TY - JOUR AB - Medullary thyroid cancer (MTC) is a relatively uncommon neuroendocrine tumor that arises from the calcitonin-secreting parafollicular cells of the thyroid gland. Unfortunately, MTC frequently metastasizes, precluding curative surgical resection and causing significant morbidity. Thus, there is an urgent need for new treatment modalities. Tautomycin and tautomycetin are antifungal antibiotics isolated from Streptomyces spiroverticillatus and Streptomyces griseochromogens, respectively. Glycogen synthase kinase-3 beta is a serine/threonine protein kinase that regulates multiple cellular processes and is important in various cancers, including MTC. Treatment with tautomycin and tautomycetin decreased neuroendocrine markers, suppressed hormonal secretion, and inhibited growth through apoptosis in MTC cells. Importantly, we describe a novel action of these compounds: inhibition of glycogen synthase kinase-3 beta. [Mol Cancer Ther 2009;8(4):914-20] AD - [Chen, Herbert] Univ Wisconsin, Dept Surg, Endocrine Surg Res Labs, Clin Sci Ctr H4 750, Madison, WI 53792 USA. [Luo, Yinggang; Ju, Jianhua; Li, Wenli; Shen, Ben] Univ Wisconsin, Div Pharmaceut Sci, Madison, WI 53792 USA. [Shen, Ben] Univ Wisconsin, Dept Chem, Natl Cooperat Drug Discovery Grp, Madison, WI 53706 USA. AN - ISI:000265204500022 AU - Adler, J. T. AU - Cook, M. AU - Luo, Y. G. AU - Pitt, S. C. AU - Ju, J. H. AU - Li, W. L. AU - Shen, B. AU - Kunnimalaiyaan, M. AU - Chen, H. DA - Apr KW - Gastrointestinal carcinoid cells neuroendocrine phenotype pathway palliation glycogen-synthase-kinase-3-beta target tumors gsk-3 Oncology LB - ISI 2009 04 30 IS - 4 N1 - English Article 1535-7163 PY - 2009 SP - 914-920 ST - Tautomycetin and tautomycin suppress the growth of medullary thyroid cancer cells via inhibition of glycogen synthase kinase-3 beta T2 - Molecular Cancer Therapeutics TI - Tautomycetin and tautomycin suppress the growth of medullary thyroid cancer cells via inhibition of glycogen synthase kinase-3 beta VL - 8 ID - 3911 ER - TY - JOUR AB - We describe a new oxaziridine-mediated approach to the amination of sp(3)-hybridized C-H bonds. In the presence of a copper(II) catalyst, N-sulfonyl oxaziridines participate in efficient intramolecular cyclization reactions to afford a variety of piperidine and tetrahydroisoquinoline structures. The aminal intermediates provide a convenient functional handle for further elaboration of these structures, demonstrating the utility of this new methodology for the rapid construction of structurally complex nitrogen-containing heterocycles. AD - [Allen, Charles P.; Benkovics, Tamas; Turek, Amanda K.; Yoon, Tehshik P.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000269735800024 AU - Allen, C. P. AU - Benkovics, T. AU - Turek, A. K. AU - Yoon, T. P. DA - Sep KW - Generated in-situ dioxiranes hydrocarbons reactivity oxidations catalysts oxyfunctionalization aminohydroxylation functionalization hydroxylation Chemistry, Multidisciplinary LB - ISI 2009 09 24 IS - 35 N1 - English Article NSF CAREER Award [CHE-0645447]; NIH [R01-GM084022]; NSF [CHE-9629688] PY - 2009 SP - 12560-+ ST - Oxaziridine-Mediated Intramolecular Amination of sp(3)-Hybridized C-H Bonds T2 - Journal of the American Chemical Society TI - Oxaziridine-Mediated Intramolecular Amination of sp(3)-Hybridized C-H Bonds VL - 131 ID - 4023 ER - TY - JOUR AB - A new strategy is presented for the synthesis of graft copolymers using only the ring-opening metathesis polymerization (ROMP). From a ROMP-derived main chain, pendant maleimide functional groups are converted into norbornene moieties via a Diels-Alder reaction with cyclopentadiene. The norbornene groups serve as sites of initiation, and subsequent ROMP from the main chain yields graft copolymers with both main and side chains derived from ROMP. This strategy offers ready access to defined graft copolymers. AD - [Allen, Matthew J.; Wangkanont, Kittikhun; Raines, Ronald T.; Kiessling, Laura L.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Raines, Ronald T.; Kiessling, Laura L.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. AN - ISI:000267048200032 AU - Allen, M. J. AU - Wangkanont, K. AU - Raines, R. T. AU - Kiessling, L. L. DA - Jun KW - Ring-opening-metathesis transfer radical polymerization comb block-copolymers functionalized norbornenes cellular internalization cylindrical brushes multivalent ligands solid-state one-pot polymers Polymer Science LB - ISI 2009 07 03 IS - 12 N1 - English Article NIH [GM049975, CA073808, 13137129, RR 13866-01]; NSF [CHE-0342998, CHE-9629688] PY - 2009 SP - 4023-4027 ST - ROMP from ROMP: A New Approach to Graft Copolymer Synthesis T2 - Macromolecules TI - ROMP from ROMP: A New Approach to Graft Copolymer Synthesis VL - 42 ID - 3948 ER - TY - JOUR AB - Vibrational spectroscopy, including infrared, Raman, sum-frequency, and ultrafast, has proven to be an exceptionally useful technique for probing the structure and dynamics of water, in the bulk liquid, and at the liquid/vapor interface. Focusing on the case of dilute HOD in D2O, we have previously analyzed infrared and Raman spectra for the bulk liquid by considering the OH frequency distribution for the ensemble of HOD molecules, and its partitioning into sub-distributions for molecules in different hydrogen-bonding environments, using one particular hydrogen-bonding definition. We have similarly analyzed the sum-frequency spectrum for the liquid/vapor interface by considering the relevant spectral density and its partitions. We show that our conclusions about the molecular origins of spectral features, and the lack of correlation in the hydrogen-bonding region between frequency and hydrogen-bonding environment, are robust, in the sense that qualitatively similar results are obtained for five other, not necessarily closely related, hydrogen-bond definitions. (C) 2009 Elsevier B.V. All rights reserved. AD - [Skinner, J. L.] Univ Wisconsin, Inst Theoret Chem, Madison, WI 53706 USA. Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000263890600003 AU - Auer, B. M. AU - Skinner, J. L. KW - Chemistry, Physical Physics, Atomic, Molecular & Chemical LB - ISI 2009 03 20 N1 - English Article MOLECULAR-DYNAMICS SIMULATIONS; SUM-FREQUENCY GENERATION; ULTRAFAST INFRARED-SPECTROSCOPY; ECHO CORRELATION SPECTROSCOPY; AB-INITIO; THEORETICAL-ANALYSIS; DILUTE HOD; INTERMOLECULAR INTERACTIONS; VAPOR/WATER INTERFACE; ORBITAL ANALYSIS FEB 24 1-3 PY - 2009 SP - 13-20 ST - Water: Hydrogen bonding and vibrational spectroscopy, in the bulk liquid and at the liquid/vapor interface T2 - Chemical Physics Letters TI - Water: Hydrogen bonding and vibrational spectroscopy, in the bulk liquid and at the liquid/vapor interface ID - 3825 ER - TY - JOUR AB - We present theoretical calculations of the vibrational sum-frequency susceptibility for the water liquid/vapor interface. Our approach builds on previous calculations by us and others, using the time-averaging approximation within the mixed quantum/classical formulation for coupled vibrational chromophores, and electric-field maps for transition frequencies, dipoles, polarizabilities, and intramolecular vibrational couplings. We compare our results for the imaginary part of the susceptibility to those from recent experiments, and comment about the effects of intermolecular vibrational coupling and the assignment of features in the spectrum. AD - [Skinner, J. L.] Univ Wisconsin, Inst Theoret Chem, Madison, WI 53706 USA. Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000264591800016 AU - Auer, B. M. AU - Skinner, J. L. DA - Apr KW - Molecular-dynamics simulations theoretical-analysis generation spectrum vapor/water interface line-shapes solid water dilute hod ir-spectra amide iir surface Chemistry, Physical LB - ISI 2009 04 09 IS - 13 N1 - English Article 1520-6106 PY - 2009 SP - 4125-4130 ST - Vibrational Sum-Frequency Spectroscopy of the Water Liquid/Vapor Interface T2 - Journal of Physical Chemistry B TI - Vibrational Sum-Frequency Spectroscopy of the Water Liquid/Vapor Interface VL - 113 ID - 3897 ER - TY - JOUR AB - The hypoxic nature of cells within solid tumors limits the efficacy of anticancer therapies such as ionizing radiation and conventional radiomimetics because their mechanisms require oxygen to induce lethal DNA breaks. For example, the conventional radiomimetic enediyne neocarzinostatin is 4-fold less cytotoxic to cells maintained in low oxygen (hypoxic) compared with normoxic conditions. By contrast, the enediyne C-1027 was nearly 3-fold more cytotoxic to hypoxic than to normoxic cells. Like other radiomimetics, C-1027 induced DNA breaks to a lesser extent in cell-free, or cellular hypoxic, compared with normoxic environments. However, the unique DNA interstrand cross-linking ability of C-1027 was markedly enhanced under the same hypoxic conditions that reduced its DNA break induction. Although the unique chemistry of C-1027 allows it to concurrently generate both DNA breaks and cross-links in normoxic cells, a low oxygen environment represses the former and promotes the latter. Thus, treatment with C-1027 offers a facile approach for overcoming the radioresistance associated with poorly oxygenated cells. AN - ISI:000262582900028 AU - Beerman, T. A. AU - Gawron, L. S. AU - Shin, S. AU - Shen, B. AU - McHught, M. M. DA - Jan DO - 10.1158/0008-5472.can-08-2753 LB - ISI 2009 03 05 (Library clean-up) IS - 2 N1 - Beerman, Terry A. Gawron, Loretta S. Shin, Seulkih Shen, Ben McHught, Mary M. PY - 2009 SN - 0008-5472 SP - 593-598 ST - C-1027, A Radiomimetic Enediyne Anticancer Drug, Preferentially Targets Hypoxic Cells T2 - Cancer Research TI - C-1027, A Radiomimetic Enediyne Anticancer Drug, Preferentially Targets Hypoxic Cells UR - ://000262582900028 VL - 69 ID - 3799 ER - TY - JOUR AB - We have discovered that the oxaziridine-mediated copper-catalyzed aminohydroxylation reaction recently discovered in our laboratories is dramatically accelerated in the presence of halide additives. The use of this more active catalyst system enables the efficient aminohydroxylation of electronically and sterically deactivated styrenes and also enables the use of nonstereogenic 3,3-dialkyl oxaziridines as terminal oxidants in the aminohydroxylation reaction. We present evidence that anionic halocuprate(II) complexes are the catalytically active species responsible for the increased reactivity under these conditions. This unexpected observation has led us to re-evaluate our mechanistic understanding of this reaction. On the basis of the results of a variety of radical trapping experiments, we propose a modified mechanism that involves a homolytic reaction of the olefin with a copper(II)-activated oxaziridine. Together, the observation that anionic additives significantly increase the oxidizing ability of oxaziridines and the recognition of the radical nature of reactions of oxaziridines under these conditions suggest that a variety of new oxidative transformations catalyzed by halocuprate(II) complexes should be possible. AD - [Benkovics, Tamas; Du, Juana; Guzei, Ilia A.; Yoon, Tehshik P.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000268480300056 AU - Benkovics, T. AU - Du, J. A. AU - Guzei, I. A. AU - Yoon, T. P. DA - Aug KW - Cross-coupling reactions cyclopropylcarbinyl-cyclopropylcarbinyl organic-compounds stereochemistry rearrangements derivatives transition halides oxidation reagents Chemistry, Organic LB - ISI 2009 08 13 IS - 15 N1 - English Article NSF [CHE-0645447, CHE-9629688]; NIH [R01-GM084022, S10 RR04981-01]; ACS Petroleum Research Fund [44783-G1] PY - 2009 SP - 5545-5552 ST - Anionic Halocuprate(II) Complexes as Catalysts for the Oxaziridine-Mediated Aminohydroxylation of Olefins T2 - Journal of Organic Chemistry TI - Anionic Halocuprate(II) Complexes as Catalysts for the Oxaziridine-Mediated Aminohydroxylation of Olefins VL - 74 ID - 3994 ER - TY - JOUR AB - Compounds that contain a late transition metal-nitrogen multiple bond represent important reactive intermediate species in many useful organic and inorganic transformations. In order to understand the role that these intermediates play in reactions, it is important to have a full understanding of their electronic structure. This paper reviews the known structural motifs that occur in late transition metal nitrido and imido compounds, and provides a correlation between geometric structure and electronic structure. Also, intermediate species that have been postulated but not yet isolated are discussed, as these compounds represent exciting targets for further efforts in synthetic inorganic chemistry. AD - Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000264097500004 AU - Berry, J. F. KW - Ray crystal-structure c-h bonds fe-n bond stereospecific vicinal oxyamination coordinated nitrene intermediate electronic absorption-spectra tert-butylimido complexes resonance raman-spectra spin-state energetics x-ray Chemistry, Inorganic & Nuclear LB - ISI 2009 03 26 IS - 1-2 N1 - English Review 0260-3594 PY - 2009 SP - 28-66 ST - Terminal Nitrido and Imido Complexes of the Late Transition Metals T2 - Comments on Inorganic Chemistry TI - Terminal Nitrido and Imido Complexes of the Late Transition Metals VL - 30 ID - 3892 ER - TY - JOUR AB - Nanoscience and nanotechnology can provide many benefits to photovoltaic and photoelectrochemical applications by combining novel nanoscale properties with processability and low cost. Taking advantage of high quality, high efficiency, yet low cost nanomaterials could potentially provide the new and transformative approaches to enable the proposed generation-III solar technologies. Nanowires are interesting because they have a long axis to absorb incident sunlight yet with a short radial distance to separate the photogenerated carriers. In this perspective, we further suggest that more "complex'' nanostructures, both in the form of hierarchically branching/hyperbranching nanowire structures and in the form of multi-component nanowire heterostructures of diverse materials, are potentially even more interesting for solar energy harvesting and conversion. The common bottom-up synthetic techniques to induce branching in nanowires to form hierarchical nanowire structures are reviewed. Several potential strategies for their incorporation into solar conversion devices are discussed and some fundamental issues and future directions are identified. AD - [Bierman, Matthew J.; Jin, Song] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000270320000003 AU - Bierman, M. J. AU - Jin, S. KW - Array photoelectrochemical cells semiconductor nanowires epitaxial-growth structural-characterization silicon nanowires pbse nanowires zno nanowires eshelby twist quantum dots zinc-oxide Chemistry, Multidisciplinary Energy & Fuels Engineering, Chemical Environmental Sciences LB - ISI 2009 10 15 IS - 10 N1 - English Article NSF [DMR-0548232]; Sloan Research Fellowship ; Research Corporation Cottrell Scholar Award ; DuPont Young Professor Grant ; Exxon Mobil Solid State Chemistry Fellowship PY - 2009 SP - 1050-1059 ST - Potential applications of hierarchical branching nanowires in solar energy conversion T2 - Energy & Environmental Science TI - Potential applications of hierarchical branching nanowires in solar energy conversion VL - 2 ID - 4037 ER - TY - JOUR AB - Lignocellulosic biomass is a plentiful and renewable resource for fuels and chemicals. Despite this potential, nearly all renewable fuels and chemicals are now produced from edible resources, such as starch, sugars, and oils; the challenges imposed by notoriously recalcitrant and heterogeneous lignocellulosic feedstocks have made their production from nonfood biomass inefficient and uneconomical. Here, we report that N,N-dimethylacetamide (DMA) containing lithium chloride (LiCI) is a privileged solvent that enables the synthesis of the renewable platform chemical 5-hydroxymethylfurfural (HMF) in a single step and unprecedented yield from untreated lignocellulosic biomass, as well as from purified cellulose, glucose, and fructose. The conversion of cellulose into HMF is unabated by the presence of other biomass components, such as lignin and protein. Mechanistic analyses reveal that loosely ion-paired halide ions in DMA-LiCl are critical for the remarkable rapidity (1-5 h) and yield (up to 92%) of this low-temperature (<= 140 degrees C) process. The simplicity of this chemical transformation of lignocellulose contrasts markedly with the complexity of extant bioprocesses and provides a new paradigm for the use of biomass as a raw material for a renewable energy and chemical industries. AD - [Binder, Joseph B.; Raines, Ronald T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Raines, Ronald T.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. AN - ISI:000264792100066 AU - Binder, J. B. AU - Raines, R. T. DA - Feb KW - Ionic liquids d-fructose reactivity cellulose chloride sucrose solvent dehydration feedstocks water Chemistry, Multidisciplinary LB - ISI 2009 04 17 IS - 5 N1 - English Article 0002-7863 PY - 2009 SP - 1979-1985 ST - Simple Chemical Transformation of Lignocellulosic Biomass into Furans for Fuels and Chemicals T2 - Journal of the American Chemical Society TI - Simple Chemical Transformation of Lignocellulosic Biomass into Furans for Fuels and Chemicals VL - 131 ID - 3881 ER - TY - JOUR AB - The crystal structure of the rare mineral fettelite was solved using intensity data collected from a twinned crystal from Chanarcillo, Copiapo Province, Chile. This study revealed that, in spite of the strong hexagonal pseudosymmetry, the structure is monoclinic (space group C2) with a= 26.0388(10), b = 15.065](8), c = 15.536](8) angstrom, beta = 90.48(1)degrees, and V= 6094.2(5) angstrom(3). The refinement of an anisotropic model led to an R index of 0.0656 for 7143 observed reflections [I > 2 sigma(I)] and 0.0759 for all 17447 independent reflections. Fettelite is intimately twinned with six twin domains. The structure consists of the stacking of two module layers along [001]: an A module layer with composition [Ag6As2S7](2-) and a B module layer with composition [Ag10HgAs2S8](2+). The As atoms form isolated AsS3 pyramids typical of sulfosalts, Hg links two Sulfur atoms in linear coordination, and Ag occupies sites with coordination ranging from quasi linear to almost tetrahedral. The A module layer found for fettelite is identical to that described for the minerals belonging to the pearceite-polybasite group. On the basis of information gained from this characterization the crystal chemical formula was revised according to the structural results, yielding [Ag(6)AS(2)S(7)][Ag10HgAs2S8] (Z = 8). AD - [Bindi, Luca] Univ Florence, Museo Storia Nat, Sez Mineral, I-50121 Florence, Italy. [Keutsch, Frank N.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Francis, Carl A.] Harvard Univ, Harvard Mineral Museum, Cambridge AN - ISI:000265157000020 AU - Bindi, L. AU - Keutsch, F. N. AU - Francis, C. A. AU - Menchetti, S. DA - Apr KW - Silver sulfosalts crystal structure chemical composition optical properties fettelite pearceite-polybasite polytypes physical properties Pearceite-polybasite group phase-transitions minerals Geochemistry & Geophysics Mineralogy LB - ISI 2009 04 30 IS - 4 N1 - English Article 0003-004X PY - 2009 SP - 609-615 ST - Fettelite, [Ag6As2S7][Ag10HgAs2S8] from Chanarcillo, Chile: Crystal structure, pseudosymmetry, twinning, and revised chemical formula T2 - American Mineralogist TI - Fettelite, [Ag6As2S7][Ag10HgAs2S8] from Chanarcillo, Chile: Crystal structure, pseudosymmetry, twinning, and revised chemical formula VL - 94 ID - 3913 ER - TY - JOUR AB - A series of silica-bound Cu(II) triazacyclononane materials was prepared to study the effect of linker length and surface hydrophobicity on the hydrolysis of phosphate esters. The general synthetic approach for these heterogeneous reagents was rhodium-catalyzed hydrosilation between an alkenyl-modified triazacyclononane and hydride-modified silica followed by metallation with a Cu(II) salt. Elemental analysis confirmed that organic functionalization of the silica gel was successful and provided an estimate of the surface concentration of triazacyclononane. EPR spectra were consistent with square pyramidal Cu(II), indicating that Cu(II) ions were bound to the immobilized macrocycles. The hydrolytic efficacies of these heterogeneous reagents were tested with bis(p-nitrophenyl) phosphate (BNPP) and diethyl 4-nitrophenyl phosphate (paraoxon). The agent that performed best was an octyl-linked, propanol-blocked material. This material had the most hydrophilic surface and the most accessible active site, achieving a rate maximum on par with the other materials, but in fewer cycles and without an induction period. AD - [Ehrbar, Anthony W.; Burstyn, Judith N.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Bodsgard, Brett R.] St Marys Univ Minnesota, Dept Chem, Winona, MN 55987 USA. [Clark, Robert W.] Univ Valparaiso, Dept Chem, Valparaiso, IN 46383 USA. AN - ISI:000264254200014 AU - Bodsgard, B. R. AU - Clark, R. W. AU - Ehrbar, A. W. AU - Burstyn, J. N. KW - Metal-chelator polymers reactive phosphates diester hydrolysis organophosphorus pesticides heterogeneous hydrolysis catalyzed-hydrolysis crystal-structure phosphodiester cleavage complexes Chemistry, Inorganic & Nuclear LB - ISI 2009 04 03 IS - 13 N1 - English Article 1477-9226 PY - 2009 SP - 2365-2373 ST - Silica-bound copper(II) triazacyclononane as a phosphate esterase: effect of linker length and surface hydrophobicity T2 - Dalton Transactions TI - Silica-bound copper(II) triazacyclononane as a phosphate esterase: effect of linker length and surface hydrophobicity ID - 3893 ER - TY - JOUR AB - Many receptors undergo ligand-induced conformational changes to initiate signal transduction. Periplasmic binding proteins (PBPs) are bacterial. receptors that exhibit dramatic conformational changes upon ligand binding. These proteins mediate a wide variety of fundamental processes including transport, chemotaxis, and quorum sensing. Despite the importance of these receptors, no PBP antagonists have been identified and characterized. In this study, we identify 3-O-methyl-D-glucose as an antagonist of glucose/galactose-binding protein and demonstrate that it inhibits glucose chemotaxis in E coli. Using small-angle X-ray scattering and X-ray crystallography, we show that this antagonist acts as a wedge. It prevents the large-scale domain closure that gives rise to the active signaling state. Guided by these results and the structures of open and closed glucose/galactose-binding protein, we designed and synthesized an antagonist composed of two linked glucose residues. These findings provide a blueprint for the design of new bacterial PBP inhibitors. Given the key role of PBPs in microbial physiology, we anticipate that PBP antagonists will have widespread uses as probes and antimicrobial agents. AD - [Zhu, Yimin; Kiessling, Laura L.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Forest, Katrina T.] Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA. Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. AN - ISI:000267207300008 AU - Borrok, M. J. AU - Zhu, Y. M. AU - Forest, K. T. AU - Kiessling, L. L. DA - Jun KW - Quorum-sensing signal escherichia-coli salmonella-typhimurium conformational-changes glucose/galactose-binding chemotactic responses ligand specificity transport-system bound structures maltose-binding Biochemistry & Molecular Biology LB - ISI 2009 07 10 IS - 6 N1 - English Article National Institutes of Health [GM059984]; W. M. Keck Foundation ; NIH Molecular Biosciences Training [GM07215] PY - 2009 SP - 447-456 ST - Structure-Based Design of a Periplasmic Binding Protein Antagonist that Prevents Domain Closure T2 - ACS Chemical Biology TI - Structure-Based Design of a Periplasmic Binding Protein Antagonist that Prevents Domain Closure VL - 4 ID - 3953 ER - TY - JOUR AB - Gas-liquid scattering experiments are used to investigate interfacial interactions of gaseous DCl with liquid glycerol containing 0.03 M tetrahexylammonium bromide (THABr), an ionic surfactant composed of hydrophobic THA(+) and hydrophilic Br- ions. Surface tension and argon scattering measurements indicate that the surface of this solution is dominated by the hexyl chains of the THA(+) ion. The hydrocarbon character of the surface is further explored by comparing Ar and DCl scattering from the THABr solution and liquid squalane. We find that the addition of THABr to glycerol alters the reactivity of DO in two ways: DO molecules that land on the surface are more likely to desorb when THA(+) and Br- are present and are less likely to dissolve, but they are also more likely to undergo rapid, interfacial DCl -> HCl exchange. Similar trends are observed when THA(+) ions are replaced by Na+ ions in a 2.7 M NaBr solution, even though THA(+) interacts weakly with glycerol OH groups and Ne binds strongly to them. These observations suggest that the THA(+) hexyl chains do not physically block DO entry and that interfacial cation-OH bonding is not essential for promoting rapid D -> H exchange when Br--OH bonding also Occurs. The use of THABr confirms that ions in the top few monolayers, and not those deeper in solution, control DO entry and rapid D -> H exchange. AD - [Brastad, Susan M.; Albert, Daniel R.; Huang, Mingwei; Nathanson, Gilbert M.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000267384500030 AU - Brastad, S. M. AU - Albert, D. R. AU - Huang, M. W. AU - Nathanson, G. M. DA - Jul KW - Aqueous tetrabutylammonium iodide molecular-dynamics simulations supercooled sulfuric-acid liquid glycerol photoelectron-spectroscopy surface-activity salty glycerol ab-initio tetraalkylammonium salts alkylammonium halides Chemistry, Physical Physics, Atomic, Molecular & Chemical LB - ISI 2009 07 31 IS - 26 N1 - English Article National Science Foundation PY - 2009 SP - 7422-7430 ST - Collisions of DCl with a Solution Covered with Hydrophobic and Hydrophilic Ions: Tetrahexylammonium Bromide in Glycerol T2 - Journal of Physical Chemistry A TI - Collisions of DCl with a Solution Covered with Hydrophobic and Hydrophilic Ions: Tetrahexylammonium Bromide in Glycerol VL - 113 ID - 3968 ER - TY - JOUR AB - Vitamin B-12 and its biologically active derivatives, 5'-deoxyadenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl), have long fascinated chemists with their elaborate structures and unusual reactivities in enzymatic systems. Due to their large size and complex electronic structures, these cofactors have posed a major challenge for Computational chemists. Yet, recent insights gained from kinetic, spectroscopic, and X-ray crystallographic studies, have established an excellent foundation for the successful completion of density functional theory studies aimed at elucidating the electronic structures of the isolated cofactors and the catalytic cycles of B-12-dependent enzymes. This review summarizes important information obtained from experimentally validated computational studies of: (i) the free AdoCbl and MeCbl cofactors in their Co3+, Co2+, and Co1+ oxidation states; (ii) the mechanism by which enzymes involved in the biosynthesis of AdoCbl accomplish the thermodynamically challenging Co2+ -> Co1+ reduction: (iii) the strategies employed by AdoCbl-dependent enzymes to achieve a trillion-fold rate acceleration for the homolytic cleavage of the cofactor's Co-C(Ado) bond: and (iv) the means by which MeCbl-dependent methyltransferases accelerate the rate of methyl transfer via heterolytic Co-C(Me) bond cleavage by as much as six orders of magnitude and reactivate the accidentally oxidized form of the cofactor. (C) 2008 Elsevier B.V. All rights reserved. AD - [Brunold, Thomas C.; Conrad, Karen S.; Liptak, Matthew D.; Park, Kiyoung] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000264701900017 AU - Brunold, T. C. AU - Conrad, K. S. AU - Liptak, M. D. AU - Park, K. DA - Mar KW - B-12-dependent enzymes Density functional theory Electronic structure description Vitamin B-12 Methylmalonyl-coa mutase dependent methionine synthase resonance raman-spectra iron-sulfur protein atp-corrinoid adenosyltransferase electron-paramagnetic-resonance carbon bond homolysis transition-metal-complexes partial proton-transfer methyl-group transfer Chemistry, Inorganic & Nuclear LB - ISI 2009 04 17 IS - 5-6 N1 - English Review 0010-8545 Sp. Iss. SI PY - 2009 SP - 779-794 ST - Spectroscopically validated density functional theory studies of the B-12 cofactors and their interactions with enzyme active sites T2 - Coordination Chemistry Reviews TI - Spectroscopically validated density functional theory studies of the B-12 cofactors and their interactions with enzyme active sites VL - 253 ID - 3885 ER - TY - JOUR AB - We report an approach to the design of reactive polymer films that can be functionalized post-fabrication to either prevent or promote the attachment and growth of cells. Our approach is based on the reactive layer-by-layer assembly of covalently crosslinked thin films using a synthetic polyamine and a polymer containing reactive azlactone functionality. Our results demonstrate (i) that the residual azlactone functionality in these films can be exploited to immobilize amine-functionalized chemical motifs similar to those that promote or prevent cell and protein adhesion when assembled as self-assembled monolayers on gold-coated surfaces and (ii) that the immobilization of these motifs changes significantly the behaviors and interactions of cells with the surfaces of these polymer films. We demonstrate that films treated with the hydrophobic molecule decylamine support the attachment and growth of mammalian cells in vitro. In contrast, films treated with the hydrophilic carbohydrate D-glucamine prevent cell adhesion and growth almost completely. The results of additional experiments suggest that these large differences in cell behavior can be understood, at least in part, in terms of differences in the abilities of these two different chemical motifs to promote or prevent the adsorption of protein onto film-coated surfaces. We demonstrate further that this approach can be used to pattern regions of these reactive films that resist the initial attachment and subsequent invasion of mammalian cells for periods of at least one month in the presence of serum-containing cell culture media. Finally, we report that films that prevent the adhesion and growth of mammalian cells also prevent the initial formation of bacterial biofilms when incubated in the presence of the clinically relevant pathogen Pseudomonas aeruginosa. The results of these studies, collectively, suggest the basis of general approaches to the fabrication and functionalization of thin films that prevent, promote, or pattern cell growth or the formation of biofilms on surfaces of interest in the contexts of both fundamental biological studies and a broad range of other practical applications. AD - [Buck, Maren E.; Breitbach, Anthony S.; Blackwell, Helen E.; Lynn, David M.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Belgrade, Sonja K.; Lynn, David M.] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA. AN - ISI:000266860700031 AU - Buck, M. E. AU - Breitbach, A. S. AU - Belgrade, S. K. AU - Blackwell, H. E. AU - Lynn, D. M. DA - Jun KW - Self-assembled monolayers pseudomonas-aeruginosa biofilms polymer-coatings polyelectrolyte multilayers biomedical applications patterning proteins ultrathin films thin-films in-vitro adsorption Biochemistry & Molecular Biology Chemistry, Organic Polymer Science LB - ISI 2009 06 26 IS - 6 N1 - English Article National Institutes of Health [EB006820, AI063326-01]; Alfred P. Sloan Foundation ; 3M Corporation ; University of Wisconsin ; Office of Naval Research [N000140710255]; Burroughs Welcome Fund ; NIH Chemistry-Biology Interface Training Grant [NIGMS T32 GM008505] PY - 2009 SP - 1564-1574 ST - Chemical Modification of Reactive Multilayered Films Fabricated from Poly(2-alkenyl azlactone)s: Design of Surfaces that Prevent or Promote Mammalian Cell Adhesion and Bacterial Biofilm Growth T2 - Biomacromolecules TI - Chemical Modification of Reactive Multilayered Films Fabricated from Poly(2-alkenyl azlactone)s: Design of Surfaces that Prevent or Promote Mammalian Cell Adhesion and Bacterial Biofilm Growth VL - 10 ID - 3946 ER - TY - JOUR AB - Raman, UV and XRD studies have been performed to characterize the structures of differently prepared samples of poly(methyl-n-propylsilane). The results demonstrate polymorphism of this polymer between T-c and T-g. At room temperature the polymer can exist in up to four modifications which comprise one amorphous disordered phase and three more ordered modifications, differing in the interchain organization and in the silicon backbone conformations. The latter are considered to be deviant, transoid and allanti, respectively. The number of the modifications present and relative amount of each strongly depends on the preparation method and thermal history of the sample as well as on the molecular weight. (C) 2009 Elsevier Ltd. All rights reserved. AD - [Bukalov, Sergey S.; Zubavichus, Yan V.; Leites, Larissa A.] Russian Acad Sci, Inst Organoelement Cpds, Sci & Tech Ctr Raman Spect, Moscow 119991, Russia. [Koe, Julian R.] Int Christian Univ, Dept Mat Sci, Tokyo 1818585, Japan. [West, Robert] Univ Wisconsin, Dept Chem, Organosilicon Res Ctr, Madison, WI 53706 USA. AN - ISI:000272959300013 AU - Bukalov, Sergey S. AU - Zubavichus, Yan V. AU - Leites, Larissa A. AU - Koe, Julian R. AU - West, Robert DA - Sep KW - Poly(methyl-n-propylsilane) Polymorphism UV, Raman, XRD methods Organosilane high polymers phase-transitions polysilane poly(di-n-hexylsilane) spectra films conformations conjugation behavior chain Polymer Science LB - ISI 2010 01 07 IS - 20 N1 - English Article Russian Academy of Sciences PY - 2009 SP - 4845-4851 ST - UV, Raman and XRD study of polymorphism of poly(methyl-n-propylsilane) T2 - Polymer TI - UV, Raman and XRD study of polymorphism of poly(methyl-n-propylsilane) VL - 50 ID - 4152 ER - TY - JOUR AB - Molecular beam scattering experiments are used to investigate collisions and reactions of HCl with deuterated sulfuric acid containing 0-0.2 M pentanoic acid (PA) and mixtures of PA and hexanol. Surface tension measurements at 296 K indicate that PA segregates to the surface of the acid, reaching coverages of 58% and 52% Of maximum packing on 60 and 68 wt % D2SO4, respectively. We find that these films increase HCl entry into the acid at low PA surface coverage at 213 K. This enhancement is attributed to the dissociation of HCl molecules that come into contact with surface COOH groups and protonate them. At higher coverages, the PA film becomes more compact and impedes HCl uptake. Comparisons with films of pure hexanol and pentanoic acid/hexanol mixtures indicate that surface OH groups are more effective than COOH groups in catalyzing HCl entry. They also suggest that the PA films consist of patchy regions of tightly packed molecules, which are pushed away from the Surface upon addition of the more surface active hexanol. HCl entry into the pure and mixed films can be analyzed quantitatively using a two-step model in which adsorbed HCl molecules penetrate between the alkyl chains and then dissociate at the surfactant-acid interface. AD - [Burden, Daniel K.; Johnson, Alexis M.; Nathanson, Gilbert M.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000272713700016 AU - Burden, Daniel K. AU - Johnson, Alexis M. AU - Nathanson, Gilbert M. DA - Dec KW - Quantum-chemical analysis air-water-interface air/water interface reactive uptake organic films diffusion-coefficients aerosol-particles cluster formation carboxylic-acids n2o5 hydrolysis Chemistry, Physical Physics, Atomic, Molecular & Chemical LB - ISI 2009 12 24 IS - 51 N1 - English Article Air Force Office of Scientific Research PY - 2009 SP - 14131-14140 ST - HCl Uptake through Films of Pentanoic Acid and Pentanoic Acid/Hexanol Mixtures at the Surface of Sulfuric Acid T2 - Journal of Physical Chemistry A TI - HCl Uptake through Films of Pentanoic Acid and Pentanoic Acid/Hexanol Mixtures at the Surface of Sulfuric Acid VL - 113 ID - 4110 ER - TY - JOUR AB - Diketopiperazines (DKPs) are a well-known class of heterocycles that have emerged as promising biologically active scaffolds. Solid-phase organic synthesis has become an important tool in the combinatorial exploration of these privileged structures, expediting the synthesis and, often, the discovery of active compounds. We recently identified several DKPs that are capable of inhibiting the luminescence response of the bacterial symbiont Vibrio fischeri, and we sought to further test the scope of this biological activity. Herein, we report the synthesis of DKP macroarrays using a SPOT-synthesis approach based on all Ugi/DeBoc/Cyclize strategy. Neither a spacer nor a linker was required for macroarray construction on cellulose support, and the cyclative cleavage produced high purity DKPs in good yields. Using this protocol, we prepared a library of 400 DKPs on cellulose support and evaluated its members as luminescence inhibitors in V. fischeri. We found six DKPs capable of inhibiting luminescence by at least 80% at 500 mu M. Collectively, this work serves to further highlight the utility of the small molecule macroarray platform for the synthesis and evaluation of focused libraries. AD - [Campbell, Jennifer; Blackwell, Helen E.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000271428500019 AU - Campbell, Jennifer AU - Blackwell, Helen E. DA - Nov-Dec KW - Small-molecule macroarrays ugi 4-component reactions gram-negative bacteria cyclic dipeptides combinatorial synthesis spot-synthesis cross-talk identification microwave phase Chemistry, Applied Chemistry, Medicinal Chemistry, Multidisciplinary LB - ISI 2009 11 19 IS - 6 N1 - English Article NIH [A1063326-01]; Research Corporation ; Burroughs Wellcome Fund ; Greater Milwaukee Foundation Shaw Scientist Program ; Johnson & Johnson, and DuPont ; Alfred P. Sloan Foundation Fellow ; Novartis Graduate Fellowship in Organic Chemistry PY - 2009 SP - 1094-1099 ST - Efficient Construction of Diketopiperazine Macroarrays Through a Cyclative-Cleavage Strategy and Their Evaluation as Luminescence Inhibitors in the Bacterial Symbiont Vibrio fischeri T2 - Journal of Combinatorial Chemistry TI - Efficient Construction of Diketopiperazine Macroarrays Through a Cyclative-Cleavage Strategy and Their Evaluation as Luminescence Inhibitors in the Bacterial Symbiont Vibrio fischeri VL - 11 ID - 4085 ER - TY - JOUR AB - Quorum sensing (QS) is under the control of N-acylated L-homoserine lactones (AHLs) and their cognate receptors (LuxR-type proteins) in Gram-negative bacteria and plays a major role in mediating host-bacteria Interactions by these species. Certain cyclic dipeptides (2,5-diketopiperazines, DKPs) have been isolated from bacteria and reported to activate or inhibit LuxR-type proteins in AHL biosensor strains, albeit at significantly higher concentrations than native lactones. These reports have prompted the proposal that Ups represent a new class of QS signals and potentially even interspecies or interkingdom signals; their mechanisms of action and physiological relevance, however, remain unknown. Here, we describe a library of synthetic DKPs that was designed to (1) determine the structural features necessary for LuxR-type protein activation and inhibition and (2) probe their mechanisms of action. These DKPs, along with several previously reported natural DKPs, were screened in bacterial reporter gene assays. In contrast to previous reports, the native DKPs failed to exhibit either antagonistic or agonistic activities in these assays. However, non-natural halogenated cyclo(L-Pro-L-Phe) derivatives were capable of inhibiting luminescence in Vibrlo fischeri. Interestingly, additional experiments revealed that these DKPs do not compete with the natural lactone signal, OHHL, to inhibit luminescence. Together, these data suggest that DKPs are not QS signals in the bacteria examined in this study. Although these compounds can influence QS-regulated outcomes, we contend that they do not do so through direct interaction with LuxR-type proteins. This work serves to refine the lexicon of naturally occurring QS signals used by Gram-negative bacteria. AD - [Campbell, Jennifer; Lin, Qi; Geske, Grant D.; Blackwell, Helen E.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000272845900009 AU - Campbell, Jennifer AU - Lin, Qi AU - Geske, Grant D. AU - Blackwell, Helen E. DA - Dec KW - Gram-negative bacteria to-cell communication acylated homoserine lactones pseudomonas-aeruginosa vibrio-fischeri gene-expression agrobacterium-tumefaciens synthetic ligands signal molecules cross-talk Biochemistry & Molecular Biology LB - ISI 2009 12 31 IS - 12 N1 - English Article National Institutes of Health [AI063326-01]; Research Corporation ; Burroughs Wellcome Foundation ; Greater Milwaukee Foundation Shaw Scientist Program ; Johnson Johnson ; DuPont ; Alfred P. Sloan Foundation ; Novartis Graduate Fellowship in Organic Chemistry ; ACS Division of Medicinal Chemistry graduate fellowship PY - 2009 SP - 1051-1059 ST - New and Unexpected Insights into the Modulation of LuxR-Type Quorum Sensing by Cyclic Dipeptides T2 - ACS Chemical Biology TI - New and Unexpected Insights into the Modulation of LuxR-Type Quorum Sensing by Cyclic Dipeptides VL - 4 ID - 4117 ER - TY - JOUR AB - Noncovalent self-assembly of biopolymers is driven by molecular interactions between functional groups oil cornplementary biopolymer surfaces, replacing interactions with water. Since individually these interactions are comparable in strength to interactions with water, they have been difficult to quantify. Solutes (osmolytes, denaturants) exert often large effects on these self-assembly interactions, determined in sign and magnitude by how well the solute competes with water to interact with the relevant biopolymer Surfaces. Here, an osmometric method and a water-accessible surface area (ASA) analysis are developed to quantify and interpret the interactions or the remarkable osmolyte glycine betaine (GB) with molecular surfaces in water. We find that GB, lacking hydrogen bond donors, is unable to compete with water to interact with anionic and amide oxygens; this explains its effectiveness as an osmolyte in the Escherichia coli cytoplasm. GB competes effectively with water to interact with amide and cationic nitrogens (hydrogen bonding) and especially with aromatic hydrocarbon (cation-pi). The large stabilizing effect of GB oil lac repressor-lac operator binding is predicted quantitatively from ASA information and shown to result largely from dehydration of anionic DNA phosphate oxygens in the protein-DNA interface. The incorporation of these results into theoretical and computational analyses will likely improve the ability to accurately model intra- and interprotein interactions. Additionally, these results pave the way for development or solutes as kinetic/mechanistic and thermodynamic probes of conformational changes and formation/disruption of molecular interfaces that occur in the steps of biomolecular self-assembly processes. AD - [Pegram, Laurel M.; Kratz, Megan; Riccardi, Demian; Wendorff, Timothy; Record, M. Thomas, Jr.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. [Capp, Michael W.; Saecker, Ruth M.; Record, M. Thomas, Jr.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Cannon, Jonathan G.; Record, M. Thomas, Jr.] Univ Wisconsin, Biophys Program, Madison, WI 53706 USA. AN - ISI:000271023500019 AU - Capp, M. W. AU - Pegram, L. M. AU - Saecker, R. M. AU - Kratz, M. AU - Riccardi, D. AU - Wendorff, T. AU - Cannon, J. G. AU - Record, M. T. DA - Nov KW - Preferential interactions protein stability lac repressor solvent accessibilities aqueous-solutions escherichia-coli nonpolar surface proline betaine urea dna Biochemistry & Molecular Biology LB - ISI 2009 10 29 IS - 43 N1 - English Article National Institutes of Health [GM147022, GM23467] PY - 2009 SP - 10372-10379 ST - Interactions of the Osmolyte Glycine Betaine with Molecular Surfaces in Water: Thermodynamics, Structural Interpretation, and Prediction of m-Values T2 - Biochemistry TI - Interactions of the Osmolyte Glycine Betaine with Molecular Surfaces in Water: Thermodynamics, Structural Interpretation, and Prediction of m-Values VL - 48 ID - 4064 ER - TY - JOUR AB - PMe3 adds selectively to the central carbon of the eta(3)-propargyl complex [C5MC5(CO)(2)Re(eta(3)- CH,C CCMe3)1[BF4] (1-t-Bu) to form the metallacyclobutene [C5Me5(CO)(2)Re(CH2C(PMe)= CCMe3)][BF4] (7). The rate of rearrangement of the metallacyclobutene 7 to eta(2)-alkyne complex [C5Me5(CO)(2)Re(eta(2)-Me3PCH2C CCMe3)][BF4] (8) is independent of phosphine concentration, consistent with a dissociative mechanism proceeding via eta(3)-propargy] complex 1-t-Bu. The rate of this rearrangement is 480 times slower than the rate of exchange of PMe3 with the labeled metal lacyclobutene 749. This rate ratio provides an indirect measurement of the regioselectivity for addition of PMe3 to the central carbon of eta(3)-propargyl complex 1-t-Bu to give 7 compared to addition to a terminal carbon to give 8. The addition of PPh3 to 1-t-Bu gives the metal lacyclobutene [C5Me5(CO)(2)Re(CH2C(PPh3)=CCMe3)][BF4] (11). Low-ternperature H-1 NMR spectra provide evidence for an equilibrium between metal lacyclobutene 11 and eta(3)-propargyl complex 1-t-Bu (K-eq approximate to 44 M-1 at -46 degrees C and Delta G degrees(0 degrees C) = -1.2 +/- 0.2 kcal mol(-1)). AD - [Casey, Charles P.; Boller, Timothy M.; Samec, Joseph S. M.; Reinert-Nash, John R.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000262177200016 AU - Casey, C. P. AU - Boller, T. M. AU - Samec, J. S. M. AU - Reinert-Nash, J. R. DA - Jan KW - Density-functional theory pi-allyl complexes central carbon transition-metal 2-bromo(pi-allyl)palladium complexes (pi-allyl)palladium complexes allenyl complexes practical tool ligand control bonding nature Chemistry, Inorganic & Nuclear Chemistry, Organic LB - ISI 2009 01 22 IS - 1 N1 - English Article 0276-7333 PY - 2009 SP - 123-131 ST - Quantitative Determination of the Regioselectivity of Nucleophilic Addition to eta(3)-Propargyl Rhenium Complexes and Direct Observation of an Equilibrium between eta(3)-Propargyl Rhenium Complexes and Rhenacyclobutenes T2 - Organometallics TI - Quantitative Determination of the Regioselectivity of Nucleophilic Addition to eta(3)-Propargyl Rhenium Complexes and Direct Observation of an Equilibrium between eta(3)-Propargyl Rhenium Complexes and Rhenacyclobutenes VL - 28 ID - 3731 ER - TY - JOUR AB - 2-Methyl-3-buten-2-ol (MBO) is an important biogenic hydrocarbon emitted in large quantities by pine forests, Atmospheric photooxidation of MBO is known to lead to oxygenated compounds, such as glycolaldehyde, which is the precursor to glyoxal. Recent studies have shown that the reactive uptake of glyoxal onto aqueous particles can lead to formation of secondary organic aerosol (SOA). In this work, MBO photooxidation under high- and low-NOx conditions was performed in dual laboratory chambers to quantify the yield of glyoxal and investigate the potential for SOA formation. The yields of glycolaldehyde and 2-hydroxy-2-methylpropanal (HMPR), fragmentation products of MBO photooxidation, were observed to be lower at lower NOx concentrations. Overall, the glyoxal yield from MBO photooxidation was 25% under high-NOx and 4% under low-NOx conditions. In the presence of wet ammonium sulfate seed and under high-NOx conditions, glyoxal uptake and SOA formation were not observed conclusively, due to relatively low (<30 ppb) glyoxal concentrations. Slight aerosol formation was observed under low-NOx and dry conditions, with aerosol mass yields on the order of 0.1%. The small amount of SOA was not related to glyoxal uptake, but is likely a result of reactions similar to those that generate isoprene SOA under low-NOx conditions. The difference in aerosol yields between MBO and isoprene photooxidation under low-NOx conditions is consistent with the difference in vapor pressures between triols (from MBO) and tetrols (from isoprene). Despite its structural similarity to isoprene, photooxidation of MBO is not expected to make a significant contribution to SOA formation. AD - [Chan, Arthur W. H.; Chhabra, Puneet S.; Flagan, Richard C.; Seinfeld, John H.] CALTECH, Dept Chem Engn, Pasadena, CA 91125 USA. [Galloway, Melissa M.; Keutsch, Frank N.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Kwan, Alan J.; Wennberg, Paul O.; Flagan, Richard C.; Seinfeld, John H.] CALTECH, Dept Environm Sci & Engn, Pasadena, CA 91125 USA. AN - ISI:000267435500008 AU - Chan, A. W. H. AU - Galloway, M. M. AU - Kwan, A. J. AU - Chhabra, P. S. AU - Keutsch, F. N. AU - Wennberg, P. O. AU - Flagan, R. C. AU - Seinfeld, J. H. DA - Jul KW - Oh-initiated oxidation atmospheric oxidation pine forest isoprene glycolaldehyde products radicals glyoxal chamber model Engineering, Environmental Environmental Sciences LB - ISI 2009 07 31 IS - 13 N1 - English Article U.S. Department of Energy Biological and Environmental Research Program [DE-FG0205ER63983]; U.S. Environmental Protection Agency STAR [RD-83374901]; U.S. National Science Foundation [ATM-0432377]; Camille and Henry Dreyfus Foundation ; National Science Foundation, Division of Atmospheric Sciences,.Atmospheric Chemistry Program [0724912]; NDSEG-ARO PY - 2009 SP - 4647-4652 ST - Photooxidation of 2-Methyl-3-Buten-2-ol (MBO) as a Potential Source of Secondary Organic Aerosol T2 - Environmental Science & Technology TI - Photooxidation of 2-Methyl-3-Buten-2-ol (MBO) as a Potential Source of Secondary Organic Aerosol VL - 43 ID - 3971 ER - TY - JOUR AB - Imaging mass spectrometry is emerging as a powerful tool that has been applied extensively for the localization of proteins, peptides, pharmaceutical compounds, metabolites, and lipids in biological tissues. In this article, a three-dimensional mass spectral imaging (3D MSI) technique was developed to examine distribution patterns of multiple neuropeptide families and lipids in the brain of the crab Cancer borealis. Different matrix/solvent combinations were compared for preferential extraction and detection of neuropeptides and lipids. Combined with morphological information, the distribution of numerous neuropeptides throughout the 3D structure of brain was determined using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF MS). Different localization patterns were observed for different neuropeptide families, and isoforms displaying unique distribution patterns that were distinct from the common family distribution trends were also detected. In addition, multiple lipids were identified and mapped from brain tissue slices. To confirm their identities, MS/MS fragmentation was performed. Different lipid species displayed distinct localization patterns, suggesting their potential different functional roles in the nervoussystem. (J Am Soc Mass Spectrom 2009, 20,1068-1077) (C) 2009 Published by Elsevier Inc. on behalf of American Society for Mass Spectrometry AD - [Li, Lingjun] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. Univ Wisconsin, Sch Pharm, Madison, WI 53706 USA. AN - ISI:000266466600020 AU - Chen, R. B. AU - Hui, L. M. AU - Sturm, R. M. AU - Li, L. J. DA - Jun KW - Stomatogastric nervous-system cancer-borealis sinus gland spectrometry tissue peptides crayfish identification lipidomics morphology Chemistry, Analytical Chemistry, Physical Spectroscopy LB - ISI 2009 06 12 IS - 6 N1 - English Article National Science Foundation CAREER Award [CHE-0449991]; National Institutes of Health [1R01DK071801]; NIH-supported Clinical Neuroengineering Training Program Predoctoral Fellowship [T90 DK070079]; Alfred P. Sloan Research Fellowship PY - 2009 SP - 1068-1077 ST - Three Dimensional Mapping of Neuropeptides and Lipids in Crustacean Brain by Mass Spectral Imaging T2 - Journal of the American Society for Mass Spectrometry TI - Three Dimensional Mapping of Neuropeptides and Lipids in Crustacean Brain by Mass Spectral Imaging VL - 20 ID - 3925 ER - TY - JOUR AB - Over the past two decades high-density DNA arrays have developed into a central technology for nucleic acid analyses. Important application areas include whole-genome gene expression studies, high throughput analyses of single nucleotide polymorphisms, and, most recently, the determination of binding site specificities for transcription factors and other critical elements involved in gene regulation. A key parameter in the performance of DNA arrays is the density of the surface-bound oligonucleotides, which strongly affects both thermodynamic and kinetic aspects of DNA hybridization. In this report, we describe an approach for the control of oligonucleotide density in photolithographically fabricated DNA arrays, based upon a controlled UV light deprotection procedure. Modulation of the UV exposure permits a desired degree of deprotection of surface synthesis sites; a subsequent capping reaction to inactivate the exposed sites leaves only a desired fraction of active sites remaining for synthesis, corresponding to a lower oligonucleotide density. It is shown that the procedure is reasonably general, in that it is readily transferable to alternative substrate materials with similar results. AD - [Chen, Siyuan; Phillips, Margaret F.; Smith, Lloyd M.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Cerrina, Franco] Univ Wisconsin, Dept Elect & Comp Engn, Madison, WI 53706 USA. AN - ISI:000266604000078 AU - Chen, S. AU - Phillips, M. F. AU - Cerrina, F. AU - Smith, L. M. DA - Jun KW - Expression analysis invasive cleavage plasmon resonance nucleic-acids human genome copy number thin-films hybridization microarrays carbon Chemistry, Physical LB - ISI 2009 06 26 IS - 11 N1 - English Article NIH [R01HG002298]; NSF [CHE-0809095]; MPS/CHE & BIO/MCB Divisions ; University of Wisconsin Industrial and Economic Development Research program PY - 2009 SP - 6570-6575 ST - Controlling Oligonucleotide Surface Density in Light-Directed DNA Array Fabrication T2 - Langmuir TI - Controlling Oligonucleotide Surface Density in Light-Directed DNA Array Fabrication VL - 25 ID - 3944 ER - TY - JOUR AB - The ability to pattern small molecules and proteins on artificial surfaces is of importance for the development of new tools including tissue engineering, cell-based drug screening, and cell-based sensors. We describe here a novel "caged" thiol-mediated strategy for the fabrication of planar Substrates patterned with biomolecules using photolithography. A thiol-bearing phosphoramidite (3-(2'-nitrobenzyl)thiopropyl (NBTP) phosphoramidite) was synthesized and coupled to a hydroxyl-terminated amorphous carbon substrate. A biocompatible oligo(ethylene glycol) spacer was used to resist nonspecific adsorption of protein and DNA and enhance flexibility of attached biomolecules. Thiol functionalities are revealed by UV irradiation of NBTP-modified surfaces. Both the surface coupling and photodeprotection were monitored by Polarization Modulation Fourier Transform Infrared Reflection Absorption Spectroscopy (PM-FTIRRAS) and X-ray Photoelectron Spectroscopy (XPS) measurements. The newly exposed thiols are chemically very active and react readily with a wide variety of groups. A series of molecules including biotin, DNA, and proteins were attached to the surfaces with retention of their biological activities, demonstrating the utility and generality of the approach. AD - [Chen, Siyuan; Smith, Lloyd M.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000270594500043 AU - Chen, S. Y. AU - Smith, L. M. DA - Oct KW - Self-assembled monolayers dna arrays carbohydrate expression gold nanoparticles lectin arrays single cells fabrication adsorption patterns films Chemistry, Multidisciplinary Chemistry, Physical Materials Science, Multidisciplinary LB - ISI 2009 10 23 IS - 20 N1 - English Article NIH [R01HG002298]; NSF [CHE-0809095]; University of Wisconsin Industrial and Economic Development Research program PY - 2009 SP - 12275-12282 ST - Photopatterned Thiol Surfaces for Biomolecule Immobilization T2 - Langmuir TI - Photopatterned Thiol Surfaces for Biomolecule Immobilization VL - 25 ID - 4055 ER - TY - JOUR AB - Fredericamycin (FDM) A, a highly oxidized aromatic penta-decaketide natural product, exhibits potent cytotoxicity and has been studied as a new anticancer drug lead. The FDM biosynthetic gene cluster has been previously cloned from Streptomyces griseus ATCC 49344 and successfully expressed in the heterologous host Streptomyces albus J1074. The fdmM and fdmM1 genes code for two proteins with high sequence homology to each other but unknown function. In-frame deletion of each of the genes from the fdm cluster was accomplished in the S. albus host. Each mutant failed to produce FDM A and the key biosynthetic intermediate FDM E but produced various new metabolites, the titers of which were dramatically increased via overexpression of an fdm pathway-specific activator fdmR1. The Delta fdmM mutant strain accumulated three new compounds FDM M-1, FDM M-2, and FDM M-3, whereas the Delta fdmM1 mutant strain produced one new compound FDM M1-1. Isolation and structural characterization of these compounds enable us to propose that FdmM and FdmM1 catalyze the C-6 and C-8 hydroxylations for FDM biosynthesis, respectively. Homologs of FdmM and FdmM1 can be found in biosynthetic gene clusters of many other aromatic polyketides, ranging from dodecaketides to pentadecaketides, but to date all of them were annotated as proteins of unknown function. Based on the findings reported here for FdmM and FdmM1, we now propose similar functions for those proteins, and FdmM and FdmM1 therefore represent an emerging family of novel oxygenases responsible for hydroxylation of aromatic polyketide natural products. AD - [Chen, Yihua; Wendt-Pienkoski, Evelyn; Rajski, Scott R.; Shen, Ben] Univ Wisconsin, Div Pharmaceut Sci, Madison, WI 53705 USA. [Shen, Ben] Univ Wisconsin, Dept Chem, Madison, WI 53705 USA. [Shen, Ben] Univ Wisconsin, Natl Cooperat Drug Discovery Grp, Madison, WI 53705 USA. AN - ISI:000269734000008 AU - Chen, Y. H. AU - Wendt-Pienkoski, E. AU - Rajski, S. R. AU - Shen, B. DA - Sep KW - Streptomyces-griseus gene-cluster identification antibiotics oxidation cofactor pathway cloning Biochemistry & Molecular Biology LB - ISI 2009 09 24 IS - 37 N1 - English Article National Institutes of Health [CA113297] PY - 2009 SP - 24735-24743 ST - In Vivo Investigation of the Roles of FdmM and FdmM1 in Fredericamycin Biosynthesis Unveiling a New Family of Oxygenases T2 - Journal of Biological Chemistry TI - In Vivo Investigation of the Roles of FdmM and FdmM1 in Fredericamycin Biosynthesis Unveiling a New Family of Oxygenases VL - 284 ID - 4024 ER - TY - JOUR AB - Yeast antibody display has found a wide variety of applications including antibody affinity maturation, epitope mapping, and library screening. Here we report a yeast display immunoprecipitation (YDIP) technique that employs yeast cells displaying single-chain antibody fragments (scFv) on their surface as affinity capture reagents to isolate and characterize antigens. We show that displayed single-chain antibody fragments are active in a variety of detergent solutions commonly used for immunoprecipitation and that the antigen-antibody interaction can be accurately quantified by YDIP coupled with flow cytometry. The YDIP method has also been optimized so that it is compatible with commonly used protein characterization tools such as Western blotting, silver staining, and mass spectrometry. From complex protein mixtures, we have used YDIP to isolate, analyze and sequence both soluble and plasma membrane antigens using tandem mass spectrometry. In the case of the membrane antigen, YDIP coupled with tandem mass spectrometry was successful in identifying neural cell adhesion molecule (NCAM) as the antigen for an antibody previously selected as binding to the plasma membranes of brain endothelial cells. The presented method therefore has potential to facilitate antibody-antigen characterization. (C) 2008 Elsevier B.V. All rights reserved. AD - [Cho, Yong Ku; Chen, Irene; Shusta, Eric V.] Univ Wisconsin, Dept Biol & Chem Engn, Madison, WI 53706 USA. [Wei, Xin; Li, Lingjun] Univ Wisconsin, Sch Pharm, Madison, WI 53705 USA. [Wei, Xin; Li, Lingjun] Univ Wisconsin, Dept Chem, Madison, WI 53705 USA. AN - ISI:000264037000012 AU - Cho, Y. K. AU - Chen, I. AU - Wei, X. AU - Li, L. J. AU - Shusta, E. V. DA - Feb KW - Immunoprecipitation Yeast display Antigen identification Surface display human-antibodies polyacrylamide-gels proteome analysis phage display proteins detergents libraries silver rna Biochemical Research Methods Immunology LB - ISI 2009 03 26 IS - 1-2 N1 - English Article 0022-1759 PY - 2009 SP - 117-126 ST - A yeast display immunoprecipitation method for efficient isolation and characterization of antigens T2 - Journal of Immunological Methods TI - A yeast display immunoprecipitation method for efficient isolation and characterization of antigens VL - 341 ID - 3890 ER - TY - JOUR AB - Noncovalent interactions define and modulate biomolecular structure, function, and dynamics. In many protein secondary structures, an intimate interaction exists between adjacent carbonyl groups of the main-chain amide bonds. As this short contact contributes to the energetics of protein conformational, stability as welt as protein-ligand interactions, understanding its nature is crucial. The intimacy of the carbonyl groups could arise from a charge-charge or dipole-dipole interaction, or n ->pi* electronic delocalization. This last putative origin, which is reminiscent of the Burgi-Dunitz trajectory, involves delocalization of the lone pairs (n) of the oxygen (Oi-1,) of a peptide bond over the antibonding orbital, (pi*) of the carbonyl group (C-r=O-i) of the subsequent peptide bond. By installing isosteric chemical substituents in a peptidic model system and using NMR spectroscopy, X-ray diffraction analysis, and ab initio calculations to analyze the consequences, the intimate interaction between adjacent carbonyl groups is shown to arise primarily from n ->pi* electronic delocalization. This finding has implications for organic, biological, and medicinal chemistry. AD - [Raines, Ronald T.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. [Raines, Ronald T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Choudhary, Amit] Univ Wisconsin, Grad Program Biophys, Madison, WI 53706 USA. [Gandla, Deepa; Krow, Grant R.] Temple Univ, Dept Chem, Philadelphia AN - ISI:000266484900020 AU - Choudhary, A. AU - Gandla, D. AU - Krow, G. R. AU - Raines, R. T. DA - Jun KW - Collagen triple-helix main-chain atoms transition structures rotational barrier polyproline-ii conformations stability backbone models forces Chemistry, Multidisciplinary LB - ISI 2009 06 19 IS - 21 N1 - English Article NIH [AR044276]; NSF [CHE 0515635] PY - 2009 SP - 7244-+ ST - Nature of Amide Carbonyl-Carbonyl Interactions in Proteins T2 - Journal of the American Chemical Society TI - Nature of Amide Carbonyl-Carbonyl Interactions in Proteins VL - 131 ID - 3935 ER - TY - JOUR AB - The ultraviolet-initiated photochemical grafting of n-alkenes to surfaces of amorphous carbon, diamond, and carbon nanofibers has recently emerged as a way to impart new surface properties to these materials. Recent studies have shown that grafting on these materials is initiated by a novel photoelectron ejection process, evidenced by a strong dependence of reaction efficiency on the electron affinity of the reactant molecules. Yet, the role of different surface functional groups and the resulting changes in valence band density of states and surface work function have not been determined previously. Understanding the influence of surface carbonyl groups is particularly significant because C=O groups increase the surface work function but are also known to catalyze certain electron-transfer processes at carbon surfaces. Here, we use infrared spectroscopy, X-ray photoelectron spectroscopy (XPS), and ultraviolet photoelectron spectroscopy (UPS) to investigate how changes in surface termination (H-termination vs O-termination) and surface annealing impact the valence electronic structure and work function of the samples, and how these changes influence the grafting of alkenes to the surfaces. Four different n-alkenes bearing terminal groups were used in order to identify the role of the molecular electron affinity, using alkenes terminated with -NHCOCF3, -NHCOO(tert-butyl), -COOMe, and -CH3 groups. By using narrowly spaced interdigitated electrodes of amorphous carbon, we are able to directly detect the UV-induced photoemission. Our results show that O-termination of amorphous carbon surfaces enhances the photochemical grafting yield compared with H-termination of surfaces, contrary to what has been found on diamond surfaces. Surfaces annealed to increase the amount of sp(2)-hybridized carbon, and therefore being most metallic in character, have the highest reactivity. The changes in reactivity are explained in terms of the changes in valence electronic structure of the samples and the influence of oxygen on the photoelectron emission process that initiates the grafting reaction. AN - ISI:000262665600054 AU - Colavita, P. E. AU - Sun, B. AU - Wang, X. Y. AU - Hamers, R. J. DA - Jan DO - 10.1021/jp805933h LB - ISI 2009 02 12 IS - 4 N1 - Colavita, Paula E. Sun, Bin Wang, Xiaoyu Hamers, Robert J. PY - 2009 SN - 1932-7447 SP - 1526-1535 ST - Influence of Surface Termination and Electronic Structure on the Photochemical Grafting of Alkenes to Carbon Surfaces T2 - Journal of Physical Chemistry C TI - Influence of Surface Termination and Electronic Structure on the Photochemical Grafting of Alkenes to Carbon Surfaces UR - ://000262665600054 VL - 113 ID - 3793 ER - TY - JOUR AB - The small molecule component of chromoprotein enediyne antitumor antibiotics is biosynthesized through a convergent route, incorporating amino acid, polyketide, and carbohydrate building blocks around a central enediyne hydrocarbon core. The naphthoic acid moiety of the enediyne neocarzinostatin plays key roles in the biological activity of the natural product by interacting with both the carrier protein and duplex DNA at the site of action. We have previously described the in vitro characterization of an S-adenosylmethionine-dependent O-methyltransferase (NcsB1) in the neocarzinostatin biosynthetic pathway [Luo, Y., Lin, S., Zhang, J., Cooke, H. A., Bruner, S. D., and Shen, B. (2008) J. Biol. Chem. 283, 14694-14702]. Here we provide a structural basis for NcsB1 activity, illustrating that the enzyme shares an overall architecture with a large family of S-adenosylmethionine-dependent proteins. In addition, NcsB1 represents the first enzyme to be structurally characterized in the biosynthetic pathway of neocarzinostatin. By cocrystallizing the enzyme with various combinations of the cofactor and substrate analogues, details of the active site structure have been established. Changes in subdomain orientation were observed via comparison of structures in the presence and absence of substrate, suggesting that reorientation of the enzyme is involved in binding of the substrate. In addition, residues important for substrate discrimination were predicted and probed through site-directed mutagenesis and in vitro biochemical characterization. AD - [Cooke, Heather A.; Guenther, Elizabeth L.; Bruner, Steven D.] Boston Coll, Dept Chem, Merkert Chem Ctr, Chestnut Hill, MA 02467 USA. [Luo, Yinggang; Shen, Ben] Univ Wisconsin, Div Pharmaceut Sci, Madison, WI 53705 USA. [Shen, Ben] Univ Wisconsin, Dept Chem, Madison, WI 53705 USA. AN - ISI:000270459100029 AU - Cooke, H. A. AU - Guenther, E. L. AU - Luo, Y. G. AU - Shen, B. AU - Bruner, S. D. DA - Oct KW - Adenosyl-l-methionine gene-cluster crystal-structure polyketide synthase streptomyces-carzinostaticus apo-neocarzinostatin ligand complexes nmr system crystallography model Biochemistry & Molecular Biology LB - ISI 2009 10 15 IS - 40 N1 - English Article Damon Runyon Cancer Research Fund ; National Institutes of Health [CA78747, CA113297] PY - 2009 SP - 9590-9598 ST - Molecular Basis of Substrate Promiscuity for the SAM-Dependent O-Methyltransferase NcsB1, Involved in the Biosynthesis of the Enediyne Antitumor Antibiotic Neocarzinostatin T2 - Biochemistry TI - Molecular Basis of Substrate Promiscuity for the SAM-Dependent O-Methyltransferase NcsB1, Involved in the Biosynthesis of the Enediyne Antitumor Antibiotic Neocarzinostatin VL - 48 ID - 4038 ER - TY - JOUR AB - CD22 is an inhibitory coreceptor on the surface of B cells that attenuates B cell antigen receptor (BCR) signaling and, therefore, B cell activation. Elucidating the molecular mechanisms underlying the inhibitory activity of CD22 is complicated by the ubiquity of CD22 ligands. Although antigens can display CD22 ligands, the receptor is known to bind to sialylated glycoproteins on the cell surface. The propinquity of CD22 and cell-surface glycoprotein ligands has led to the conclusion that the inhibitory properties of the receptor are due to cis interactions. Here, we examine the functional consequences of trans interactions by employing sialylated multivalent antigens that can engage both CD22 and the BCR. Exposure of B cells to sialylated antigens results in the inhibition of key steps in BCR signaling. These results reveal that antigens bearing CD22 ligands are powerful suppressors of B cell activation. The ability of sialylated antigens to inhibit BCR signaling through trans CD22 interactions reveals a previously unrecognized role for the Siglec-family of receptors as modulators of immune signaling. AD - [Courtney, Adam H.; Puffer, Erik B.; Kiessling, Laura L.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000263652900008 AU - Courtney, A. H. AU - Puffer, E. B. AU - Pontrello, J. K. AU - Yang, Z. Q. AU - Kiessling, L. L. DA - Feb KW - B cell antigen receptor multivalency sialic acid siglec autoimmunity Protein-tyrosine phosphorylation co-receptors cis ligands binding syk kinase recognition lymphocytes complexes shp-1 Multidisciplinary Sciences LB - ISI 2009 03 13 IS - 8 N1 - English Article 0027-8424 PY - 2009 SP - 2500-2505 ST - Sialylated multivalent antigens engage CD22 in trans and inhibit B cell activation T2 - Proceedings of the National Academy of Sciences of the United States of America TI - Sialylated multivalent antigens engage CD22 in trans and inhibit B cell activation VL - 106 ID - 3817 ER - TY - JOUR AB - Ultrafast transient absorption experiments monitor the reaction of CN radicals with 16 different alkane, alcohol, and chloroalkane solutes in CH2Cl2 and with a smaller number of representative solutes in CHCl3 and CH3CCl3. In these experiments, 267-nm photolysis generates CN radicals, and transient electronic absorption at 400 nm probes their time evolution. A crucial feature of the reactions of CN radicals is their rapid formation of two different types of complexes with the solvent that have different stabilities and reactivities. The signature of the formation of these complexes is the CN transient absorption disappearing more slowly than the infrared transient absorption of the HCN product appears. Studying both the growth of HCN and the decay of the CN-solvent complexes in the reaction of CN with pentane in CHCl2 and CHCl3 solutions provides the information needed to build a kinetic model that accounts for the reaction of both complexes. This model permits analysis of the reaction of each of the 16 different solutes using only the decay of the CN transient absorption. The reaction of CN-solvent complexes with alkanes and chloroalkanes is slower than the corresponding reactions of Cl. However, the reactions of alcohols with both CN and Cl occur at about the same rate, likely reflecting additional complexation of the CN radical or its ICN precursor by the alcohol. The rates for the reactions of CN with the chloroalkanes decrease with increasing Cl content of the solute, in keeping with previous observations for the reactions of Cl in both gases and liquids. AD - [Crowther, Andrew C.; Carrier, Stacey L.; Preston, Thomas J.; Crim, F. Fleming] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000265383200006 AU - Crowther, A. C. AU - Carrier, S. L. AU - Preston, T. J. AU - Crim, F. F. DA - Apr KW - Bromine atom complexes organic-compounds spectroscopy dynamics recombination abstraction icn photodissociation dissociation reactivity Chemistry, Physical Physics, Atomic, Molecular & Chemical IS - 16 N1 - English Article National Science Foundation 1089-5639 PY - 2009 SP - 3758-3764 ST - Time-Resolved Studies of the Reactions of CN Radical Complexes with Alkanes, Alcohols, and Chloroalkanes T2 - Journal of Physical Chemistry A TI - Time-Resolved Studies of the Reactions of CN Radical Complexes with Alkanes, Alcohols, and Chloroalkanes VL - 113 ID - 3918 ER - TY - JOUR AB - Mass uptake of water vapor was measured as a function of relative humidity for indomethacin glasses prepared using physical vapor deposition at different substrate temperatures. Highly stable glasses were produced on substrates at 265 K (0.84T(g)) by depositing at 0.2 nm/s while samples similar to melt-cooled glasses were produced at 315 K and 5 nm/s. Samples deposited at 315 K absorb approximately the same amount of water as glasses prepared by supercooling the melt while stable glasses absorb a factor of 5 less water. Unexpectedly, the diffusion of water in the stable glass samples is 5-10 times faster than in the glass prepared by cooling the liquid. AD - [Dawson, Kevin J.; Kearns, Kenneth L.; Ediger, M. D.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Sacchetti, Mark J.; Zografi, George D.] Univ Wisconsin, Sch Pharm, Madison, WI 53706 USA. AN - ISI:000263529500027 AU - Dawson, K. J. AU - Kearns, K. L. AU - Ediger, M. D. AU - Sacchetti, M. J. AU - Zografi, G. D. KW - Chemistry, Physical LB - ISI 2009 03 05 N1 - English Article PARTIAL MOLAR VOLUME; SMALL MOLECULES; AMORPHOUS STATE; TRANSPORT-PROPERTIES; PHYSICAL-PROPERTIES; POLYMER GLASSES; SORBED WATER; PART I; T-G; DIFFUSION FEB 26 8 PY - 2009 SP - 2422-2427 ST - Highly Stable Indomethacin Glasses Resist Uptake of Water Vapor T2 - Journal of Physical Chemistry B TI - Highly Stable Indomethacin Glasses Resist Uptake of Water Vapor ID - 3765 ER - TY - JOUR AB - Mass uptake of water vapor was measured as a function of relative humidity for indomethacin glasses prepared using physical vapor deposition at different substrate temperatures. Highly stable glasses were produced on substrates at 265 K (0.84T(g)) by depositing at 0.2 nm/s while samples similar to melt-cooled glasses were produced at 315 K and 5 nm/s. Samples deposited at 315 K absorb approximately the same amount of water as glasses prepared by supercooling the melt while stable glasses absorb a factor of 5 less water. Unexpectedly, the diffusion of water in the stable glass samples is 5-10 times faster than in the glass prepared by cooling the liquid. AN - ISI:000263529500027 AU - Dawson, K. J. AU - Kearns, K. L. AU - Ediger, M. D. AU - Sacchetti, M. J. AU - Zografi, G. D. DA - Feb DO - 10.1021/jp808838t LB - ISI 2009 03 05 (Library clean-up) IS - 8 N1 - Dawson, Kevin J. Kearns, Kenneth L. Ediger, M. D. Sacchetti, Mark J. Zografi, George D. PY - 2009 SN - 1520-6106 SP - 2422-2427 ST - Highly Stable Indomethacin Glasses Resist Uptake of Water Vapor T2 - Journal of Physical Chemistry B TI - Highly Stable Indomethacin Glasses Resist Uptake of Water Vapor UR - ://000263529500027 VL - 113 ID - 3772 ER - TY - JOUR AB - Stable glasses of indomethacin (IMC) were prepared by using physical vapor deposition. Wide-angle X-ray scattering measurements were performed to characterize the average local structure. IMC glasses prepared at a substrate temperature of 0.84 T-g (where T-g is the glass transition temperature) and a deposition rate of 0.2 nm/s show a broad, high-intensity peak at low q values that is not present in the supercooled liquid or melt-quenched glasses. When annealed slightly above T-g, the new WAXS pattern transforms into the melt-quenched glass pattern, but only after very long annealing times. For a series of samples prepared at the lowest deposition rate, the new local packing arrangement is present only for deposition temperatures below T-g - 20 K, suggesting an underlying first-order liquid-to-liquid phase transition. AD - [Dawson, Kevin J.; Kearns, Kenneth L.; Ediger, M. D.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Yu, Lian] Univ Wisconsin, Sch Pharm, Madison, WI 53705 USA. [Steffen, Werner] Max Planck Inst Polymer Res, D-55128 Mainz, Germany. AN - ISI:000269632400016 AU - Dawson, K. J. AU - Kearns, K. L. AU - Yu, L. AU - Steffen, W. AU - Ediger, M. D. DA - Sep KW - entropy glass liquid-liquid transition supercooled X-ray scattering Glass-forming liquids supercooled liquids indomethacin polymorphs energy landscape polymer melts free-volume transition temperature dynamics phase Multidisciplinary Sciences LB - ISI 2009 09 17 IS - 36 N1 - English Article National Science Foundation [CHE-0724062, DMR-0804786, CHE-0605136] PY - 2009 SP - 15165-15170 ST - Physical vapor deposition as a route to hidden amorphous states T2 - Proceedings of the National Academy of Sciences of the United States of America TI - Physical vapor deposition as a route to hidden amorphous states VL - 106 ID - 4016 ER - TY - JOUR AB - The DUF1094 family contains over 100 bacterial proteins, all containing a conserved CXC motif, with unknown function. We solved the crystal structure of the Bacillus subtilis representative, the product of the yphP gene. The protein shows remarkable structural similarity to thioredoxins, with a canonical alpha beta alpha beta alpha beta beta alpha topology, despite low amino acid sequence identity to thioredoxin. The CXC motif is found in the loop immediately downstream of the first beta-strand, in a location equivalent to the CXXC motif of thioredoxins, with the first Cys occupying a position equivalent to the first Cys in canonical thioredoxin. The experimentally determined reduction potential of YphP is E-o' = -130 mV, significantly higher than that of thioredoxin and consistent with disulfide isomerase activity. Functional assays confirmed that the protein displays a level of isomerase activity that might be biologically significant. We propose a mechanism by which the members of this family catalyze isomerization using the CXC catalytic site. AD - [Gorres, Kelly L.; Raines, Ronald T.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. [Raines, Ronald T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Derewenda, Urszula; Boczek, Tomasz; Cooper, David; Derewenda, Zygmunt S.] Univ Virginia, Sch Med, Dept Mol Physiol & Biol Phys, Charlottesville, VA 22908 USA. [Derewenda, Urszula; Boczek, Tomasz; Cooper, David; Derewenda, Zygmunt S.] Univ Virginia, Sch Med, ISFI PSI2 Ctr, Charlottesville, VA 22908 USA. [Hung, Li-wei] Univ Calif Berkeley, Lawrence Berkeley Lab, Phys Biosci Div, Berkeley, CA 94720 USA. [Hung, Li-wei] Los Alamos Natl Lab, Div Phys, Los Alamos, NM 87545 USA. [Joachimiak, Andrzej] Argonne Natl Lab, Biosci Div, Midwest Ctr Struct Genom, Argonne, IL 60439 USA. [Joachimiak, Andrzej] Argonne Natl Lab, Struct Biol Ctr, Argonne, IL 60439 USA. AN - ISI:000269485500019 AU - Derewenda, U. AU - Boczek, T. AU - Gorres, K. L. AU - Yu, M. AU - Hung, L. W. AU - Cooper, D. AU - Joachimiak, A. AU - Raines, R. T. AU - Derewenda, Z. S. DA - Sep KW - Rational protein crystallization automated structure solution electron-density maps crystal-structure high-throughput cxxc-motif refinement fold site superfamily Biochemistry & Molecular Biology LB - ISI 2009 09 10 IS - 36 N1 - English Article NIH [U54 GM074946-01US, GM044783, U54 GM074942, T32 BM008505]; U.S. Department of Energy [DE-AC02-05CH11231] PY - 2009 SP - 8664-8671 ST - Structure and Function of Bacillus subtilis YphP, a Prokaryotic Disulfide Isomerase with a CXC Catalytic Motif T2 - Biochemistry TI - Structure and Function of Bacillus subtilis YphP, a Prokaryotic Disulfide Isomerase with a CXC Catalytic Motif VL - 48 ID - 4015 ER - TY - JOUR AB - The ribonuclease inhibitor (RI) is a cytosolic protein and a potent inhibitor of bovine pancreatic ribonuclease (RNase A). Amphibian homologues and variants of RNase A that evade RI are cytotoxic. Here, we employ RNA interference along with amphibian and:mammalian ribonucleases to demonstrate that RI protects cells against exogenous ribonucleases. These data indicate an imperative for the molecular evolution of RI and suggest a means of enhancing the cytotoxicity of mammalian ribonucleases. AD - [Dickson, Kimberly A.; Raines, Ronald T.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. [Raines, Ronald T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000266860400001 AU - Dickson, K. A. AU - Raines, R. T. DA - Jun KW - Human pancreatic ribonuclease protein-protein interfaces catalytic-activity rna interference mammalian-cells a variants onconase oocytes Biochemistry & Molecular Biology LB - ISI 2009 06 26 IS - 23 N1 - English Article National Institutes of Health [CA073808]; Louis and Elsa Thomsen Wisconsin Distinguished Fellowship ; College of Agricultural arid Life Sciences at the University of Wisconsin PY - 2009 SP - 5051-5053 ST - Silencing an Inhibitor Unleashes a Cytotoxic Enzyme T2 - Biochemistry TI - Silencing an Inhibitor Unleashes a Cytotoxic Enzyme VL - 48 ID - 3947 ER - TY - JOUR AB - Astrocytes are important regulators of normal brain function in mammals, including roles in synaptic signaling, synapse formation, and neuronal health and survival. Many of these functions are executed via secreted proteins. To analyze the astrocyte secretome, a combination of shotgun proteomics and bioinformatics was employed to analyze conditioned media from primary murine astrocyte cultures. Both two- and one-dimensional LC-MS/MS were used to analyze astrocyte secreted proteins, resulting in the identification of over 420 proteins. To refine our results, the intracellular protein contaminants were removed in silico using a cytoplasmic control. In additional rounds of refinement, putative secreted proteins were subjected to analysis by SignalP, SecretomeP, and gene ontology analysis, yielding a refined list of 187 secreted proteins. In conclusion, the use of shotgun proteomics combined with multiple rounds of data refinement produced a high quality catalog of astrocyte secreted proteins. AD - [Dowell, James A.; Johnson, Jeffrey A.; Li, Lingjun] Univ Wisconsin, Sch Pharm, Madison, WI 53705 USA. [Johnson, Jeffrey A.] Univ Wisconsin, Mol & Environm Toxicol Ctr, Madison, WI 53705 USA. [Johnson, Jeffrey A.; Li, Lingjun] Univ Wisconsin, Waisman Ctr, Madison, WI 53705 USA. [Johnson, Jeffrey A.; Li, Lingjun] Univ Wisconsin, Ctr Neurosci, Madison, WI 53705 USA. [Li, Lingjun] Univ Wisconsin, Dept Chem, Madison, WI 53705 USA. AN - ISI:000268661800036 AU - Dowell, J. A. AU - Johnson, J. A. AU - Li, L. J. DA - Aug KW - Astrocyte secreted proteins secretome proteomics mass spectrometry bioinformatics Growth-factor expression cancer-cell-lines hippocampal-neurons reactive astrocytes neurotrophic factor breast-cancer rat striatum glial-cells lc-ms/ms in-vivo Biochemical Research Methods LB - ISI 2009 08 13 IS - 8 N1 - English Article National Institutes of Environmental Health Sciences [ES08089, ES10042]; American Foundation for Pharmaceutical Education (AFPE) ; Alfred P. Sloan Research Fellowship PY - 2009 SP - 4135-4143 ST - Identification of Astrocyte Secreted Proteins with a Combination of Shotgun Proteomics and Bioinformatics T2 - Journal of Proteome Research TI - Identification of Astrocyte Secreted Proteins with a Combination of Shotgun Proteomics and Bioinformatics VL - 8 ID - 3992 ER - TY - JOUR AB - Efficient [2+2] heterodimerizations of dissimilar acyclic enones can be accomplished upon visible light irradiation in the presence of a ruthenium(II) photocatalyst. Similar cycloadditions under standard UV photolysis conditions are inefficient and unselective. Nevertheless, a diverse range of unsymmetrical tri- and tetrasubstituted cyclobutane structures can be produced in good yields and excellent diastereoselectivities using this new method. The reaction is promoted by any visible light source, and efficient, gram-scale cycloadditions can be conducted upon irradiating with ambient sunlight. AD - [Du, Juana; Yoon, Tehshik P.] Univ Wisconsin, Dept Chem, Madison, WI 53705 USA. AN - ISI:000271271800003 AU - Du, J. AU - Yoon, T. P. DA - Oct KW - Intramolecular cyclobutanation electron-transfer bis(enones) mechanism pathways Chemistry, Multidisciplinary LB - ISI 2009 11 12 IS - 41 N1 - English Article Beckman Foundation and the Research Corporation ; NSF [CHE-9208463, CHE9629688]; NIH [RR08389-01] PY - 2009 SP - 14604-+ ST - Crossed Intermolecular [2+2] Cycloadditions of Acyclic Enones via Visible Light Photocatalysis T2 - Journal of the American Chemical Society TI - Crossed Intermolecular [2+2] Cycloadditions of Acyclic Enones via Visible Light Photocatalysis VL - 131 ID - 4069 ER - TY - JOUR AB - Epstein-Barr virus (EBV) is the causative agent of infectious mononucleosis and a risk factor for developing a variety of lymphomas and carcinomas. EBV nuclear antigen 1 (EBNA1) is the only viral protein found in all EBV-related malignancies. It plays a key role in establishing and maintaining the altered state of cells transformed with EBV. EBNA1 is required for a variety of functions, including gene regulation, replication and maintenance of the viral genome, but the regulation of EBNA1's functions is poorly understood. We demonstrate that phosphorylation affects the functions of EBNA1. By using electron-transfer dissociation tandem mass spectrometry, ten specific phosphorylated EBNA1 residues were identified. A mutant derivative preventing the phosphorylation of all ten phosphosites retained the unusually long half-life and the ability to translocate, into the nucleus of wild-type EBNA1. This phosphorylation-deficient mutant, however, had a significantly reduced ability to activate transcription and to maintain EBV's plasmids in cells. AD - [Duellman, Sarah J.; Burgess, Richard R.] Univ Wisconsin, McArdle Lab Canc Res, Madison, WI 53706 USA. [Thompson, Katie L.; Coon, Joshua J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Coon, Joshua J.] Univ Wisconsin, Dept Biomol Chem, Madison, WI 53706 USA. AN - ISI:000269676300022 AU - Duellman, S. J. AU - Thompson, K. L. AU - Coon, J. J. AU - Burgess, R. R. DA - Sep KW - Electron-transfer dissociation orbitrap mass-spectrometer nuclear antigen 1 dna-replication bovine papillomavirus sequence-analysis latent infection stable replication escherichia-coli plasmid origin Biotechnology & Applied Microbiology Virology LB - ISI 2009 09 17 N1 - English Article The Beckman Foundation ; Eli Lilly ; National Institutes of Health [1R01GM080148] Part 9 PY - 2009 SP - 2251-2259 ST - Phosphorylation sites of Epstein-Barr virus EBNA1 regulate its function T2 - Journal of General Virology TI - Phosphorylation sites of Epstein-Barr virus EBNA1 regulate its function VL - 90 ID - 4020 ER - TY - JOUR AB - UDP-Galactopyranose mutase (UGM or Glf), which catalyzes the interconversion of UDP-galactopyranose and UDP-galactofuranose, is implicated in the viability and virulence of multiple pathogenic microorganisms. Here we report the synthesis of high-affinity ligands for UGM homologues from Klebsiella pneumoniae and Mycobacterium tuberculosis. The potency of these compounds stems from their ability to access both the substrate binding pocket and an adjacent site. AD - [Dykhuizen, Emily C.; Kiessling, Laura L.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. USA. AN - ISI:000262018700049 AU - Dykhuizen, E. C. AU - Kiessling, L. L. DA - Jan KW - Cell-wall core mycobacterium-tuberculosis efficient synthesis inhibitors probes galactofuranose identification spectroscopy mechanism analogs Chemistry, Organic LB - ISI 2009 01 22 IS - 1 N1 - English Article 1523-7060 PY - 2009 SP - 193-196 ST - Potent Ligands for Prokaryotic UDP-Galactopyranose Mutase That Exploit an Enzyme Subsite T2 - Organic Letters TI - Potent Ligands for Prokaryotic UDP-Galactopyranose Mutase That Exploit an Enzyme Subsite VL - 11 ID - 3733 ER - TY - JOUR AB - We still know very little about how proteins achieve their native three-dimensional structure in vitro and in the cell. Folding studies as proteins emerge from the mega Dalton-sized ribosome pose special challenges due to the large size and complicated nature of the ribosome-nascent chain complex. This work introduces a combination of three-component analysis of fluorescence depolarization decays (including the presence of two local motions) and in-cone analysis of diffusive local dynamics to investigate the spatial constraints experienced by a protein emerging from the ribosomal tunnel. We focus on E. coli ribosomes and an all-alpha-helical nascent globin in the presence and absence of the cotranslationally active chaperones DnaK and trigger factor. The data provide insights on the dynamic nature and structural plasticity of ribosome-nascent chain complexes. We find that the sub-ns motions of the N-terminal fluorophore, reporting on the globin dynamics in the vicinity of the N terminus, are highly constrained both inside and outside the ribosomal tunnel, resulting in high-order parameters (>0.85) and small cone semiangles (<30 degrees). The shorter globin chains buried inside the tunnel are less spatially constrained than those of a reference sequence from a natively unfolded protein, suggesting either that the two nascent chain sequences have a different secondary structure and therefore sample different regions of the tunnel or that the tunnel undergoes local structural adjustments to accommodate the globin sequence. Longer globins emerging out of the ribosomal tunnel are also found to have highly spatially constrained slow (ns) motions. There are no observable spectroscopic changes in the absence of bound chaperones. AD - [Ellis, Jamie P.; Culviner, Peter H.; Cavagnero, Silvia] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000270501400001 AU - Ellis, J. P. AU - Culviner, P. H. AU - Cavagnero, S. DA - Oct KW - protein folding ribosome globin nascent chain dynamics frequency domain fluorometry cone angle analysis Trigger factor-binding exit tunnel cryoelectron microscopy different conformations molecular-mechanism chain protein polypeptide chaperones recognition Biochemistry & Molecular Biology LB - ISI 2009 10 15 IS - 10 N1 - English Article National Institutes of Health [R21GM071012]; National Science Foundation [MCB-0544182] PY - 2009 SP - 2003-2015 ST - Confined dynamics of a ribosome-bound nascent globin: Cone angle analysis of fluorescence depolarization decays in the presence of two local motions T2 - Protein Science TI - Confined dynamics of a ribosome-bound nascent globin: Cone angle analysis of fluorescence depolarization decays in the presence of two local motions VL - 18 ID - 4034 ER - TY - JOUR AB - The title compound ([3,5-Me(2)bpzaH(2)][AuCl4]Cl, 1) (Me(2)bpza = bis(3,5-dimethylpyrazolyl)acetic acid), was prepared by reacting H[AuCl4] with 3,5-Me(2)bpza; and spectroscopically and structurally characterized. In the solid state structure of 1, the pyrazolyl ligand is doubly protonated to form two strong charge assisted hydrogen bonds of the type N*-H center dot center dot center dot Cl- with the single chloride anion whilst the [AuCl4](-) anion remains discrete. The anti-HIV-1 activity of 1 was determined by a colorimetric direct enzyme reverse transcriptase (RT) assay and a fluorogenic protease (PR) assay. Compound 1 significantly (p < 0.05) inhibited RT over a concentration range of 5-250 mu M and inhibited HIV-1 protease at 100 mu M. Compound 1 inhibited two very important HIV-1 enzymes (RT and PR) in direct enzyme assays and therefore warrants further evaluation. (C) 2008 Elsevier Inc. All rights reserved. AN - ISI:000262919700005 AU - Fonteh, P. N. AU - Keter, F. K. AU - Meyer, D. AU - Guzei, I. A. AU - Darkwa, J. DA - Feb DO - 10.1016/j.jinorgbio.2008.10.001 LB - ISI 2009 02 20 IS - 2 N1 - Fonteh, Pascaline N. Keter, Frankline K. Meyer, Debra Guzei, Ilia A. Darkwa, James PY - 2009 SN - 0162-0134 SP - 190-194 ST - Tetra-chloro-(bis-(3,5-dimethylpyrazolyl)methane)gold(III) chloride: An HIV-1 reverse transcriptase and protease inhibitor T2 - Journal of Inorganic Biochemistry TI - Tetra-chloro-(bis-(3,5-dimethylpyrazolyl)methane)gold(III) chloride: An HIV-1 reverse transcriptase and protease inhibitor UR - ://000262919700005 VL - 103 ID - 3784 ER - TY - JOUR AB - Oligomers of N-substituted glycine, or peptoids, are versatile tools to probe biological processes and hold promise as therapeutic agents. An underlying theme in the majority of recent peptoid research is the connection between peptoid function and peptoid structure. For certain applications, well-folded peptoids are essential for activity, while unstructured peptoids appear to suffice, or even are superior, for other applications. Currently, these structure-function connections are largely made after the design, synthesis, and characterization process. However, as guidelines for peptoid folding are elucidated and the known biological activities are expanded, we anticipate these connections will provide a pathway toward the de novo design of functional peptoids. In this perspective, we review several of the peptoid structure-function relationships that have been delineated over the past five years. AD - [Fowler, Sarah A.; Blackwell, Helen E.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000265195100002 AU - Fowler, S. A. AU - Blackwell, H. E. KW - Solid-phase synthesis relative cell-permeability aromatic side-chains zinc-binding antimicrobial peptides nonbiological polymer staphylococcus-aureus regulatory particle secondary structure drug-delivery Chemistry, Organic LB - ISI 2009 04 30 IS - 8 N1 - English Article 1477-0520 PY - 2009 SP - 1508-1524 ST - Structure-function relationships in peptoids: Recent advances toward deciphering the structural requirements for biological function T2 - Organic & Biomolecular Chemistry TI - Structure-function relationships in peptoids: Recent advances toward deciphering the structural requirements for biological function VL - 7 ID - 3910 ER - TY - JOUR AB - N-Substituted glycine oligomers, or peptoids, have emerged as an important class of foldamers for the study of biomolecular interactions and for potential use as therapeutic agents. However, the design of peptoids with well-defined conformations a priori remains a formidable challenge. New approaches are required to address this problem, and the systematic study of the role of individual monomer units in the global peptoid folding process represents one strategy. Here, we report our efforts toward this approach through the design, synthesis, and characterization of peptoids containing nitroaromatic monomer units. This work required the synthesis of a new chiral amine building block, (S)-1-(2-nitrophenyl)ethanamine (s2ne), which could be readily installed into peptoids using standard solid-phase peptoid synthesis techniques. We designed a series of peptoid nonamers that allowed us to probe the effects of this relatively electron-deficient and sterically encumbered alpha-chiral side chain on peptoid structure, namely, the peptoid threaded loop and helix. Circular dichroism spectroscopy of the peptoids revealed that the nitroaromatic monomer has a significant effect on peptoid secondary structure. Specifically, the threaded loop structure was disrupted in a nonamer containing alternating N-(S)-1-phenylethylglycine (Nspe) and Ns2ne monomers, and the major conformation was helical instead. Indeed, placement of a single Ns2ne at the N-terminal position of (Nspe)(9) resulted in a destabilized form of the threaded loop structure relative to the homononamer (Nspe)(9). Conversely, we observed that incorporation of N-(S)-1-(4-nitrophenyl)ethylglycine (Nsnp, a p-nitro monomer) at the N-terminal position stabilized the threaded loop structure relative to (Nspe())9. Additional experiments revealed that nitroaromatic side chains can influence peptoid nonamer folding by modulating the strength of key intramolecular hydrogen bonds in the peptoid threaded loop structure. Steric interactions were also implicated for the Ns2ne monomer. Overall, this study provides further evidence that aromatic side-chain structure, even if perturbed in a single monomer unit, can strongly influence local peptoid backbone conformation. AN - ISI:000263316600002 AU - Fowler, S. A. AU - Luechapanichkul, R. AU - Blackwell, H. E. DA - Feb DO - 10.1021/jo8023363 LB - ISI 2009 02 26 IS - 4 N1 - Fowler, Sarah A. Luechapanichkul, Rinrada Blackwell, Helen E. PY - 2009 SN - 0022-3263 SP - 1440-1449 ST - Synthesis and Characterization of Nitroaromatic Peptoids: Fine Tuning Peptoid Secondary Structure through Monomer Position and Functionality T2 - Journal of Organic Chemistry TI - Synthesis and Characterization of Nitroaromatic Peptoids: Fine Tuning Peptoid Secondary Structure through Monomer Position and Functionality UR - ://000263316600002 VL - 74 ID - 3777 ER - TY - JOUR AB - Well-defined molecular layers can be formed on the surface of nanocrystalline anatase TiO2 by photochemically grafting organic molecules bearing a terminal vinyl group. The molecular layers produced are shown to have minimal oxidation and are able to be patterned and uniformly grafted through optically thick nanocrystalline films. Stability tests show that the layers have excellent stability in deionized water at 80 degrees C, aqueous solutions at pH = 1.0 and pH = 10.3 at 65 degrees C, and acetonitrile for time scales approaching 1200 h. Degradation of the films in deionized water occurs using a AM1.5 full-spectrum solar simulator as an illumination Source but is partially suppressed by filtering with a 400 nm UV blocking filter which blocks the above-bandgap light. A mechanism is proposed for the grafting reaction in which the Surface hydroxyl groups trap photoexcited holes, facilitating reaction with the vinyl group. AD - [Franking, Ryan A.; Landis, Elizabeth C.; Hamers, Robert J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000269655000038 AU - Franking, R. A. AU - Landis, E. C. AU - Hamers, R. J. DA - Sep KW - Self-assembled monolayers sensitized solar-cells charge-transfer sensitizers porous vycor glass titanium-dioxide diamond surfaces thin-films protein adsorption hydroxyl-groups photocatalytic hydrogenation Chemistry, Physical LB - ISI 2009 09 17 IS - 18 N1 - English Article National Science Foundation [CHE-0613010, DMR0520527]; Merck, Inc. PY - 2009 SP - 10676-10684 ST - Highly Stable Molecular Layers on Nanocrystalline Anatase TiO2 through Photochemical Grafting T2 - Langmuir TI - Highly Stable Molecular Layers on Nanocrystalline Anatase TiO2 through Photochemical Grafting VL - 25 ID - 4018 ER - TY - JOUR AB - Approaches to the fabrication of surfaces that combine methods for the topographic patterning of soft materials with opportunities for facile, post-fabrication chemical functionalization could contribute significantly to advances in biotechnology and a broad range of other areas. Here, we report methods that can be used to introduce well-defined nano- and microscale topographic features to thin films of reactive polymers containing azlactone functionality using nanoimprint lithography (NIL). We demonstrate that NIL can be used to imprint topographic patterns into thin films of poly(2-vinyl-4,4-dimethylazlactone) and a copolymer of methyl methacrylate and 2-vinyl-4,4-dimethylazlactone using silicon masters having patterns of grooves and ridges ranging in width from 400 nm to 2 mu m, demonstrating the potential of this method to transfer patterns to films of these reactive polymers over a range of feature sizes and densities. We demonstrate further that the azlactone functionality of these polymers survives temperatures and pressures associated with NIL, and that topographically patterned films can be readily functionalized post-fabrication by treatment of surface-accessible azlactone functionality with small molecules and polymers containing primary amines. The results of experiments in which NIH-3T3 cells were seeded onto films imprinted with lined patterns having a pitch of 4 mu um demonstrated that cells attach and proliferate on these azlactone-containing films and that they align in the direction of the imprinted pattern. Finally, we demonstrate that the treatment of these materials with amine-functionalized poly(ethylene glycol) (PEG) can be used to create regions of topographically patterned films that prevent cell adhesion. The results of this study suggest approaches to the functionalization of topographically patterned surfaces with a broad range of chemical functionality (e.g., peptides, proteins, carbohydrates, etc.) of biotechnological interest. The ability to manipulate and define both the physical topography and chemical functionality of these reactive materials could provide opportunities to investigate the combined effects of substrate topography and chemical functionality on cell behavior and may also be useful in a broad range of other applications. AD - [Fredin, Nathaniel J.; Broderick, Adam H.; Lynn, David M.] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA. [Buck, Maren E.; Lynn, David M.] Univ Wisconsin, Dept Chem, Madison AN - ISI:000265098800047 AU - Fredin, N. J. AU - Broderick, A. H. AU - Buck, M. E. AU - Lynn, D. M. DA - Apr KW - Self-assembled monolayers corneal epithelial-cells block-copolymer films protein adsorption soft lithography recent progress mu-cp surfaces adhesion chemistry Biochemistry & Molecular Biology Chemistry, Organic Polymer Science LB - ISI 2009 04 30 IS - 4 N1 - English Article 1525-7797 PY - 2009 SP - 994-1003 ST - Nanoimprinted Thin Films of Reactive, Azlactone-Containing Polymers: Combining Methods for the Topographic Patterning of Cell Substrates with Opportunities for Facile Post-Fabrication Chemical Functionalization T2 - Biomacromolecules TI - Nanoimprinted Thin Films of Reactive, Azlactone-Containing Polymers: Combining Methods for the Topographic Patterning of Cell Substrates with Opportunities for Facile Post-Fabrication Chemical Functionalization VL - 10 ID - 3912 ER - TY - JOUR AB - Pairs of short peptide strands can be induced to adopt an antiparallel beta-sheet secondary structure in aqueous solution via a macrocyclic constraint, as illustrated by many natural and designed peptides. We show that an analogous strategy is successful for creation of small units of parallel beta-sheet secondary structure in aqueous solution. Cyclization in this case requires nonpeptide segments for N-to-N and C-to-C interstrand linkage. Surprisingly, we find that only one of these segments needs to be preorganized. AD - [Freire, Felix; Gellman, Samuel H.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000267623100017 AU - Freire, F. AU - Gellman, S. H. DA - Jun KW - Protein secondary structure diffusion nmr-spectroscopy nuclear-magnetic-resonance model systems aqueous-solution chemical-models peptides water defensins hairpins Chemistry, Multidisciplinary LB - ISI 2009 07 17 IS - 23 N1 - English Article NIH [GM61238]; MEC-Fulbright Post-Doctoral Fellowship ; NSF PY - 2009 SP - 7970-+ ST - Macrocyclic Design Strategies for Small, Stable Parallel beta-Sheet Scaffolds T2 - Journal of the American Chemical Society TI - Macrocyclic Design Strategies for Small, Stable Parallel beta-Sheet Scaffolds VL - 131 ID - 3958 ER - TY - JOUR AB - The ligand solid angle approach has been successfully applied to the analysis of the catecholate complexes of Sb(III) and Sb(V). The Sb(III) complexes possess an electron lone pair that influences their molecular structure but does not behave as a classic "ligand" when intermolecular interactions are concerned. The Sb(III) complexes in solid state form numerous intermolecular interactions that effectively increase metal shielding, and herein we analyze the effects of the lone pair of electrons on the complex coordination geometry. In the five-coordinate R(3)CatSb(V) complexes (Cat = catecholate ligand, R = Ph, Me, Cl) the metal is shielded by 87(3)% and multiple intermolecular contacts are observed. The central metal in the six-coordinate antimony(V) complexes R(3)CatSb(V) center dot A L is shielded to the extent of 89(2)% and no strong attractive intermolecular interactions are detected in solid state. Thus, the metal shielding in excess of 85% is required to prevent complex dimerization or additional ligation of the central atom by a nucleophile. AD - [Fukin, Georgy K.; Baranov, Evgenii V.; Domrachev, Georgy A.] Russian Acad Sci, GA Razuvaev Inst Organomet Chem, Nizhnii Novgorod 603950, Russia. [Guzei, Ilia A.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000267593400012 AU - Fukin, G. K. AU - Guzei, I. A. AU - Baranov, E. V. AU - Domrachev, G. A. DA - Aug KW - Catecholate complexes of Sb(III) and Sb(V) Supramolecular structure Steric saturation of the metal coordination environment The ligand solid angle approach Transition-metal-complexes pentacoordinated molecules 5-coordinated antimony guanidinate complexes crystal-structure coordination stacking geometry oxygen Chemistry, Multidisciplinary Chemistry, Physical Crystallography LB - ISI 2009 07 17 IS - 4 N1 - English Article RFBR [06-0332728a, 1396.2008.3] PY - 2009 SP - 643-654 ST - Analysis of the supramolecular structures of Sb(III) and Sb(V) catecholate complexes from the viewpoint of ligand solid angles T2 - Structural Chemistry TI - Analysis of the supramolecular structures of Sb(III) and Sb(V) catecholate complexes from the viewpoint of ligand solid angles VL - 20 ID - 3956 ER - TY - JOUR AB - Chamber studies of glyoxal uptake onto ammonium sulphate aerosol were performed under dark and irradiated conditions to gain further insight into processes controlling glyoxal uptake onto ambient aerosol. Organic fragments from glyoxal dimers and trimers were observed within the aerosol under dark and irradiated conditions. Glyoxal monomers and oligomers were the dominant organic compounds formed under the conditions of this study; glyoxal oligomer formation and overall organic growth were found to be reversible under dark conditions. Analysis of high-resolution time-of-flight aerosol mass spectra provides evidence for irreversible formation of carbon-nitrogen (C-N) compounds in the aerosol. We have identified 1H-imidazole-2-carboxaldehyde as one C-N product. To the authors' knowledge, this is the first time C-N compounds resulting from condensed phase reactions with ammonium sulphate seed have been detected in aerosol. Organosulphates were not detected under dark conditions. However, active photochemistry was found to occur within aerosol during irradiated experiments. Carboxylic acids and organic esters were identified within the aerosol. An organosulphate, which had been previously assigned as glyoxal sulphate in ambient samples and chamber studies of isoprene oxidation, was observed only in the irradiated experiments. Comparison with a laboratory synthesized standard and chemical considerations strongly suggest that this organosulphate is glycolic acid sulphate, an isomer of the previously proposed glyoxal sulphate. Our study shows that reversibility of glyoxal uptake should be taken into account in SOA models and also demonstrates the need for further investigation of C-N compound formation and photochemical processes, in particular organosulphate formation. AD - [Galloway, M. M.; Keutsch, F. N.] Univ Wisconsin, Dept Chem, Madison AN - ISI:000266556000007 AU - Galloway, M. M. AU - Chhabra, P. S. AU - Chan, A. W. H. AU - Surratt, J. D. AU - Flagan, R. C. AU - Seinfeld, J. H. AU - Keutsch, F. N. KW - Secondary organic aerosol mass-spectrometry high-resolution tropospheric aerosols oligomer formation absorption-model aqueous glyoxal real-time photooxidation phase Meteorology & Atmospheric Sciences LB - ISI 2009 06 19 IS - 10 N1 - English Article Camille and Henry Dreyfus Foundation ; NDSEG-ARO, the US Department of Energy [DE-FG0205ER63 983]; US Environmental Protection Agency STAR [RD-83 374 901]; National Science Foundation, Division of Atmospheric Sciences, Atmospheric Chemistry Program [0 724 912, CHE-0 541 745]; NDSEG-ARO PY - 2009 SP - 3331-3345 ST - Glyoxal uptake on ammonium sulphate seed aerosol: reaction products and reversibility of uptake under dark and irradiated conditions T2 - Atmospheric Chemistry and Physics TI - Glyoxal uptake on ammonium sulphate seed aerosol: reaction products and reversibility of uptake under dark and irradiated conditions VL - 9 ID - 3940 ER - TY - JOUR AB - A dual pressure linear ion trap mass spectrometer was modified to permit infrared multiphoton dissociation (IRMPD) in each of the two cells-the first a high pressure cell operated at nominally 5 x 10(-3) Torr and the second a low pressure cell operated at nominally 3 x 10(-4) Torr. When IRMPD was performed in the high pressure cell, most peptide ions did not undergo significant photodissociation; however, in the low pressure cell peptide cations were efficiently dissociated with less than 25 ms of IR irradiation regardless of charge state. IRMPD of peptide cations allowed the detection of low m/z product ions including the y(1) fragments and immonium ions which are not typically observed by ion trap collision induced dissociation (CID). Photodissociation efficiencies of similar to 100% and MS/MS (tandem mass spectrometry) efficiencies of greater than 60% were observed for both multiply and singly protonated peptides. In general, higher sequence coverage of peptides was obtained using IRMPD over CID. Further, greater than 90% of the product ion current in the IRMPD mass spectra of doubly charged peptide ions was composed of singly charged product ions compared to the CID mass spectra in which the abundances of the multiply and singly charged product ions were equally divided. Highly charged primary product ions also underwent efficient photodissociation to yield singly charged secondary product ions, thus simplifying the IRMPD product ion mass spectra. AD - [Gardner, Myles W.; Smith, Suncerae I.; Madsen, James A.; Brodbelt, Jennifer S.] Univ Texas Austin, Dept Chem & Biochem, Austin, TX 78751 USA. [Schwartz, Jae C.; Stafford, George C., Jr.] Thermo Fisher Sci, San Jose, CA 95134 USA. [Coon, Joshua J.] Univ Wisconsin, Dept Biomol Chem, Madison, WI 53706 USA. [Ledvina, Aaron R.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000270361100037 AU - Gardner, M. W. AU - Smith, S. I. AU - Ledvina, A. R. AU - Madsen, J. A. AU - Coon, J. J. AU - Schwartz, J. C. AU - Stafford, G. C. AU - Brodbelt, J. S. DA - Oct KW - Collisionally activated dissociation protonated peptides protein-structure photodissociation nm fragmentation ionization proteomics Chemistry, Analytical LB - ISI 2009 10 15 IS - 19 N1 - English Article NSF [CHE-0718320]; NIH [R01 TGM080148]; Welch Foundation [F1155] PY - 2009 SP - 8109-8118 ST - Infrared Multiphoton Dissociation of Peptide Cations in a Dual Pressure Linear Ion Trap Mass Spectrometer T2 - Analytical Chemistry TI - Infrared Multiphoton Dissociation of Peptide Cations in a Dual Pressure Linear Ion Trap Mass Spectrometer VL - 81 ID - 4039 ER - TY - JOUR AB - As stringent tests for the molecular model and computational protocol, microscopic pK(a) calculations are performed for the key residue, Glu286, in cytochrome c oxidase (CcO) using a combined quantum mechanical/molecular mechanical (QM/MM) potential and a thermodynamic integration protocol. The impact of the number of water molecules in the hydrophobic cavity and protonation state of several key residues (e.g., His334, Cu-B-bound water, and PRDa3) on the computed microscopic pK(a) values of Glu286 has been systematically examined. To help evaluate the systematic errors in the QM/MM-based protocol, microscopic pK(a) calculations have also been carried out for sites in a soluble protein (Asp70 in T4 lysozyme) and a better-characterized membrane protein (Asp85 in bacteriorhodopsin). Overall, the results show a significant degree of internal consistency and reproducibility that support the effectiveness of the computational framework. Although the number of water molecules in the hydrophobic cavity does not greatly influence the computed pK(a) of Glu286, the protonation states of several residues, some of which are rather far away, have more significant impacts. Adopting the standard protonation state for all titratable residues leaves a large net charge on the system and a significantly elevated pK(a) for Glu286, highlighting that any attempt to address the energetics of proton transfers in CcO at a microscopic level should carefully select the protonation state of residues, even those not in the immediate neighborhood of the active site. The calculations indirectly argue against the deprotonation of His334 for the proton pumping process, although further studies that explicitly compute its pK(a) are required for a more conclusive statement. Finally, the deprotonated Glu286 is found to be in a stable water-mediated connection with PRDa3 for at least several nanoseconds when this presumed pumping site is protonated. This does not support the proposed role of Glu286 as a robust gating valve that prevents proton leakage, although a conclusive statement awaits a more elaborate characterization of the Glu286-PRDa3 connectivity with free energy simulations and a protonated PRDa3. The large sets of microscopic simulations performed here have provided useful guidance to the establishment of a meaningful molecular model and effective computational protocol for explicitly analyzing the proton transfer kinetics in CcO, which is required for answering key questions regarding the pumping function of this fascinating and complex system. AD - [Ghosh, Nilanjan; Prat-Resina, Xavier; Cui, Qiang] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Gunner, M. R.] CUNY, Dept Phys, New York, NY 10031 USA. AN - ISI:000264272700021 AU - Ghosh, N. AU - Prat-Resina, X. AU - Gunner, M. R. AU - Cui, Q. DA - Mar KW - Heme-copper oxidases effective core potentials proton-transfer reactions functional tight-binding monte-carlo simulations retinal schiff-base free-energy electron-transfer computer-simulation qm/mm simulations Biochemistry & Molecular Biology LB - ISI 2009 04 03 IS - 11 N1 - English Review 0006-2960 PY - 2009 SP - 2468-2485 ST - Microscopic pK(a) Analysis of Glu286 in Cytochrome c Oxidase (Rhodobacter sphaeroides): Toward a Calibrated Molecular Model T2 - Biochemistry TI - Microscopic pK(a) Analysis of Glu286 in Cytochrome c Oxidase (Rhodobacter sphaeroides): Toward a Calibrated Molecular Model VL - 48 ID - 3894 ER - TY - JOUR AB - Helix bundles are among the most widely studied tertiary and quaternary structural motifs in proteins. Here we present the crystal structure of an alpha/beta-peptide foldamer that adopts a tetrameric helix-bundle quaternary structure with a hydrophobic core composed solely of beta-amino acids. The structure displays features that are unprecedented among all known helix bundles composed of either a-peptides or peptidic foldamers. The tetramer is characterized by an asymmetry of interaction between neighboring hetices, and the side-chain packing within the hydrophobic core differs fundamentally from the knobs-into-holes arrangement typical of most helix bundles. AD - [Giuliano, Michael W.; Horne, W. Seth; Gellman, Samuel H.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000268395000001 AU - Giuliano, M. W. AU - Horne, W. S. AU - Gellman, S. H. DA - Jul KW - Coiled coils specificity proteins design stability foldamers bonds Chemistry, Multidisciplinary LB - ISI 2009 08 13 IS - 29 N1 - English Article PY - 2009 SP - 9860-+ ST - An alpha/beta-Peptide Helix Bundle with a Pure beta(3)-Amino Acid Core and a Distinctive Quaternary Structure T2 - Journal of the American Chemical Society TI - An alpha/beta-Peptide Helix Bundle with a Pure beta(3)-Amino Acid Core and a Distinctive Quaternary Structure VL - 131 ID - 3990 ER - TY - JOUR AB - Tandem mass spectra (MS/MS) produced using electron transfer dissociation (ETD) differ from those derived from collision-activated dissociation (CAD) in several important ways. Foremost, the predominant fragment ion series are different: c- and z(center dot)-type ions are favored in ETD spectra while b- and y-type ions comprise the bulk of the fragments in CAD spectra. Additionally, ETD spectra possess charge-reduced precursors and unique neutral losses. Most database search algorithms were designed to analyze CAD spectra, and have only recently been adapted to accommodate c- and z(center dot)-type ions; therefore, inclusion of these additional spectral features can hinder identification, leading to lower confidence scores and decreased sensitivity. Because of this, it is important to pre-process spectral data before submission to a database search to remove those features that cause complications. Here, we demonstrate the effects of removing these features on the number Of unique peptide identifications at a 1% false discovery rate (FDR) using the open mass spectrometry search algorithm (OMSSA). When analyzing two biologic replicates of a yeast protein extract in three total analyses, the number of unique identifications with a similar to 1% FDR increased from 4611 to 5931 upon spectral preprocessing-an increase of similar to 28.6%. We outline the most effective pre-processing methods, and provide free software containing these algorithms. (J Am Soc Mass Spectrom 2009, 20, 1435-1440) (C) 2009 American Society for Mass Spectrometry AD - [Good, David M.; Wenger, Craig D.; McAlister, Graeme C.; Coon, Joshua J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Bai, Dina L.; Hunt, Donald F.] Univ Virginia, Dept Chem, Charlottesville, VA USA. [Hunt, Donald F.] Univ Virginia, Dept Pathol, Charlottesville, VA 22903 USA. [Coon, Joshua J.] Univ Wisconsin, Dept Biomol Chem, Madison, WI 53706 USA. AN - ISI:000268739900007 AU - Good, D. M. AU - Wenger, C. D. AU - McAlister, G. C. AU - Bai, D. L. AU - Hunt, D. F. AU - Coon, J. J. DA - Aug KW - Electron-transfer dissociation tandem mass-spectrometry side-chain losses capture dissociation sequence-analysis proteomics Chemistry, Analytical Chemistry, Physical Spectroscopy LB - ISI 2009 08 20 IS - 8 N1 - English Article NIH [5T32GM08349]; University of Wisconsin ; Beckman Foundation ; Eli Lilly ; National Institutes of Health [IR01GM080148] PY - 2009 SP - 1435-1440 ST - Post-Acquisition ETD Spectral Processing for Increased Peptide Identifications T2 - Journal of the American Society for Mass Spectrometry TI - Post-Acquisition ETD Spectral Processing for Increased Peptide Identifications VL - 20 ID - 4004 ER - TY - JOUR AB - Prolyl 4-hydroxylase (P4H) is a nonheme iron dioxygenase that catalyzes the posttranslational hydroxylation of (2S)-proline (Pro) residues in protocollagen strands. The resulting (2S,4R)-4-hydroxyproline (Hyp) residues are essential for the folding, secretion, and stability of the collagen triple helix. P4H uses alpha-ketoglutarate and O-2 as cosubstrates, and forms succinate and CO2 as well as Hyp. Described herein is the first assay for P4H that continuously and directly detects turnover of the proline-containing Substrate. This assay is based on (2S,4S)-4-fluoroproline (flp), a proline analogue that is transformed into (2S)-4-ketoproline (Kep) and inorganic fluoride by P4H. The fluoride ion, and thus turnover by P4H, is detected by a fluoride ion-selective electrode. Using this assay, steady-state kinetic parameters for the human P4H-catalyzed turnover of a flp-containing peptide were determined and found to be comparable to those obtained with a discontinuous HPLC-based assay. In addition, this assay can be used to Characterize P4H variants, as demonstrated by a comparison of catalysis by D414A P4H and the wild-type enzyme. Finally, the use of the assay to identify small-molecule inhibitors of P4H was verified by an analysis of catalysis in the presence of 2,4-pyridine dicarboxylate, an analogue of alpha-ketoglutarate. Thus, the assay described herein Could facilitate biochemical analyses of this essential enzyme. (C) 2008 Elsevier Inc. All rights reserved. AD - [Gorres, Kelly L.; Raines, Ronald T.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. AN - ISI:000263789500007 AU - Gorres, K. L. AU - Raines, R. T. DA - Mar KW - Fluoride ion-selective electrode 4-Fluoroproline Fluorohydrin alpha-Ketoglutarate Peptide Non-heme iron dioxygenase Prolyl 4-hydroxylase 2,4-Pyridine dicarboxylate Collagen proline hydroxylase enzymatic hydroxylation caenorhabditis-elegans escherichia-coli triple-helix bound iron ascorbate enzymes 2-oxoglutarate sites Biochemical Research Methods Biochemistry & Molecular Biology Chemistry, Analytical LB - ISI 2009 03 13 IS - 2 N1 - English Article 0003-2697 PY - 2009 SP - 181-185 ST - Direct and continuous assay for prolyl 4-hydroxylase T2 - Analytical Biochemistry TI - Direct and continuous assay for prolyl 4-hydroxylase VL - 386 ID - 3824 ER - TY - JOUR AB - The recently synthesized sterically constrained copper(l) complex [Cu(dtbp)(2)](+) (1), where dtbp is 2,9-di-tert-butyl-1,10-phenanthroline, exhibits unique photophysical and reactivity properties. Complex 1 (lambda(abs), 425 nm; epsilon, 3100 L M-1 cm(-1); lambda(emission), 599 nm) has the longest metal-to-ligand charge-transfer (MLCT) emission lifetime (tau, 3260 ns) and largest quantum yield (phi, 5.6%) of all (Cu(R(2)phen)(2)](+) complexes, Complex 1 also exhibits a large positive reduction potential for the [Cu2+(dtbp)(2)]I[Cu+(dtbp)(2)] couple (E-1/2 = 0.70 V vs Fc(+/0)) and a large negative excited-state reduction potential for the [Cu2+(dtbp)(dtbp(-center dot))]I[Cu2+(dtbp)(2)] couple (E-1/2 = -1.66 V vs Fc(+/0)), indicating that this complex is a potent photoreductant in the excited state. The steric constraint imposed by the t-butyl substituents in 1 enables unusual ligand replacement reactivity. Either CH3CN or CO replaces one of the dtbp ligands, a reaction that is readily followed by loss of the unique emission signature of 1. Monodentate CH3CN binds to the copper(l) center with an affinity 2 orders of magnitude greater than that of the displaced dtbp, despite the fact that the displaced ligand is bidentate. CO-induced displacement of dtbp from 1 is reversible, but only in the presence of I equiv of unbound dtbp. The exceptionally strong donor ligand CH3NC displaces both dtbp ligands from 1. In contrast to the facile ligand displacement reactivity With good donor ligands, 1 does not react readily with O-2, by either a ligand displacement or an oxidative pathway. Rather, O-2 induces partial quenching of emission via an outer-sphere interaction with 1. AD - [Green, Omar; Gandhi, Bhavesh A.; Burstyn, Judith N.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000267507400021 AU - Green, O. AU - Gandhi, B. A. AU - Burstyn, J. N. DA - Jul KW - Excited-states bis(phenanthroline) complex coordination-compounds molecular machines transition-metals systems photochemistry 1,10-phenanthroline spectroscopy distortion Chemistry, Inorganic & Nuclear LB - ISI 2009 08 06 IS - 13 N1 - English Article American Chemical Society Petroleum Research Fund [ACS-PRF, 42041-AC3] PY - 2009 SP - 5704-5714 ST - Photophysical Characteristics and Reactivity of Bis(2,9-di-tert-butyl-1,10-phenanthroline) copper(I) T2 - Inorganic Chemistry TI - Photophysical Characteristics and Reactivity of Bis(2,9-di-tert-butyl-1,10-phenanthroline) copper(I) VL - 48 ID - 3988 ER - TY - JOUR AB - Galactofuranose (Galf) residues are present in cell wall glycoconjugates of numerous pathogenic microbes. Uridine 5'-diphosphate (UDP) Galf, the biosynthetic precursor of Galf-containing glycoconjugates, is produced from UDP-galactopyranose (UDP-Galp) by the flavoenzyme UDP-galactopyranose mutase (UGM). The gene encoding UGM (glf) is essential for the viability of pathogens, including Mycobacterium tuberculosis, and this finding underscores the need to understand how UGM functions. Considerable effort has been devoted to elucidating the catalytic mechanism of UGM, but progress has been hindered by a lack of structural data for an enzyme-substrate complex. Such data could reveal not only substrate binding interactions but how UGM can act preferentially on two very different substrates, UDP-Galp and UDP-Galf, yet avoid other structurally related UDP sugars present in the cell. Herein, we describe the first structure of a UGM-ligand complex, which provides insight into the catalytic mechanism and molecular basis for substrate selectivity. The structure of UGM from Klebsiella pneumoniae bound to the substrate analog UDP-glucose (UDP-Glc) was solved by X-ray crystallographic methods and refined to 2.5 angstrom resolution. The ligand is proximal to the cofactor a finding that is consistent with a proposed mechanism in which the reduced flavin engages in covalent catalysis. Despite this proximity, the glucose ring of the substrate analog is positioned such that it disfavors covalent catalysis. This orientation is consistent with data indicating that UDP-Glc is not a substrate for UGM. The relative binding orientations of UDP-Galp and UDP-Glc were compared using saturation transfer difference NMR. The results indicate that the uridine moiety occupies a similar location in both ligand complexes, and this relevant binding mode is defined by our structural data. In contrast, the orientations of the glucose and galactose sugar moieties differ. To understand the consequences of these differences, we derived a model for the productive UGM-substrate complex that highlights interactions that can contribute to catalysis and substrate discrimination. (C) 2009 Elsevier Ltd. All rights reserved. AD - [Forest, Katrina T.] Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA. [Gruber, Todd D.; Borrok, M. Jack; Kiessling, Laura L.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. [Westler, William M.] Univ Wisconsin, Natl Magnet Resonance Facil Madison, Madison, WI 53706 USA. [Kiessling, Laura L.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000269227300007 AU - Gruber, T. D. AU - Borrok, M. J. AU - Westler, W. M. AU - Forest, K. T. AU - Kiessling, L. L. DA - Aug KW - UDP-galactopyranose mutase glf cell wall biosynthesis mycobacteria galactofuranose Std-nmr spectroscopy escherichia-coli catalytic mechanism aspergillus-fumigatus leishmania-major o-antigen galactofuranose identification protein growth Biochemistry & Molecular Biology LB - ISI 2009 09 03 IS - 2 N1 - English Article National Institutes of Health (NIH) [AI 063596, GM08349, GM07215, RR 007707, P41RR02301, P41GM66326, RR02781, RR08438]; National Science Foundation [DMB-8415048, OIA-9977486, BUZ-9214394]; United States Department of Agriculture PY - 2009 SP - 327-340 ST - Ligand Binding and Substrate Discrimination by UDP-Galactopyranose Mutase T2 - Journal of Molecular Biology TI - Ligand Binding and Substrate Discrimination by UDP-Galactopyranose Mutase VL - 391 ID - 4008 ER - TY - JOUR AB - The flavoenzyme uridine 5'-diphosphate galactopyranose mutase (UGM or Glf) catalyzes the interconversion of UDP-galactopyra nose and UDP-galactofuranose. The latter Is a key building block for cell wall construction in numerous pathogens, including Mycobacterium tuberculosis. Mechanistic studies of UGM suggested a novel role for the flavin, and we previously provided evidence that the catalytic mechanism proceeds through a covalent flavin-galactose iminium. Here, we describe 2.3 and 2.5 resolution X-ray crystal structures of the substrate-bound enzyme in oxidized and reduced forms, respectively. In the latter, Cl of the substrate is 3.6 angstrom from the nucleophilic flavin N5 position. This orientation is consistent with covalent catalysis by flavin. AD - Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. Univ Wisconsin, Dept Bacteriol & Chem, Madison, WI 53706 USA. Univ Wisconsin, Natl Magnet Resonance Facil Madison, Madison, WI 53706 USA. AN - ISI:000270136600001 AU - Gruber, T. D. AU - Westler, W. M. AU - Kiessling, L. L. AU - Forest, K. T. DA - Oct KW - Std-nmr spectroscopy escherichia-coli galactofuranose mechanism biosynthesis mycobacteria dynamics binding growth Biochemistry & Molecular Biology LB - ISI 2009 10 09 IS - 39 N1 - English Article National Institutes of Health [063596, T32 GM08349]; W M. Keck Foundation PY - 2009 SP - 9171-9173 ST - X-ray Crystallography Reveals a Reduced Substrate Complex of UDP-Galactopyranose Mutase Poised for Covalent Catalysis by Flavin T2 - Biochemistry TI - X-ray Crystallography Reveals a Reduced Substrate Complex of UDP-Galactopyranose Mutase Poised for Covalent Catalysis by Flavin VL - 48 ID - 4033 ER - TY - JOUR AB - A highly stereosetective synthesis of novel cyclically constrained gamma-amino acid residues is presented. The key step involves organocatalytic Michael addition of an aldehyde to 1-nitrocyclohexene. After aldehyde reduction, this approach provides optically active beta-substituted delta-nitro alcohols (96-99% ee), which can be converted to gamma-amino acid residues with a variety of substituents at the a position. We have used these new building blocks to prepare alpha/gamma-peptide foldamers that adopt a specific helical conformation in solution and in the solid state. AD - [Guo, Li; Chi, Yonggui; Almeida, Aaron M.; Guzei, Ilia A.; Parker, Brian K.; Gellman, Samuel H.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000271513700027 AU - Guo, Li AU - Chi, Yonggui AU - Almeida, Aaron M. AU - Guzei, Ilia A. AU - Parker, Brian K. AU - Gellman, Samuel H. DA - Nov KW - Asymmetric conjugate addition protein surface recognition short alpha/beta-peptides michael additions crystallographic characterization heterogeneous backbones beta-peptides aldehydes residue nitroalkenes Chemistry, Multidisciplinary LB - ISI 2009 11 19 IS - 44 N1 - English Article NSF [CHE-0848847]; NIH PY - 2009 SP - 16018-+ ST - Stereospecific Synthesis of Conformationally Constrained gamma-Amino Acids: New Foldamer Building Blocks That Support Helical Secondary Structure T2 - Journal of the American Chemical Society TI - Stereospecific Synthesis of Conformationally Constrained gamma-Amino Acids: New Foldamer Building Blocks That Support Helical Secondary Structure VL - 131 ID - 4084 ER - TY - JOUR AB - The title compound (Ti((C5H4Bu)-Bu-t)(2)Cl-2, 1) exists in three polymorphs and undergoes two enantiotropic phase transitions between them. The low-temperature, non-merohedrally twinned monoclinic phase III (space group P2(1)) Undergoes a first-order phase transition into an orthorhombic phase II (space group P2(1)2(1)2(1)) at 147(l) K. Subsequent heating of the crystal results in a gradual second-order k2 transformation of this phase into the high-temperature orthorhombic phase I (P2(1)2(1)2). This phase transition is completed at similar to 330 K. The phase transitions were monitored by single-crystal X-ray diffraction, differential scanning calorimetry and powder diffraction; however, the II --> I transition did not register on the differential scanning calorimetry curve or powder patterns. The molecular conformations and mutual arrangement of molecule,, in the crystal in the three phases are very similar. The location of the ancillary ligands relative to the Cl-Ti-Cl wedge in the solid-state structures of 1 and 32 related Ti(C5H4R)(2)Cl-2 complexes seems to be principally determined by weak C-H center dot center dot center dot Cl intrarnolecular interactions between the R substituents and Cl ligands rather than by steric factors. Ail example of an advanced structural refinement technique Using SHELXL to compute standard uncertainties on mathematically derived parameters is also given. AD - [Guzei, Ilia A.; Mitra, Amitabha; Spencer, Lara C.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000265892200041 AU - Guzei, I. A. AU - Mitra, A. AU - Spencer, L. C. DA - May KW - Phase-transition variable-temperature crystal complexes spin Chemistry, Multidisciplinary Crystallography Materials Science, Multidisciplinary LB - ISI 2009 05 29 IS - 5 N1 - English Article PY - 2009 SP - 2287-2292 ST - Concomitant Twinning and Polymorphism of Ti((C5H4Bu)-Bu-t)(2)Cl-2 T2 - Crystal Growth & Design TI - Concomitant Twinning and Polymorphism of Ti((C5H4Bu)-Bu-t)(2)Cl-2 VL - 9 ID - 3923 ER - TY - JOUR AB - The title compound, C16H16N4O2S, crystallizes with two symmetry-independent half-molecules in the asymmetric unit. All non-H atoms in each molecule lie in a crystallographic mirror plane. The molecules form sheets in the ac plane, which then form stacks along the b axis. The sheets are connected via pi-pi stacking interactions [centroid-centroid distance between pyrazolato rings = 3.6949 (8) angstrom]. AD - [Guzei, Ilia A.; Spencer, Lara C.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Tshivashe, Mmboneni G.; Darkwa, James] Univ Johannesburg, Dept Chem, ZA-2006 Johannesburg, South Africa. AN - ISI:000271977700055 AU - Guzei, Ilia A. AU - Spencer, Lara C. AU - Tshivashe, Mmboneni G. AU - Darkwa, James DA - Nov KW - Complexes palladium(ii) catalysts Crystallography LB - ISI 2009 11 26 N1 - English Article National Research Foundation (South Africa) Part 11 PY - 2009 SP - O2743-U699 ST - (3,5-Dimethylpyrazol-1-yl)[5-(3,5-dimethylpyrazol-1-ylcarbonyl)-2-thieny l]methanone T2 - Acta Crystallographica Section E-Structure Reports Online TI - (3,5-Dimethylpyrazol-1-yl)[5-(3,5-dimethylpyrazol-1-ylcarbonyl)-2-thieny l]methanone VL - 65 ID - 4093 ER - TY - JOUR AB - The title compound, [Na(C18H36N2O6)]ClO4, was isolated and crystallized to understand more fully the ligand's binding specificity to cations. The cation and anion reside at an intersection of crystallographic twofold and threefold axes. The carbon atoms in the cation are disordered over two positions in a 3:2 ratio, and the anion is equally disordered over two positions. The geometries of the cation and anion are typical. The compound packs in alternating sheets of discrete cations and anions stacked along the c axis, separated by a distance equal to one-sixth the length of the c axis. AD - [Guzei, Ilia A.; Spencer, Lara C.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Su, Joe W.] DR SUSS CORP, Las Vegas, NV 89120 USA. [Burnette, Ronald R.] Univ Wisconsin, Sch Pharm, Madison, WI 53705 USA. AN - ISI:000271906600099 AU - Guzei, Ilia A. AU - Su, Joe W. AU - Spencer, Lara C. AU - Burnette, Ronald R. DA - Nov KW - Cation strontium Crystallography LB - ISI 2009 11 26 N1 - English Article National Science Foundation Part 11 PY - 2009 SP - M1381-U1303 ST - (4,7,13,16,21,24-Hexaoxa-1,10-diazabicyclo[8.8.8]hexacosane)sodium perchlorate T2 - Acta Crystallographica Section E-Structure Reports Online TI - (4,7,13,16,21,24-Hexaoxa-1,10-diazabicyclo[8.8.8]hexacosane)sodium perchlorate VL - 65 ID - 4092 ER - TY - JOUR AB - The title compound, C40H64O12, crystallizes in a pseudomerohedrally twinned primitive monoclinic cell with similar contributions of the two twin components. There are two symmetry-independent half-molecules of nonactin in the asymmetric unit. Each molecule has a pseudo-S-4 symmetry and resides on a crystallographic twofold axis; the axes pass through the molecular center of mass and are perpendicular to the plane of the macrocycle. The literature description of the room-temperature structure of nonactin as an order-disorder structure in an orthorhombic unit cell is corrected. We report a low-temperature high-precision ordered structure of 'free' nonactin that allowed for the first time precise determination of its bond distances and angles. It possesses an unfolded and more planar geometry than its complexes with encapsulated Na+, K+, Cs+, Ca2+ or NH4+ cations that exhibit more isometric overall conformations. AD - [Guzei, Ilia A.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Wang, Cheng; Zhan, Yulian; Cheng, Yi-Qiang] Univ Wisconsin, Dept Biol Sci, Milwaukee, WI 53211 USA. [Dolomanov, Oleg V.] Univ Durham, Dept Chem, Durham DH1 3LE, England. [Cheng, Yi-Qiang] Univ Wisconsin, Dept Chem & Biochem, Milwaukee, WI 53211 USA. AN - ISI:000270387600025 AU - Guzei, I. A. AU - Wang, C. AU - Zhan, Y. L. AU - Dolomanov, O. V. AU - Cheng, Y. Q. DA - Oct KW - Stoffwechselprodukte von actinomyceten orthorhombic diffraction patterns crystal-structure complex Crystallography LB - ISI 2009 10 15 N1 - English Article US National Institute of Health [R03 AI073498] Part 10 PY - 2009 SP - O521-O524 ST - Pseudomerohedrally twinned monoclinic structure of unfolded 'free' nonactin: comparative analysis of its large conformational change upon encapsulation of alkali metal ions T2 - Acta Crystallographica Section C-Crystal Structure Communications TI - Pseudomerohedrally twinned monoclinic structure of unfolded 'free' nonactin: comparative analysis of its large conformational change upon encapsulation of alkali metal ions VL - 65 ID - 4040 ER - TY - JOUR AB - Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement(1). To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population(1). Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion(2). Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars(3,4). Here we report the sequence of the P. infestans genome, which at similar to 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for similar to 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential. AD - [Kamoun, Sophien; Cano, Liliana M.; Raffaele, Sylvain; Bozkurt, Tolga O.; Jones, Alexandra M. E.; Jones, Jonathan D. G.; MacLean, Daniel; Schornack, Sebastian; Schwessinger, Ben; Silvar, Cristina; Studholme, David J.; Thines, Marco; Win, Joe] Sainsbury Lab, Norwich NR4 7UH, Norfolk, England. [Haas, Brian J.; Zody, Michael C.; Handsaker, Robert E.; Grabherr, Manfred; Kodira, Chinnappa D.; Alvarado, Lucia; Gnerre, Sante; Karlsson, Elinor K.; Ma, LiJun; O'Neill, Keith; Sharpe, Ted; Sykes, Sean; Nusbaum, Chad] Broad Inst MIT & Harvard, Cambridge, MA 02141 USA. [Kamoun, Sophien; Torto-Alalibo, Trudy; Bos, Jorunn I. B.; Cakir, Cahid; Huitema, Edgar; Liu, Zhenyu; Song, Jing; Young, Carolyn] Ohio State Univ, Ohio Agr Res & Dev Ctr, Dept Plant Pathol, Wooster, OH 44691 USA. [Zody, Michael C.] Uppsala Univ, Dept Med Biochem & Microbiol, SE-75124 Uppsala, Sweden. [Jiang, Rays H. Y.; Meijer, Harold J. G.; van de Vondervoort, Peter J. I.; Weide, Rob; Govers, Francine] Univ Wageningen & Res Ctr, Phytopathol Lab, NL-6708 PB Wageningen, Netherlands. [Ah-Fong, Audrey M. V.; Roy, Sourav; Judelson, Howard S.] Univ Calif Riverside, Dept Plant Pathol & Microbiol, Riverside, CA 92521 USA. [Anderson, Vicky L.; Grenville-Briggs, Laura J.; Horner, Neil R.; Schumann, Ulrike D.; Wawra, Stephan; van West, Pieter] Univ Aberdeen, Aberdeen Oomycete Lab, Coll Life Sci & Med, Inst Med Sci, Aberdeen AB25 2ZD, Scotland. [Armstrong, Miles R.; Avrova, Anna; Boevink, Petra C.; Gilroy, Eleanor M.; Pritchard, Leighton; Whisson, Stephen C.] Scottish Crop Res Inst, Plant Pathol Programme, Dundee DD2 5DA, Scotland. [Baxter, Laura; Beynon, Jim] Univ Warwick, Warwick CV35 9EF, England. [Bollmann, Stephanie R.; Gruenwald, Niklaus J.] ARS, USDA, Hort Crops Res Lab, Corvallis, OR 97330 USA. [Bulone, Vincent; Fugelstad, Johanna] AlbaNova Univ Ctr, Sch Biotechnol, Royal Inst Technol KTH, SE-10691 Stockholm, Sweden. [Cai, Guohong; Fry, William] Cornell Univ, Dept Plant Pathol & Plant Microbe Biol, Ithaca, NY 14853 USA. [Carrington, James C.; Fahlgren, Noah] Oregon State Univ, Dept Bot & Plant Pathol, Corvallis, OR 97331 USA. [Carrington, James C.; Fahlgren, Noah] Oregon State Univ, Ctr Genome Res & Biocomp, Corvallis, OR 97331 USA. [Chawner, Megan; Griffith, John; Horn, Karolyn; McWalters, Jessica; Ospina-Giraldo, Manuel; Seyer, Lauren] Lafayette Coll, Dept Biol, Easton, PA 18042 USA. [Conti, Lucio; Ewan, Richard; Sadanandom, Ari] Univ Glasgow, Plant Mol Sci Fac Biomed & Life Sci, Glasgow G12 8QQ, Lanark, Scotland. [Costanzo, Stefano] ARS, USDA, Dale Bumpers Natl Rice Res Ctr, Stuttgart, AR 72160 USA. [Fischbach, Michael A.] Massachusetts Gen Hosp, Dept Mol Biol, Boston, MA 02114 USA. [Green, Pamela J.; Jeong, Dong-Hoon; Meyers, Blake C.] Univ Delaware, Delaware Biotechnol Inst, Newark, DE 19711 USA. [Hu, Chia-Hui; Ristaino, Jean] N Carolina State Univ, Dept Plant Pathol, Raleigh, NC 27695 USA. [Jones, Richard W.] ARS, USDA, Beltsville, MD 20705 USA. [Kunjeti, Sridhara G.] Univ Delaware, Dept Plant & Soil Sci, Newark, DE 19716 USA. [Lamour, Kurt] Univ Tennessee, Dept Entomol & Plant Pathol, Knoxville, TN 37996 USA. [Chibucos, Marcus C.] Univ Maryland, Sch Med, Inst Genome Sci, Baltimore, MD 21201 USA. [McDonald, Hayes] Vanderbilt Univ, Dept Biochem, Sch Med, Nashville, TN 37232 USA. [Morgan, William] Coll Wooster, Dept Biol, Wooster, OH 44691 USA. [Morris, Paul F.; Phuntumart, Vipaporn] Bowling Green State Univ, Dept Biol Sci, Bowling Green, OH 43403 USA. [Munro, Carol A.] Univ Aberdeen, Sch Med Sci, Coll Life Sci & Med, Inst Med Sci, Aberdeen AB25 2ZD, Scotland. [Pinzon, Andres; Restrepo, Silvia] Univ Los Andes, Mycol & Phytopathol Lab, Bogota, Colombia. [Ramsahoye, Bernard] Univ Edinburgh, Western Gen Hosp, Inst Genet & Mol Med, Canc Res Ctr, Edinburgh EH4 2XU, Midlothian, Scotland. [Schwartz, David C.; Zhou, Shiguo] Univ Wisconsin, Dept Chem, Genet Lab, Ctr Biotechnol,Lab Mol & Computat Genom, Madison, WI 53706 USA. [Thines, Marco] Univ Hohenheim, Inst Bot 210, D-70593 Stuttgart, Germany. [Birch, Paul R. J.] Univ Dundee, SCRI, Coll Life Sci, Div Plant Sci, Dundee DD2 5DA, Scotland. [Ren, Qinghu] J Craig Venter Inst, Rockville, MD 20850 USA. [Savidor, Alon] Tel Aviv Univ, Dept Plant Sci, IL-69978 Tel Aviv, Israel. AN - ISI:000269828100039 AU - Haas, B. J. AU - Kamoun, S. AU - Zody, M. C. AU - Jiang, R. H. Y. AU - Handsaker, R. E. AU - Cano, L. M. AU - Grabherr, M. AU - Kodira, C. D. AU - Raffaele, S. AU - Torto-Alalibo, T. AU - Bozkurt, T. O. AU - Ah-Fong, A. M. V. AU - Alvarado, L. AU - Anderson, V. L. AU - Armstrong, M. R. AU - Avrova, A. AU - Baxter, L. AU - Beynon, J. AU - Boevink, P. C. AU - Bollmann, S. R. AU - Bos, J. I. B. AU - Bulone, V. AU - Cai, G. H. AU - Cakir, C. AU - Carrington, J. C. AU - Chawner, M. AU - Conti, L. AU - Costanzo, S. AU - Ewan, R. AU - Fahlgren, N. AU - Fischbach, M. A. AU - Fugelstad, J. AU - Gilroy, E. M. AU - Gnerre, S. AU - Green, P. J. AU - Grenville-Briggs, L. J. AU - Griffith, J. AU - Grunwald, N. J. AU - Horn, K. AU - Horner, N. R. AU - Hu, C. H. AU - Huitema, E. AU - Jeong, D. H. AU - Jones, A. M. E. AU - Jones, J. D. G. AU - Jones, R. W. AU - Karlsson, E. K. AU - Kunjeti, S. G. AU - Lamour, K. AU - Liu, Z. Y. AU - Ma, L. J. AU - MacLean, D. AU - Chibucos, M. C. AU - McDonald, H. AU - McWalters, J. AU - Meijer, H. J. G. AU - Morgan, W. AU - Morris, P. F. AU - Munro, C. A. AU - O'Neill, K. AU - Ospina-Giraldo, M. AU - Pinzon, A. AU - Pritchard, L. AU - Ramsahoye, B. AU - Ren, Q. H. AU - Restrepo, S. AU - Roy, S. AU - Sadanandom, A. AU - Savidor, A. AU - Schornack, S. AU - Schwartz, D. C. AU - Schumann, U. D. AU - Schwessinger, B. AU - Seyer, L. AU - Sharpe, T. AU - Silvar, C. AU - Song, J. AU - Studholme, D. J. AU - Sykes, S. AU - Thines, M. AU - van de Vondervoort, P. J. I. AU - Phuntumart, V. AU - Wawra, S. AU - Weide, R. AU - Win, J. AU - Young, C. AU - Zhou, S. G. AU - Fry, W. AU - Meyers, B. C. AU - van West, P. AU - Ristaino, J. AU - Govers, F. AU - Birch, P. R. J. AU - Whisson, S. C. AU - Judelson, H. S. AU - Nusbaum, C. DA - Sep KW - Effector proteins rxlr effectors cell-death plant avirulence avr3a resistance infection genes Multidisciplinary Sciences LB - ISI 2009 09 24 IS - 7262 N1 - English Article National Research Initiative of the USDA Cooperative State Research, Education and Extension Service [2004-35600-15024, 2006-35600-16623]; National Science Foundation [EF-0333274, EF-0523670]; Gatsby Charitable Foundation PY - 2009 SP - 393-398 ST - Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans T2 - Nature TI - Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans VL - 461 ID - 4022 ER - TY - JOUR AB - We report the induction of perpendicularly oriented cylindrical domains in PS-b-PMMA block copolymer (BCP) films thicker than 100 nm by thermally annealing oil a substrate modified with it random copolymer. The effects of annealing temperature, composition of the substrate-modifying random copolymer, and BCP film thickness on the morphology of PMMA cylinder forming PS-b-PMMA were Studied. For BCP films thicker than 100 nm, the fabrication of perpendicular PMMA cylinders is highly dependent on both the substrate-modifying random copolymer and the annealing temperature as these two parameters control the interactions of the BCP with the substrate and the free surface, respectively, We found the best perpendicular structures to be created by using it random copolymer brush with a styrene fraction (P's,) near 0.70 and an annealing temperature near 230 degrees C. Perpendicular cylinder structures were achieved in similar to 300 nm thick Films using these conditions. When the BCP film was thicker than 300 rim, nucleation and growth of the microdomains proceeded independently from each interface. We present scanning electron microscope (SEM) and cross-sectional transmission electron microscope (TEM) images of these perpendicular Structures and explain the results oil the basis of previous simulation reports. AD - [Han, Eungnak; Leolukman, Melvina; Gopalan, Padma] Univ Wisconsin, Dept Mat Sci & Engn, Madison, WI 53706 USA. [Stuen, Karl O.; Liu, Chi-Chun; Nealey, Paul F.] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA. AN - ISI:000268138500077 AU - Han, E. AU - Stuen, K. O. AU - Leolukman, M. AU - Liu, C. C. AU - Nealey, P. F. AU - Gopalan, P. DA - Jul KW - Confined diblock copolymers microdomain orientation lithography arrays fabrication templates surfaces nanorods brushes layers Polymer Science LB - ISI 2009 07 31 IS - 13 N1 - English Article National Science Foundation [DMR-0537588, DMR0425880]; center on Functional Engineered Nano Architectonics (FENA) PY - 2009 SP - 4896-4901 ST - Perpendicular Orientation of Domains in Cylinder-Forming Block Copolymer Thick Films by Controlled Interfacial Interactions T2 - Macromolecules TI - Perpendicular Orientation of Domains in Cylinder-Forming Block Copolymer Thick Films by Controlled Interfacial Interactions VL - 42 ID - 3965 ER - TY - JOUR AB - Renal activity and smoldering disease is difficult to assess in anti-neutrophil cytoplasmic antibody-associated vasculitis (AAV) because of renal scarring. Even repeated biopsies suffer from sampling errors in this focal disease especially in patients with chronic renal insufficiency. We applied capillary electrophoresis coupled to mass spectrometry toward urine samples from patients with active renal AAV to identify and validate urinary biomarkers that enable differential diagnosis of disease and assessment of disease activity. The data were compared with healthy individuals, patients with other renal and non-renal diseases, and patients with AAV in remission. 113 potential biomarkers were identified that differed significantly between active renal AAV and healthy individuals and patients with other chronic renal diseases. Of these, 58 could be sequenced. Sensitivity and specificity of models based on 18 sequenced biomarkers were validated using blinded urine samples of 40 patients with different renal diseases. Discrimination of AAV from other renal diseases in blinded samples was possible with 90% sensitivity and 86.7-90% specificity depending on the model. 10 patients with active AAV were followed for 6 months after initiation of treatment. Immunosuppressive therapy led to a change of the proteome toward "remission." 47 biomarkers could be sequenced that underwent significant changes during therapy together with regression of clinical symptoms, normalization of C-reactive protein, and improvement of renal function. Proteomics analysis with capillary electrophoresis-MS represents a promising tool for fast identification of patients with active AAV, indication of renal relapses, and monitoring for ongoing active renal disease and remission without renal biopsy. Molecular & Cellular Proteomics 8: 2296-2307, 2009. AD - [Haubitz, Marion; Woywodt, Alexander; Haller, Hermann] Hannover Med Sch, Dept Nephrol, D-30625 Hannover, Germany. [Good, David M.; Coon, Joshua J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Coon, Joshua J.] Univ Wisconsin, Dept Biomol Chem, Madison, WI 53706 USA. [Rupprecht, Harald] Univ Munich, Dept Nephrol, D-80336 Munich, Germany. [Theodorescu, Dan] Univ Virginia, Dept Urol, Charlottesville, VA 22908 USA. [Dakna, Mohammed; Mischak, Harald] Mosaiques Diagnost GmbH, D-30625 Hannover, Germany. AN - ISI:000270492700008 AU - Haubitz, M. AU - Good, D. M. AU - Woywodt, A. AU - Haller, H. AU - Rupprecht, H. AU - Theodorescu, D. AU - Dakna, M. AU - Coon, J. J. AU - Mischak, H. DA - Oct KW - Electron-transfer dissociation circulating endothelial-cells anca-associated vasculitis mass-spectrometry capillary-electrophoresis proteome analysis wegeners-granulomatosis sequence-analysis discovery disease Biochemical Research Methods LB - ISI 2009 10 15 IS - 10 N1 - English Article National Institutes of Health [5T32GM08349]; Biotechnology Training Program PY - 2009 SP - 2296-2307 ST - Identification and Validation of Urinary Biomarkers for Differential Diagnosis and Evaluation of Therapeutic Intervention in Anti-neutrophil Cytoplasmic Antibody-associated Vasculitis T2 - Molecular & Cellular Proteomics TI - Identification and Validation of Urinary Biomarkers for Differential Diagnosis and Evaluation of Therapeutic Intervention in Anti-neutrophil Cytoplasmic Antibody-associated Vasculitis VL - 8 ID - 4036 ER - TY - JOUR AB - Bis(imino)acenaphthenes (BIAN) have been known for many years. However, it is only since the 1990s that such compounds have been recognized as robust ligands for the support of catalytically active transition metal centers. More recently, the unique stereoelectronic properties of the BIAN ligand class are beginning to be appreciated and exploited for some fascinating new developments in synthetic, structural and catalytic s- and p-block chemistry. AD - [Cowley, Alan H.] Univ Texas Austin, Dept Chem & Biochem, Austin, TX 78712 USA. [Hill, Nicholas J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000261807400002 AU - Hill, N. J. AU - Vargas-Baca, I. AU - Cowley, A. H. KW - Chemistry, Inorganic & Nuclear LB - ISI 2009 01 09 N1 - English Review ALPHA-DIIMINE LIGANDS; RIGID NITROGEN LIGAND; TRANSITION-METAL-COMPLEXES; ALKYL TRANSFER PRODUCTS; ASTERISK EXCITED-STATE; RAY CRYSTAL-STRUCTURES; AMIDO-IMINO LIGAND; MOLECULAR-STRUCTURES; STRUCTURAL-CHARACTERIZATION; CALCIUM COMPLEXES 2 PY - 2009 SP - 240-253 ST - Recent developments in the coordination chemistry of bis(imino)acenaphthene (BIAN) ligands with s- and p-block elements T2 - Dalton Transactions TI - Recent developments in the coordination chemistry of bis(imino)acenaphthene (BIAN) ligands with s- and p-block elements ID - 3706 ER - TY - JOUR AB - We report the self-assembly of organic-inorganic block copolymers (BCP) in thin-films by simple solvent annealing on unmodified substrates. The resulting vertically oriented lamellae and cylinders are converted to a hard silica mask by single-step, highly selective oxygen plasma etching. The size of the resulting nanostructures in the case of cylinders is less than 10 nm. AD - [Hirai, Tomoyasu; Ishida, Yoshihito; Hayakawa, Teruaki; Kakimoto, Masa-aki] Tokyo Inst Technol, Dept Organ & Polymer Mat, Eguro Ku, Tokyo 1528552, Japan. [Liu, Chi Chun; Nealey, Paul F.] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA. [Leolukman, Melvina; Han, Eungnak; Kim, Yun Jun; Gopalan, Padma] Univ Wisconsin, Dept Mat Sci & Engn, Madison, WI 53706 USA. AN - ISI:000272504300003 AU - Hirai, Tomoyasu AU - Leolukman, Melvina AU - Liu, Chi Chun AU - Han, Eungnak AU - Kim, Yun Jun AU - Ishida, Yoshihito AU - Hayakawa, Teruaki AU - Kakimoto, Masa-aki AU - Nealey, Paul F. AU - Gopalan, Padma DA - Nov KW - Thin-films lithography fabrication resists media nm Chemistry, Multidisciplinary Chemistry, Physical Nanoscience & Nanotechnology Materials Science, Multidisciplinary Physics, Applied Physics, Condensed Matter LB - ISI 2009 12 17 IS - 43 N1 - English Article Nanoscale Science and Engineering Center [DMR-0425880]; NSF-DMR-CAREER [0449688]; Center of Functional Engineered Nano Architectonics (FENA) ; Mitsubishi Chemical Corporation Fund PY - 2009 SP - 4334-+ ST - One-Step Direct-Patterning Template Utilizing Self-Assembly of POSS-Containing Block Copolymers T2 - Advanced Materials TI - One-Step Direct-Patterning Template Utilizing Self-Assembly of POSS-Containing Block Copolymers VL - 21 ID - 4079 ER - TY - JOUR AB - The lowest energy optical electronic absorption band of the three-chromophore system tris(4-bromophenyl)-amine radical cation is analyzed. The lowest energy electronic transition corresponds to a p-bromophenyl orbital to nitrogen p orbital transition that places the positive charge on three equivalent p-bromophenyl chromophores. The excited electronic state is an example of excited-state mixed valence (ESMV), and the spectrum is interpreted using two ESMV models. The simplest model invokes the concept of an "effective coupling" between the three identical chromophores with an excited-state energy splitting equal to three times the coupling. A more accurate model, the "neighboring orbital model", utilizes the coupling between the bridge's and charge-bearing unit's orbitals closest in energy. The three-chromophore system provides a striking illustration of the failure of an effective coupling term to account for ESMV splitting. The calculated relative energies of the diabatic and adiabatic states are different, but the calculated absorption spectra of the two models show nearly identical vibrational fine structure. Resonance Raman data and the time-dependent theory of electronic and resonance Raman spectroscopies are used to calculate the spectra. AD - [Weaver, Michael N.; Nelsen, Stephen F.] Univ Wisconsin, Dept Chem, [Hoekstra, Ryan M.; Dibrell, Marcelle M.; Zink, Jeffrey .] Univ Calif AN - ISI:000262324300011 AU - Hoekstra, R. M. AU - Dibrell, M. M. AU - Weaver, M. N. AU - Nelsen, S. F. AU - Zink, J. DA - Jan KW - Triarylaminium cation radicals hyperfine coupling-constants electron-transfer pathways aromatic free radicals optical-spectra raman-scattering spectroscopic consequences excitation profiles resonance-spectra single hole Chemistry, Physical Physics, Atomic, Molecular & Chemical LB - ISI 2008 01 29 IS - 2 N1 - English Article 1089-5639 PY - 2009 SP - 456-463 ST - Three-Chromophore Excited-State Mixed Valence T2 - Journal of Physical Chemistry A TI - Three-Chromophore Excited-State Mixed Valence VL - 113 ID - 3736 ER - TY - JOUR AB - Unnatural oligomers that can mimic protein surfaces offer a potentially useful strategy for blocking biomedically important protein-protein interactions. Here we evaluate an approach based on combining alpha- and beta-amino acid residues in the context of a polypeptide sequence from the HIV protein gp41, which represents an excellent testbed because of the wealth of available structural and biological information. We show that alpha/beta-peptides can mimic structural and functional properties of a critical gp41 subunit. Physical studies in solution, crystallographic data, and results from cell-fusion and virus-infectivity assays collectively indicate that the gp41-mimetic alpha/beta-peptides effectively block HIV-cell fusion via a mechanism comparable to that of gp41-derived alpha-peptides. An optimized alpha/beta-peptide is far less susceptible to proteolytic degradation than is an analogous alpha-peptide. Our findings show how a two-stage design approach, in which sequence-based alpha ->beta replacements are followed by site-specific backbone rigidification, can lead to physical and biological mimicry of a natural biorecognition process. AD - [Horne, W. Seth; Johnson, Lisa M.; Gellman, Samuel H.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Ketas, Thomas J.; Klasse, Per Johan; Moore, John P.] Cornell Univ, Weill Med Coll, Dept Microbiol & Immunol, New York, NY 10021 USA. [Lu, Min] Cornell Univ, Weill Med Coll, Dept Biochem, New York, NY 10021 USA. AN - ISI:000269481000006 AU - Horne, W. S. AU - Johnson, L. M. AU - Ketas, T. J. AU - Klasse, P. J. AU - Lu, M. AU - Moore, J. P. AU - Gellman, S. H. DA - Sep KW - alpha/beta-peptides HIV protein folding protein-protein interactions Immunodeficiency-virus type-1 hiv-1 entry fusion inhibitor envelope glycoprotein bh3-recognition cleft atomic-structure mediated fusion membrane-fusion helix mimicry coiled-coil Multidisciplinary Sciences LB - ISI 2009 09 10 IS - 35 N1 - English Article National Institutes of Health [GM56414, CA119875, AI42382, AI45463, AI76982]; Chemistry-Biology Training Program [T32GM008505]; U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-AC02-06CH11357] PY - 2009 SP - 14751-14756 ST - Structural and biological mimicry of protein surface recognition by alpha/beta-peptide foldamers T2 - Proceedings of the National Academy of Sciences of the United States of America TI - Structural and biological mimicry of protein surface recognition by alpha/beta-peptide foldamers VL - 106 ID - 4009 ER - TY - JOUR AB - Direct, in situ detection of gas phase formaldehyde (HCHO) via laser induced fluorescence in a White-type multipass cell is demonstrated with a (3 sigma) limit of detection of similar to 0.051 parts per billion by volume in a 1 s sampling time. Calibration is performed in two ways: using permeation tubes and with air bubbled through an aqueous solution of HCHO. The concentration of HCHO output from the bubbler is measured by cavity ring-down spectroscopy. Measurement of ambient HCHO is carried out at the University of Wisconsin, Madison for a period of several days. AN - ISI:000262926400044 AU - Hottle, J. R. AU - Huisman, A. J. AU - Digangi, J. P. AU - Kammrath, A. AU - Galloway, M. M. AU - Coens, K. L. AU - Keutsch, F. N. DA - Feb DO - 10.1021/es801621f LB - ISI 2009 02 20 IS - 3 N1 - Hottle, John R. Huisman, Andrew J. Digangi, Joshua P. Kammrath, Aster Galloway, Melissa M. Coens, Katherine L. Keutsch, Frank N. PY - 2009 SN - 0013-936X SP - 790-795 ST - A Laser Induced Fluorescence-Based Instrument for In-Situ Measurements of Atmospheric Formaldehyde T2 - Environmental Science & Technology TI - A Laser Induced Fluorescence-Based Instrument for In-Situ Measurements of Atmospheric Formaldehyde UR - ://000262926400044 VL - 43 ID - 3787 ER - TY - JOUR AB - Resonant two-photon ionization (R2PI), UV hole-burning (UVHB), and resonant ion-dip infrared (RIDIR) spectroscopies have been used to record single-conformation infrared and ultraviolet spectra of three model synthetic foldamers with heterogeneous backbones, alpha/beta-peptides Ac-beta(3)-hAla-L-Phe-NHMe (beta alpha L), Ac-beta(3)-hAla-D-Phe-NHMe (beta alpha D), and Ac-L-Phe-beta(3)-hAla-NHMe (alpha beta L), isolated and cooled in a supersonic expansion. beta alpha L and beta alpha D are diastereomers, differing only in the configuration of the a-amino acid residue; beta alpha L and alpha beta L contain the same residues, but differ in residue order. In all three alpha/beta-peptides the beta(3)-residue has S absolute configuration. UVHB spectroscopy is used to determine that there are six conformers of each molecule and to locate and characterize their SO-S, transitions in the origin region. RIDIR spectra in the amide NH stretch region reflect the number and strength of intramolecular H-bonds present. Comparison of the RIDIR spectra with scaled, harmonic vibrational frequencies and infrared intensities leads to definite assignments for the conformational families involved. C8/C7(eq) double-ring structures are responsible for three conformers of beta alpha L and four of beta alpha D, including those with the most intense transitions in the R2PI spectra. This preference for C8/C7(eq) double rings appears to be dictated by the C7(eq) ring of the alpha-peptide subunit. Three of the conformers of beta alpha L and beta alpha D form diastereomeric pairs (A/A', C/C', and G/G') that have nearly identical SO-S, origin positions in the UV and belong to the same conformational family, indicating no significant change associated with the change in chirality of the a-peptide subunit. However, beta alpha L favors formation of a C6/C5 conformer over C11, while the reverse preference holds in beta alpha D. Calculations indicate that the selective stabilization of the lowest-energy C11 (g(+)) structure in beta alpha D occurs because this structure minimizes steric effects between the beta(2) methylene group and C=O(1). In the alpha/beta-peptide alpha beta L, two conformers dominate the spectrum, one assigned to a C5/C8 bifurcated double-ring, and the other to a C5/C6 double-ring structure. This preference for C5 rings in the alpha/beta-peptide occurs because the C5 ring is further stabilized by an amide NH center dot center dot center dot pi interaction involving an NH group on the adjacent amide, as it is in the alpha-peptides. Comparison of the NH stretch spectra of C8/C7(eq) structures in beta alpha L with their C7(eq)/C8 counterparts in alpha beta L shows that the central amide NH stretch is shifted to lower frequency by. some 50-70 cm(-1) due to cooperative effects associated with the central amide accepting and donating a H-borid to neighboring amide groups. This swaps the ordering of the C8 and C7 NH stretch fundamentals in the two molecules. AD - [James, William H., III; Baquero, Esteban E.; Shubert, V. Alvin; Zwier, Timothy S.] Purdue Univ, Dept Chem, W Lafayette, IN 47907 USA. [Choi, Soo Hyuk; Gellman, Samuel H.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000265939200060 AU - James, W. H. AU - Baquero, E. E. AU - Shubert, V. A. AU - Choi, S. H. AU - Gellman, S. H. AU - Zwier, T. S. DA - May KW - Double-resonance spectroscopy secondary structure elements gas-phase formation o=c hydrogen-bond beta-peptides density functionals heterogeneous backbones ab-initio temperature-dependence quaternary structure Chemistry, Multidisciplinary LB - ISI 2009 05 29 IS - 18 N1 - English Article National Science Foundation [NSF-CHE0551075, CHE-0551920]; Samsung Scholarship Foundation PY - 2009 SP - 6574-6590 ST - Single-Conformation and Diastereomer Specific Ultraviolet and Infrared Spectroscopy of Model Synthetic Foldamers: alpha/beta-Peptides T2 - Journal of the American Chemical Society TI - Single-Conformation and Diastereomer Specific Ultraviolet and Infrared Spectroscopy of Model Synthetic Foldamers: alpha/beta-Peptides VL - 131 ID - 3921 ER - TY - JOUR AB - Attractive interactions between two carboxamide groups in a "stacked" geometry are explored under isolated molecule conditions. Infrared spectra of single conformations of a small gamma-peptide, Ac-gamma(2)-hPhe-NHMe, reveal the presence of a conformation in which the two amide planes are approximately parallel with the amide dipoles in an antialigned orientation. This stacked conformation is energetically comparable to conformations that contain an intramolecutar amide-amide H-bond. Amide stacking interactions can compete with H-bonding in circumstances where the amide groups can be brought into a stacking configuration with minimal strain, opening the way for its use in the design of future foldamer structures. AD - [James, William H., III; Mueller, Christian W.; Buchanan, Evan G.; Nix, Michael G. D.; Slipchenko, Lyudmila V.; Zwier, Timothy S.] Purdue Univ, Dept Chem, W Lafayette, IN 47907 USA. [Guo, Li; Gellman, Samuel H.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Roskop, Luke; Gordon, Mark S.] Iowa State Univ, Dept Chem, Ames, IA 50011 USA. AN - ISI:000271271500055 AU - James, William H., III AU - Mueller, Christian W. AU - Buchanan, Evan G. AU - Nix, Michael G. D. AU - Guo, Li AU - Roskop, Luke AU - Gordon, Mark S. AU - Slipchenko, Lyudmila V. AU - Gellman, Samuel H. AU - Zwier, Timothy S. DA - Oct KW - Model synthetic foldamers single-conformation ultraviolet fragment potential method main-chain atoms infrared-spectroscopy peptides molecules proteins Chemistry, Multidisciplinary LB - ISI 2009 11 13 IS - 40 N1 - English Article NSF [CHE0909619, CHE-0848847]; Purdue University ; Air Force Office of Scientific Research PY - 2009 SP - 14243-+ ST - Intramolecular Amide Stacking and Its Competition with Hydrogen Bonding in a Small Foldamer T2 - Journal of the American Chemical Society TI - Intramolecular Amide Stacking and Its Competition with Hydrogen Bonding in a Small Foldamer VL - 131 ID - 4082 ER - TY - JOUR AB - Attractive interactions between two carboxamide groups in a "stacked" geometry are explored under isolated molecule conditions. Infrared spectra of single conformations of a small gamma-peptide, Ac-gamma(2)-hPhe-NHMe, reveal the presence of a conformation in which the two amide planes are approximately parallel with the amide dipoles in an antialigned orientation. This stacked conformation is energetically comparable to conformations that contain an intramolecutar amide-amide H-bond. Amide stacking interactions can compete with H-bonding in circumstances where the amide groups can be brought into a stacking configuration with minimal strain, opening the way for its use in the design of future foldamer structures. AD - [James, William H., III; Mueller, Christian W.; Buchanan, Evan G.; Nix, Michael G. D.; Slipchenko, Lyudmila V.; Zwier, Timothy S.] Purdue Univ, Dept Chem, W Lafayette, IN 47907 USA. [Guo, Li; Gellman, Samuel H.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Roskop, Luke; Gordon, Mark S.] Iowa State Univ, Dept Chem, Ames, IA 50011 USA. AN - ISI:000271271500055 AU - James, W. H. AU - Muller, C. W. AU - Buchanan, E. G. AU - Nix, M. G. D. AU - Guo, L. AU - Roskop, L. AU - Gordon, M. S. AU - Slipchenko, L. V. AU - Gellman, S. H. AU - Zwier, T. S. DA - Oct KW - Model synthetic foldamers single-conformation ultraviolet fragment potential method main-chain atoms infrared-spectroscopy peptides molecules proteins Chemistry, Multidisciplinary LB - ISI 2009 11 12 IS - 40 N1 - English Article NSF [CHE0909619, CHE-0848847]; Purdue University ; Air Force Office of Scientific Research PY - 2009 SP - 14243-+ ST - Intramolecular Amide Stacking and Its Competition with Hydrogen Bonding in a Small Foldamer T2 - Journal of the American Chemical Society TI - Intramolecular Amide Stacking and Its Competition with Hydrogen Bonding in a Small Foldamer VL - 131 ID - 4068 ER - TY - JOUR AB - Recent infrared pump-probe studies on alcohol oligomers in CCl4 solution reveal that, following OH stretch excitation, ultrafast hydrogen bond (H-bond) breaking takes place on a time scale of 1 ps. To shed light on the mechanism of the H-bond breaking, we consider vibrational predissociation of the H-bonded methanol dimer. We construct a four-dimensional model for the dimer including the H-bond stretch, the donor OH stretch, the donor COH bend, and the OH rotation about the CO axis of the donor. Predissociation rates are calculated with Fermi's golden rule and close coupling approaches. Our results indicate that the predissociation leads to products with highly excited OH rotations. The predissociation rates strongly depend on the hydrogen bond strength. From our results, a simple nonadiabatic curve crossing picture for the predissociation process emerges, which provides a framework for future studies of solvent-assisted vibrational predissociation. AD - [Sibert, Edwin L., III] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. Univ Wisconsin, Inst Theoret Chem, Madison, WI 53706 USA. AN - ISI:000267384500013 AU - Jiang, R. M. AU - Sibert, E. L. DA - Jul KW - Vibrational-energy relaxation der-waals molecules infrared-spectroscopy hydroxyl stretch configurational uniformity structural dynamics methanol oligomers liquid methanol diabatic states ir spectroscopy Chemistry, Physical Physics, Atomic, Molecular & Chemical LB - ISI 2009 07 31 IS - 26 N1 - English Article National Science Foundation [CHE-0615165] PY - 2009 SP - 7275-7285 ST - How Do Hydrogen Bonds Break in Small Alcohol Oligomers? T2 - Journal of Physical Chemistry A TI - How Do Hydrogen Bonds Break in Small Alcohol Oligomers? VL - 113 ID - 3967 ER - TY - JOUR AB - Much of modern biology relies on the strategic manipulation of molecules for creating ordered arrays prior to high throughput molecular analysis. Normally, DNA arrays involve deposition on surfaces, or confinement in nanochannels; however, we show that microfluidic devices can present stretched molecules within a controlled flow in ways complementing surface modalities, or extreme confinement conditions. Here we utilize pressure-driven oscillatory shear flows generated in microchannels as a new way of stretching DNA molecules for imaging "arrays'' of individual DNA molecules. Fluid shear effects both stretch DNA molecules and cause them to migrate away from the walls becoming focused in the centerline of a channel. We show experimental findings confirming simulations using Brownian dynamics accounting for hydrodynamic interactions between molecules and channel-flow boundary conditions. Our findings characterize DNA elongation and migration phenomena as a function of molecular size, shear rate, oscillatory frequency with comparisons to computer simulation studies. AD - [Jo, Kyubong] Sogang Univ, Dept Chem, Seoul 121742, South Korea. [Jo, Kyubong] Sogang Univ, Interdisciplinary Program Integrated Biotechnol, Seoul 121742, South Korea. [Chen, Yeng-Long] Acad Sinica, Inst Phys, Taipei, Taiwan. [de Pablo, Juan J.] Univ Wisconsin, Dept Biol & Chem Engn, Madison AN - ISI:000268370400011 AU - Jo, K. AU - Chen, Y. L. AU - de Pablo, J. J. AU - Schwartz, D. C. KW - Induced polymer migration escherichia-coli o157-h7 brownian dynamics genome sequence stretching dna surface confinement system maps Biochemical Research Methods Chemistry, Multidisciplinary Nanoscience & Nanotechnology LB - ISI 2009 08 06 IS - 16 N1 - English Article National Science Foundation (NSEC; USA) ; National Institute of Health (NHGRI; USA) ; Sogang University [200810019.01] PY - 2009 SP - 2348-2355 ST - Elongation and migration of single DNA molecules in microchannels using oscillatory shear flows T2 - Lab on a Chip TI - Elongation and migration of single DNA molecules in microchannels using oscillatory shear flows VL - 9 ID - 3986 ER - TY - JOUR AB - Sphere-forming polystyrene-block-poly(t-butyl acrylate) (PS-b-PtBA) diblock copolymer with catalytic amounts of photo-acid generator (PAG) formulated a pixelated photoresist. In thin films with single-sphere thickness, hexagonal arrays of spheres (similar to 20 nm diameter on a 40 nm pitch) of PS within a matrix of PAG segregated in PtBA was obtained through solvent annealing. Upon exposure and post-exposure baking, the soluble PtBA matrix was converted to insoluble poly(acrylic acid), such that a negative pattern could be formed in the chlorobenzene developer. The concept of pixelation was demonstrated by exposing line and space patterns with increasing widths. In contrast to the width of the exposure fields that increased monotonically, the widths of the pixelated resist structures after development were quantized with respect to an integer number of rows of spheres. Furthermore, line edge roughness could be correlated with the size of each pixel (diameter of spherical domain). AD - [Kang, Huiman; Nealey, Paul F.] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA. [Kim, Yun Jun; Gopalan, Padma] Univ Wisconsin, Dept Mat Sci & Engn, Madison, WI 53706 USA. AN - ISI:000272803400134 AU - Kang, Huiman AU - Kim, Yun Jun AU - Gopalan, Padma AU - Nealey, Paul F. DA - Nov KW - annealing catalysis photoresists polymer blends thin films Chemically amplified resists positive-tone sidewall roughness lithography nanolithography nanostructures fabrication features Engineering, Electrical & Electronic Nanoscience & Nanotechnology Physics, Applied LB - ISI 2009 12 31 IS - 6 N1 - English Article Intel Corporation ; NSF UW Nanoscale Science and Engineering Center [DMR-0425880]; NSF [DMR-0084402]; UW Center for Nanotechnology PY - 2009 SP - 2993-2997 ST - Control of the critical dimensions and line edge roughness with pre-organized block copolymer pixelated photoresists T2 - Journal of Vacuum Science & Technology B TI - Control of the critical dimensions and line edge roughness with pre-organized block copolymer pixelated photoresists VL - 27 ID - 4115 ER - TY - JOUR AB - beta-Peptides (beta-amino acid oligomers) that mimic the amphiphilic, helical, and cationic properties of natural antimicrobial peptides have previously been shown to display antifungal activity against planktonic Candida albicans cells. beta-Peptides offer several advantages over conventional peptides composed of alpha-amino acid residues, including conformational stability, resistance to proteases, and activity at physiological salt concentrations. We examined sequence-activity relationships toward both planktonic C. albicans cells and C. albicans biofilms, and the results suggest a toxicity mechanism involving membrane disruption. A strategy for fluorescently labeling a beta-peptide without diminishing antifungal activity was devised; labeled beta-peptides penetrated the cell membrane and accumulated in the cytoplasm of both planktonic and biofilm-associated cells. The labeled beta-peptide was detected only in metabolically inactive cells, which suggests that beta-peptide entry is correlated with cell death. The presence of a beta-peptide at a concentration near the minimum inhibitory concentration completely prevented planktonic C. albicans cells from forming a biofilm, suggesting that beta-peptides may be useful in preventing fungal colonization and biofilm formation. AD - [Pomerantz, William C.; Gellman, Samuel H.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Karlsson, Amy J.; Neilsen, Keane J.; Palecek, Sean P.] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA. AN - ISI:000268233000009 AU - Karlsson, A. J. AU - Pomerantz, W. C. AU - Neilsen, K. J. AU - Gellman, S. H. AU - Palecek, S. P. DA - Jul KW - Cationic antimicrobial peptides de-novo design in-vitro antifungal agents membrane resistance antibacterial stability mechanism chlorhexidine Biochemistry & Molecular Biology LB - ISI 2009 07 31 IS - 7 N1 - English Article PY - 2009 SP - 567-579 ST - Effect of Sequence and Structural Properties on 14-Helical beta-Peptide Activity against Candida albicans Planktonic Cells and Biofilms T2 - ACS Chemical Biology TI - Effect of Sequence and Structural Properties on 14-Helical beta-Peptide Activity against Candida albicans Planktonic Cells and Biofilms VL - 4 ID - 3978 ER - TY - JOUR AB - Indomethacin glasses of varying stabilities were prepared by physical vapor deposition onto substrates at 265 K. Enthalpy relaxation and the mobility onset temperature, were assessed with differential scanning calorimetry (DSC). Quasi-isothermal temperature-modulated DSC was used to measure the reversing heat capacity during annealing above the glass transition temperature T-g. At deposition rates near 8 angstrom/s, scanning DSC shows two enthalpy relaxation peaks and quasi-isothermal DSC shows a two-step change in the reversing heat capacity. We attribute these features to two distinct local packing structures in the vapor-deposited glass, and this interpretation is supported by the strong correlation between the two calorimetric signatures of the glassy to liquid transformation. At lower deposition rates, a larger fraction of the sample is prepared in the more stable local packing. The transformation of the vapor-deposited glasses into the supercooled liquid above Tg is exceedingly slow, as much as 4500 times slower than the structural relaxation time of the liquid. AN - ISI:000263134500005 AU - Kearns, K. L. AU - Swallen, S. F. AU - Ediger, M. D. AU - Sun, Y. AU - Yu, L. DA - Feb DO - 10.1021/jp808665t LB - ISI 2009 02 20 IS - 6 N1 - Kearns, Kenneth L. Swallen, Stephen F. Ediger, M. D. Sun, Ye Yu, Lian PY - 2009 SN - 1520-6106 SP - 1579-1586 ST - Calorimetric Evidence for Two Distinct Molecular Packing Arrangements in Stable Glasses of Indomethacin T2 - Journal of Physical Chemistry B TI - Calorimetric Evidence for Two Distinct Molecular Packing Arrangements in Stable Glasses of Indomethacin UR - ://000263134500005 VL - 113 ID - 3780 ER - TY - JOUR AB - Oxidation of the pyrazol-1-yldithiocarbamate compounds {[3,5-R2C3HN2CS2](-) (R = H, Me) and indazol-1-lydithiocarbamate by iodine produces the sulfur-sulfur coupling compounds {R'C(S)S-S(S)CR') (R' = pyrazolyl, 3,5-dimethylpyrazolyl, indazolyl). All compounds were spectroscopically characterised, and, in some cases, structurally characterised. The X-ray structures reveal that these compounds contain a disulfide bridging the pyrazolylthiocarbonyl units. Two of the three disulfide compounds showed very good anticancer activities against HeLa cells at micromolar concentrations, with the most active compound active being 9.6 times more selective in its activity towards tumour cells than normal cells. AD - [Keter, Frankline K.; Omondi, Bernard; Darkwa, James] Univ Johannesburg, Dept Chem, ZA-2006 Auckland Pk, South Africa. [Nell, Margo J.] Univ Pretoria, Dept Pharmacol, ZA-0002 Pretoria, South Africa. [Guzei, Ilia A.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000267448400016 AU - Keter, F. K. AU - Nell, M. J. AU - Guzei, I. A. AU - Omondi, B. AU - Darkwa, J. DA - May KW - dithiocarbamates pyrazolyl indazolyl disulfide anticancer HeLa cells Tetraethylthiuram disulfide antialcoholism drug proteasome activity crystal-structure in-vitro inhibition diethyldithiocarbamate growth agent lines Chemistry, Multidisciplinary LB - ISI 2009 07 17 IS - 5 N1 - English Article PY - 2009 SP - 322-325 ST - Anticancer activities of bis(pyrazol-1-ylthiocarbonyl)disulfides against HeLa cells T2 - Journal of Chemical Research-S TI - Anticancer activities of bis(pyrazol-1-ylthiocarbonyl)disulfides against HeLa cells ID - 3961 ER - TY - JOUR AB - A series of pyrazolyl palladium(II), platinum(II) and gold(III) complexes, [PdCl2(3,5-R(2)bpza)] {R = H (1), R = Me (2), bpza = bis-pyrazolyl acetic acid}, [PtCl2(3,5-R(2)bpza)] {R = H (3a), R = Me (4)}, [AuCl2(3,5-R(2)bpza)] Cl {R = H (5a), R = Me (6a)} and [PdCl2(3,5-R(2)bpzate)] {R = Me (7)} have been synthesised and structurally characterised. Single crystal X-ray crystallography showed that the pyrazolyl ligands exhibit N boolean AND N-coordination with the metals. Anticancer activities of six complexes 1-6a were investigated against CHO cells and were found to have low activities. Substitution reactions of selected complexes 1, 2, 3a and 5a with L-cysteine show that the low anticancer activities compounds and that the rate of substitution with sulfur-containing compounds is not the cause of the low anticancer activities. (C) 2008 Elsevier B.V. All rights reserved. AD - [Keter, Frankline K.; Ojwach, Stephen O.; Darkwa, James] Univ Johannesburg, Dept Chem, ZA-2006 Auckland Pk, South Africa. [Oyetunji, Olayinka A.] Univ Botswana, Dept Chem, Gaborone, Botswana. [Guzei, Ilia A.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000265509200012 AU - Keter, F. K. AU - Ojwach, S. O. AU - Oyetunji, O. A. AU - Guzei, I. A. AU - Darkwa, J. DA - Jun KW - Bis(pyrazolyl)acetic acid compounds Cytotoxicity Pseudo first-order Substitution L-cysteine Dna-binding properties biologically relevant nucleophiles coordination chemistry heteroscorpionate ligands aqueous-solution cytotoxicity kinetics mechanism reactivity design Chemistry, Inorganic & Nuclear LB - ISI 2009 05 14 IS - 8 N1 - English Article Southern & Eastern African Network of Analytical Chemists (SEANAC) PY - 2009 SP - 2595-2602 ST - Bis(pyrazolyl) palladium(II), platinum(II) and gold(III) complexes: Syntheses, molecular structures and substitution reactions with L-cysteine T2 - Inorganica Chimica Acta TI - Bis(pyrazolyl) palladium(II), platinum(II) and gold(III) complexes: Syntheses, molecular structures and substitution reactions with L-cysteine VL - 362 ID - 3983 ER - TY - JOUR AB - "Hastite", the orthorhombic dimorph of CoSe2, formerly considered as a valid mineral species occurring in the Trogtal quarries, Harz Mountains, Germany, is discredited as being identical with ferroselite, orthorhombic FeSe2. The discreditation has been unanimously approved by the IMA Commission on New Minerals, Nomenclature and Classification (CNMNC) (IMA No. 07-E). We also provide observations on the composition, homogeneity, and origin of trogtalite (cubic CoSe2) from its type locality. AD - [Keutsch, Frank N.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Foerster, Hans-Juergen] Univ Potsdam, Inst Earth Sci, D-14415 Potsdam, Germany. [Stanley, Chris J.] Nat Hist Museum, Dept Mineral, London SW7 5BD, England. [Rhede, Dieter] Deutsch GeoForschungsZentrum, Dept Inorgan & Isotope Geochem, D-14473 Potsdam, Germany. AN - ISI:000269726000018 AU - Keutsch, F. N. AU - Forster, H. J. AU - Stanley, C. J. AU - Rhede, D. DA - Aug KW - "hastite" ferroselite trogtalite electron-microprobe data reflectance data Trogtal Harz Mountains Germany Selenides kolwezi congo mine Mineralogy LB - ISI 2009 09 24 IS - 4 N1 - English Article PY - 2009 SP - 969-976 ST - THE DISCREDITATION OF HASTITE, THE ORTHORHOMBIC DIMORPH OF CoSe2, AND OBSERVATIONS ON TROGTALITE, CUBIC CoSe2, FROM THE TYPE LOCALITY T2 - Canadian Mineralogist TI - THE DISCREDITATION OF HASTITE, THE ORTHORHOMBIC DIMORPH OF CoSe2, AND OBSERVATIONS ON TROGTALITE, CUBIC CoSe2, FROM THE TYPE LOCALITY VL - 47 ID - 4026 ER - TY - JOUR AB - Reduction of elemental sulfur by a monovalent nickel precursor leads to a trans-1,2-mu-disulfidodinickel(II) complex assigned based on a combination of advanced spectroscopic methods in conjunction with density functional theory calculations. The disulfido linkage is characterized by an intense optical S -> Ni charge transfer transition at 650 nm, which causes a significant distortion of the Ni2S2 core along an isotope-sensitive v(S-S) mode at 474 cm(-1), as demonstrated by the resonance Raman excitation profile of this vibrational feature. AD - [Kieber-Emmons, Matthew T.; Riordan, Charles G.] Univ Delaware, Dept Chem & Biochem, Newark, DE 19716 USA. [Van Heuvelen, Katherine M.; Brunold, Thomas C.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000262521800022 AU - Kieber-Emmons, M. T. AU - Van Heuvelen, K. M. AU - Brunold, T. C. AU - Riordan, C. G. DA - Jan KW - Transition-metal-complexes side-on sulfur reactivity nickel ligand activation dioxygen core Chemistry, Multidisciplinary LB - ISI 2009 04 17 IS - 2 N1 - English Article 0002-7863 PY - 2009 SP - 440-+ ST - Synthesis and Spectroscopic Identification of a mu-1,2-Disulfidodinickel Complex T2 - Journal of the American Chemical Society TI - Synthesis and Spectroscopic Identification of a mu-1,2-Disulfidodinickel Complex VL - 131 ID - 3879 ER - TY - JOUR AB - The effect of peptides on the growth of ice crystals are studied using molecular dynamics simulations. The growth of the ice crystal is simulated at a supercooling of 14 K, and the effect of a single tetrapeptide on the growth rate is calculated. For pure ice the simulated crystal grows at a rate comparable to experiment. When a peptide molecule is added near the interface, the growth rate is diminished significantly, by up to a factor of 5 for Gly-Pro-Ala-Gly and a factor of 3 for Gly-Gly-Ala-Gly. The retardation occurs via the binding of the peptide to the ice surface, suppression of ice growth near the binding site, and eventual growth of the crystal around the bound peptide. The peptide with a proline residue is more effective in retarding the crystal growth, and this can be understood from the conformation of the peptide within the frozen ice phase after overgrowth. The simulations suggest that short peptides can be effective antifreeze agents. AD - [Yethiraj, Arun] Univ Wisconsin, Inst Theoret Chem, Madison, WI 53706 USA. [Yethiraj, Arun] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Damodaran, Srinivasan] Univ Wisconsin, Dept Food Sci, Madison, WI 53706 USA. [Kim, Jun Soo] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000265383200086 AU - Kim, J. S. AU - Damodaran, S. AU - Yethiraj, A. DA - Apr KW - Molecular-dynamics simulations particle mesh ewald antifreeze protein supercooled water potential functions crystal-growth hexagonal ice liquid water force-field inhibition Chemistry, Physical Physics, Atomic, Molecular & Chemical IS - 16 N1 - English Article United States Department of Agriculture National Research Initiative Program [2006-35503-16998]; National Science Foundation [CHE-0717569] 1089-5639 PY - 2009 SP - 4403-4407 ST - Retardation of Ice Crystallization by Short Peptides T2 - Journal of Physical Chemistry A TI - Retardation of Ice Crystallization by Short Peptides VL - 113 ID - 3919 ER - TY - JOUR AB - The effect of macromolecular crowding on the rates of association reactions are investigated using theory and computer simulations. Reactants and crowding agents are both hard spheres, and when two reactants collide they form product with a reaction probability, p(rxn). A value of p(rxn) < 1 crudely mimics the fact that proteins must be oriented properly for an association reaction to occur. The simulations show that the dependence of the reaction rate on the volume fraction of crowding agents varies with the reaction probability. For reaction probabilities close to unity where most of encounters between reactants lead to a reaction, the reaction rate always decreases as the volume fraction of crowding agents is increased due to the reduced diffusion coefficient of reactants. On the other hand, for very small reaction probabilities where, in most of encounters, the reaction does not occur, the reaction rate increases with the volume fraction of crowding agents-in this case, due to the increase probability of a recollision. The Smoluchowski theory refined with the radiation boundary condition and the radial distribution function at contact is in quantitative agreement with simulations for the reaction rate constant and allows the quantitative analysis of both effects separately. AD - [Yethiraj, Arun] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. Univ Wisconsin, Inst Theoret Chem, Madison, WI USA. AN - ISI:000266377800010 AU - Kim, J. S. AU - Yethiraj, A. DA - Feb KW - Diffusion-controlled reactions molecular-dynamics simulation orientation constraints biochemical reactions actin-filaments protein association cytoplasm models volume Biophysics LB - ISI 2009 06 12 IS - 4 N1 - English Article National Science Foundation [CHE-0717569] PY - 2009 SP - 1333-1340 ST - Effect of Macromolecular Crowding on Reaction Rates: A Computational and Theoretical Study T2 - Biophysical Journal TI - Effect of Macromolecular Crowding on Reaction Rates: A Computational and Theoretical Study VL - 96 ID - 3928 ER - TY - JOUR AD - [Kim, Yun Jun; Leolukman, Melvina; Gopalan, Padma] Univ Wisconsin, Dept Mat Sci & Engn, Madison, WI 53706 USA. [Kang, Huiman; Nealey, Paul F.] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA. AN - ISI:000268174400002 AU - Kim, Y. J. AU - Kang, H. M. AU - Leolukman, M. AU - Nealey, P. F. AU - Gopalan, P. DA - Jul KW - Chemically amplified resists block-copolymers radical polymerization raft process thin-films lithography chemistry blends Chemistry, Physical Materials Science, Multidisciplinary LB - ISI 2009 07 31 IS - 14 N1 - English Article Intel Corporation PY - 2009 SP - 3030-3032 ST - Synthesis of Photoacid Generator-Containing Patternable Diblock Copolymers by Reversible Addition-Fragmentation Transfer Polymerization T2 - Chemistry of Materials TI - Synthesis of Photoacid Generator-Containing Patternable Diblock Copolymers by Reversible Addition-Fragmentation Transfer Polymerization VL - 21 ID - 3972 ER - TY - JOUR AB - The applications of block copolymers are myriad, ranging from electronics to functionalized resins to therapeutics. The ring-opening metathesis polymerization (ROMP) is an especially valuable reaction for block copolymer assembly because each block can be generated with length control. We sought to use this polymerization to expand the repertoire of block copolymers by implementing a strategy that involves postpolymerization modification of a backbone bearing selectively reactive groups. To this end, we demonstrate that ROMP can be used to synthesize a block copolymer scaffold that possesses three types of functional groups-a succinimidyl ester, an alpha-chloroacetamide group, and a ketone-each of which can be modified independently. Thus, a single scaffold can be elaborated to afford a wide range of block copolymers. Exploiting this synthetic approach and the length control offered by ROMP, we assemble block copolymers capable of traversing the membrane and entering mammalian cells. AD - [Kolonko, Erin M.; Pontrello, Jason K.; Mangold, Shane L.; Kiessling, Laura L.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Kiessling, Laura L.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. AN - ISI:000266484900032 AU - Kolonko, E. M. AU - Pontrello, J. K. AU - Mangold, S. L. AU - Kiessling, L. L. DA - Jun KW - Ring-opening-metathesis controlled molecular-weight olefin-metathesis multivalent ligands radical polymerization polyvalent inhibitors reactive polymers catalysts polynorbornenes neoglycopolymers Chemistry, Multidisciplinary LB - ISI 2009 06 19 IS - 21 N1 - English Article NIGMS of the NIH [GM049975]; NIH [GM008505, RR 13866]; NSF [CHE-0342998, CHE-9629688] PY - 2009 SP - 7327-7333 ST - General Synthetic Route to Cell-Permeable Block Copolymers via ROMP T2 - Journal of the American Chemical Society TI - General Synthetic Route to Cell-Permeable Block Copolymers via ROMP VL - 131 ID - 3936 ER - TY - JOUR AB - Multinuclear NMR spectroscopic studies at low temperature (-110 to -150 degrees C) revealed that lithium p-fluorophenolate and the lithium enolates of cyclohexanone, cyclopentanone and 4-fluoroacetophenone have tetrameric structures in THF/Et2O and THF/Et2O-HMPA by study of the effects of the addition of HMPA. The Z and E isomers of the lithium enolate of 1,3-bis-(4-fluorophenyl)-2-propanone (5F-Li) show divergent behavior. The Z isomer is completely dimeric in. pure diethyl ether, and mostly dimeric in 3:2 THF/ether, where monomer could be detected in small amounts. TMTAN and P, MDTA convert Z-5F-Li to a monomeric amine complex, and HMPA converts it partially to m, and partially to lithiate species (RO)(2)Li- and (RO)(3)Li2-. Better characterized solutions of these lithiates were prepared by addition of phosphazenium enolates (using P4-Bu-t base) to the lithium enolate in 1:1 ratio to form triple ion (RO)(2)Li(-)P4H(+), or 2:1 ratio to form the higher lithiate (RO)(3)Li2- (P4H(+))(2)) (quadruple ions). The E isomer of 5F-Li is also dimeric in 3:2 THF/Et2O solution, but is not delectably converted to monomer either by PMDTA or HMPA. In contrast to Z-5F-Li, the E isomer is tetrameric in diethyl ether even in the presence of excess HMPA. Thus for the two isomers of 5F six different enolate structures were characterized: tetramer, dimer, CIP-monomer, SIP-monomer, triple ion, and quadruple ion. AD - [Kolonko, Kristopher J.; Biddle, Margaret M.; Guzei, Ilia A.; Reich, Hans J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000269379200058 AU - Kolonko, K. J. AU - Biddle, M. M. AU - Guzei, I. A. AU - Reich, H. J. DA - Aug KW - Aryllithium reagents-structure nuclear-magnetic-resonance dynamic-behavior organolithium compounds coupling-constants aggregation states crystal-structure sec-butyllithium cyclic dimers li-6 nmr Chemistry, Multidisciplinary LB - ISI 2009 09 10 IS - 32 N1 - English Article NSF [CHE-0074657, CHE-0717954, CHE-9709065, CHE-9304546] PY - 2009 SP - 11525-11534 ST - Solution Structures of Lithium Enolates of Cyclopentanone, Cyclohexanone, Acetophenones, and Benzyl Ketones. Triple Ions and Higher Lithiate Complexes T2 - Journal of the American Chemical Society TI - Solution Structures of Lithium Enolates of Cyclopentanone, Cyclohexanone, Acetophenones, and Benzyl Ketones. Triple Ions and Higher Lithiate Complexes VL - 131 ID - 4012 ER - TY - JOUR AB - Facile diffusion of globular proteins within a cytoplasm that is dense with biopolymers is essential to normal cellular biochemical activity and growth. Remarkably, Escherichia coli grows in minimal medium over a wide range of external osmolalities (0.03 to 1.8 osmol). The mean cytoplasmic biopolymer volume fraction () for such adapted cells ranges from 0.16 at 0.10 osmol to 0.36 at 1.45 osmol. For cells grown at 0.28 osmol, a similar range is obtained by plasmolysis (sudden osmotic upshift) using NaCl or sucrose as the external osmolyte, after which the only available cellular response is passive loss of cytoplasmic water. Here we measure the effective axial diffusion coefficient of green fluorescent protein (D-GFP) in the cytoplasm of E. coli cells as a function of for both plasmolyzed and adapted cells. For plasmolyzed cells, the median D-GFP (D-GFP(m)) decreases by a factor of 70 as increases from 0.16 to 0.33. In sharp contrast, for adapted cells, D-GFP(m) decreases only by a factor of 2.1 as increases from 0.16 to 0.36. Clearly, GFP diffusion is not determined by alone. By comparison with quantitative models, we show that the data cannot be explained by crowding theory. We suggest possible underlying causes of this surprising effect and further experiments that will help choose among competing hypotheses. Recovery of the ability of proteins to diffuse in the cytoplasm after plasmolysis may well be a key determinant of the time scale of the recovery of growth. AD - [Konopka, Michael C.; Sochacki, Kem A.; Bratton, Benjamin P.; Shkel, [Record, M. Thomas] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. AN - ISI:000261628100024 AU - Konopka, M. C. AU - Sochacki, K. A. AU - Bratton, B. P. AU - Shkel, I. A. AU - Record, M. T. AU - Weisshaar, J. C. DA - Jan KW - Green fluorescent protein concentration-dependence diffusion coefficients self-diffusion in-vivo dna bacteria model cell organization Microbiology LB - ISI 2009 01 09 IS - 1 N1 - English Article 0021-9193 PY - 2009 SP - 231-237 ST - Cytoplasmic Protein Mobility in Osmotically Stressed Escherichia coli T2 - Journal of Bacteriology TI - Cytoplasmic Protein Mobility in Osmotically Stressed Escherichia coli VL - 191 ID - 3698 ER - TY - JOUR AB - Facile diffusion of globular proteins within a cytoplasm that is dense with biopolymers is essential to normal cellular biochemical activity and growth. Remarkably, Escherichia coli grows in minimal medium over a wide range of external osmolalities (0.03 to 1.8 osmol). The mean cytoplasmic biopolymer volume fraction () for such adapted cells ranges from 0.16 at 0.10 osmol to 0.36 at 1.45 osmol. For cells grown at 0.28 osmol, a similar range is obtained by plasmolysis (sudden osmotic upshift) using NaCl or sucrose as the external osmolyte, after which the only available cellular response is passive loss of cytoplasmic water. Here we measure the effective axial diffusion coefficient of green fluorescent protein (D-GFP) in the cytoplasm of E. coli cells as a function of for both plasmolyzed and adapted cells. For plasmolyzed cells, the median D-GFP (D-GFP(m)) decreases by a factor of 70 as increases from 0.16 to 0.33. In sharp contrast, for adapted cells, D-GFP(m) decreases only by a factor of 2.1 as increases from 0.16 to 0.36. Clearly, GFP diffusion is not determined by alone. By comparison with quantitative models, we show that the data cannot be explained by crowding theory. We suggest possible underlying causes of this surprising effect and further experiments that will help choose among competing hypotheses. Recovery of the ability of proteins to diffuse in the cytoplasm after plasmolysis may well be a key determinant of the time scale of the recovery of growth. AD - [Konopka, Michael C.; Sochacki, Kem A.; Bratton, Benjamin P.; Shkel, Irina A.; Record, M. Thomas; Weisshaar, James C.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Record, M. Thomas] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. AN - ISI:000261628100024 AU - Konopka, M. C. AU - Sochacki, K. A. AU - Bratton, B. P. AU - Shkel, I. A. AU - Record, M. T. AU - Weisshaar, J. C. KW - Microbiology LB - ISI 2009 01 09 N1 - English Article GREEN FLUORESCENT PROTEIN; CONCENTRATION-DEPENDENCE; DIFFUSION COEFFICIENTS; SELF-DIFFUSION; IN-VIVO; DNA; BACTERIA; MODEL; CELL; ORGANIZATION JAN 1 PY - 2009 SP - 231-237 ST - Cytoplasmic Protein Mobility in Osmotically Stressed Escherichia coli T2 - Journal of Bacteriology TI - Cytoplasmic Protein Mobility in Osmotically Stressed Escherichia coli ID - 3705 ER - TY - JOUR AB - Nucleophilic displacements of 5(6)-anti-bromo substituents in 2-azabicyclo[2.1.1]hexanes (methanopyrrolidines) have been accomplished. These displacements have produced 5-anti-X-6-anti-Y-difunctionalized-2-azabicyclo[2.1.1]hexanes containing bromo, fluoro, acetoxy, hydroxy, azido, imidazole, thiophenyl, and iodo substituents. Such displacements of anti-bromide ions require an amine nitrogen and tire it function of the solvent and the choice of metal salt. Reaction rates were Faster and product yields were higher in DMSO when compared to DMF and with CsOAc compared to NaOAc. Sodium or lithium salts gave products, except with NaF, where silver fluoride in nitromethane was best for Substitution by fluoride. The presence of electron-withdrawing F, OAc, N-3, Br, or SPh substituents in the 6-anti-position slows bromide displacements at the 5-anti-position. AD - [Krow, Grant R.; Edupuganti, Ram; Gandla, Deepa; Lin, Guoliang; Sonnet, Philip E.; DeBrosse, Charles] Temple Univ, Dept Chem, Philadelphia, PA 19122 USA. [Choudhary, Amit] Univ Wisconsin, Grad Program Biophys, Madison, WI 53706 USA. [Raines, Ronald T.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. [Raines, Ronald T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Cannon, Kevin C.] Penn State Abington, Dept Chem, Abington, PA 19104 USA. [Ross, Charles W., III] Merck & Co Inc, Dept Med Chem, Merck Res Labs, West Point, PA 19486 USA. AN - ISI:000271113400025 AU - Krow, G. R. AU - Edupuganti, R. AU - Gandla, D. AU - Choudhary, A. AU - Lin, G. L. AU - Sonnet, P. E. AU - DeBrosse, C. AU - Ross, C. W. AU - Cannon, K. C. AU - Raines, R. T. DA - Nov KW - Neighboring group participation acetylcholine-receptor ligands glutamic-acid analog 2,4-methanoproline 2-carboxy-2,4-methanopyrrolidine rearrangement route conformational properties dimethyl-sulfoxide aqueous-solution proline analogs n-alkylation Chemistry, Organic LB - ISI 2009 11 05 IS - 21 N1 - English Article National Science Foundation [CHE 0515635] PY - 2009 SP - 8232-8242 ST - 5(6)-anti-Substituted-2-azabicyclo[2.1.1]hexanes: A Nucleophilic Displacement Route T2 - Journal of Organic Chemistry TI - 5(6)-anti-Substituted-2-azabicyclo[2.1.1]hexanes: A Nucleophilic Displacement Route VL - 74 ID - 4065 ER - TY - JOUR AB - Electrospray ionization (ESI) of denatured proteins produces a broad distribution of multiply-charged ions leading to multiple peaks in the mass spectrum. We investigated changes in the positive-mode ESI charge state distribution produced by several chemical modifications of denatured proteins. Capping carboxylic acid groups with neutral functional groups yields little change in charge state distribution compared with unmodified proteins. The results indicate that carboxyl groups do not play a significant role in the positive charging of denatured proteins in ESI. The modification of proteins with additional basic sites or fixed positive charges generates substantially higher charge states, providing evidence that the number of ionizable sites, rather than molecular size and shape, determines ESI charging for denatured proteins. Fixed charge modification also significantly reduces the number of protons acquired by a protein, in that the charge state envelope is not increased by the full number of fixed charges appended. This result demonstrates that Coulombic repulsion between positive charges plays a significant role in determining charge state distribution by affecting the gas-phase basicity of ionizable sites. Addition of fixed-charge moieties to a protein is a useful approach for shifting protein charge state distributions to higher charge states, and with further work, it may help limit the distribution of protein ions to fewer charge states. (J Am Soc Mass Spectrorn 2009, 20, 1617-1625) (C) 2009 American Society for Mass Spectrometry AD - [Frey, Brian L.; Belshaw, Peter J.; Smith, Lloyd M.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Krusemark, Casey J.; Belshaw, Peter J.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. AN - ISI:000270836800004 AU - Krusemark, C. J. AU - Frey, B. L. AU - Belshaw, P. J. AU - Smith, L. M. DA - Sep KW - Ion-molecule reactions gas-phase top-down globular-proteins native proteins ubiquitin ions cytochrome-c complexes deprotonation peptides Chemistry, Analytical Chemistry, Physical Spectroscopy LB - ISI 2009 10 29 IS - 9 N1 - English Article NIH Biotechnology Training Grant Fellowship ; National Heart Lung Blood Institute (NHLBI) [N01HV-28,182]; NIH [R01GM065406, R33DK070297] PY - 2009 SP - 1617-1625 ST - Modifying the Charge State Distribution of Proteins in Electrospray Ionization Mass Spectrometry by Chemical Derivatization T2 - Journal of the American Society for Mass Spectrometry TI - Modifying the Charge State Distribution of Proteins in Electrospray Ionization Mass Spectrometry by Chemical Derivatization VL - 20 ID - 4058 ER - TY - JOUR AB - Bacterial cells can differentiate into states that allow them to respond efficiently to their environment. An example of such a transformation is the differentiation of planktonic bacteria into highly motile swarmer cells, The hyper-flagellated, filamentous swarmer cells can use coordinated movement to seek out and colonize new sites for pathogenic infection. Because the chemotaxis proteins are essential for swarmer differentiation, we sought to probe the relationship between differentiation and chemoattractants. To this end, we developed a method to screen large populations of swarmer cells using flow cytometry. Using this approach, we found that highly potent multivalent chemoattractants can induce the dedifferentiation of swarmer cells. Our results indicate that chemotactic signaling functions as a target for agents that interfere with bacterial swarming, In addition, the identification of ligands that promote the dedifferentiation of swarmer cells offers new strategies for modulating this multicellular behavior. AD - [Lamanna, Allison C.; Kiessling, Laura L.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. [Kiessling, Laura L.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000272562000003 AU - Lamanna, Allison C. AU - Kiessling, Laura L. DA - Oct KW - Enterica serovar typhimurium escherichia-coli bacterial chemoreceptors proteus-mirabilis bacillus-subtilis chemotactic responses dna-content motility size differentiation Biochemistry & Molecular Biology LB - ISI 2009 12 24 IS - 10 N1 - English Article NIH [R01 GM055984, T32 GM072125]; NSF PY - 2009 SP - 828-833 ST - Flow Cytometry Reveals that Multivalent Chemoattractants Effect Swarmer Cell Dedifferentiation T2 - ACS Chemical Biology TI - Flow Cytometry Reveals that Multivalent Chemoattractants Effect Swarmer Cell Dedifferentiation VL - 4 ID - 4113 ER - TY - JOUR AB - Electrochemically active ferrocene groups were covalently linked to vertically aligned carbon nanofibers (VACNFs) in a simple and efficient manner via the Cu(I)-catalyzed azide alkyne cycloaddition (CuAAC), one form of "click" chemistry. The VACNFs were terminated with azide groups followed by the attachment of ethynylferrocene through a 1,4-disubstituted 1,2,3-triazole linkage. Our results show that the CuAAC reaction goes to completion in one hour and provides highly stable attachment of electrochemically active ferrocene groups to the nanofibers. X-ray photoelectron spectroscopy measurements of the density of surface-bound ferrocene molecules are in good agreement with those determined by cyclic voltammetry. The rates of electron transfer were found to be slightly faster than those measured previously through alkyl linkages to the VACNF surface. Stability tests show that the covalently grafted ferrocene groups are stable for more than 1500 repeated cyclic voltammograms and over a potential window of > 1.5 V, limited by the solvent. These results suggest that the use of "click" chemistry with VACNFs provides a facile route toward synthesis of high-surface-area electrodes with high stability and tailored electrochemical properties. AD - [Landis, Elizabeth C.; Hamers, Robert J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000263431600019 AU - Landis, E. C. AU - Hamers, R. J. KW - Chemistry, Physical Materials Science, Multidisciplinary LB - ISI 2009 03 05 N1 - English Article ELECTRON-TRANSFER KINETICS; SELF-ASSEMBLED MONOLAYERS; FERROCENYL ALKYL THIOLS; BIOCHEMICAL FUNCTIONALIZATION; TERMINATED MONOLAYERS; SURFACE MODIFICATION; GRAPHITE-ELECTRODES; NANOTUBES; GOLD; VOLTAMMETRY FEB 24 4 PY - 2009 SP - 724-730 ST - Covalent Grafting of Redox-Active Molecules to Vertically Aligned Carbon Nanofiber Arrays via "Click" Chemistry T2 - Chemistry of Materials TI - Covalent Grafting of Redox-Active Molecules to Vertically Aligned Carbon Nanofiber Arrays via "Click" Chemistry ID - 3767 ER - TY - JOUR AB - Electrochemically active ferrocene groups were covalently linked to vertically aligned carbon nanofibers (VACNFs) in a simple and efficient manner via the Cu(I)-catalyzed azide alkyne cycloaddition (CuAAC), one form of "click" chemistry. The VACNFs were terminated with azide groups followed by the attachment of ethynylferrocene through a 1,4-disubstituted 1,2,3-triazole linkage. Our results show that the CuAAC reaction goes to completion in one hour and provides highly stable attachment of electrochemically active ferrocene groups to the nanofibers. X-ray photoelectron spectroscopy measurements of the density of surface-bound ferrocene molecules are in good agreement with those determined by cyclic voltammetry. The rates of electron transfer were found to be slightly faster than those measured previously through alkyl linkages to the VACNF surface. Stability tests show that the covalently grafted ferrocene groups are stable for more than 1500 repeated cyclic voltammograms and over a potential window of > 1.5 V, limited by the solvent. These results suggest that the use of "click" chemistry with VACNFs provides a facile route toward synthesis of high-surface-area electrodes with high stability and tailored electrochemical properties. AN - ISI:000263431600019 AU - Landis, E. C. AU - Hamers, R. J. DA - Feb DO - 10.1021/cm802869b LB - ISI 2009 03 05 (Library clean-up) IS - 4 N1 - Landis, Elizabeth C. Hamers, Robert J. PY - 2009 SN - 0897-4756 SP - 724-730 ST - Covalent Grafting of Redox-Active Molecules to Vertically Aligned Carbon Nanofiber Arrays via "Click" Chemistry T2 - Chemistry of Materials TI - Covalent Grafting of Redox-Active Molecules to Vertically Aligned Carbon Nanofiber Arrays via "Click" Chemistry UR - ://000263431600019 VL - 21 ID - 3774 ER - TY - JOUR AB - Growth of extensively aligned hierarchical lead sulfide (PbS) nanowires with hyperbranched morphology has been achieved by synthesizing nanowires epitaxially on single crystal NaCl, rutile TiO2 (001), and muscovite mica in a chemical vapor deposition process. The morphology of as-grown PbS nanowires has been examined using scanning electron microscopy. Epitaxial match with the (100) plane of PbS has been observed on all substrates, and epitaxial match with PbS (111) was also observed on mica. In addition, the preferred orientation of nanowires led to particularly strong (200) reflections from PbS in powder X-ray diffraction. The potential epitaxial relationship and lattice match are proposed and discussed. PbS nanowires of the pine tree morphology can only be formed nonepitaxially in the presence of epitaxial hyperbranched clusters. The difficulty of forming epitaxial nanowire pine trees suggested that epitaxial growth might not be conducive to the creation of dislocations that drive the formation of pine tree nanowires. Electrical properties of PbS nanowires have also been investigated. AN - ISI:000263113500013 AU - Lau, Y. K. A. AU - Chernak, D. J. AU - Bierman, M. J. AU - Jin, S. DO - 10.1039/b818187j LB - ISI 2009 02 20 IS - 7 N1 - Lau, Y. K. Albert Chernak, Davin J. Bierman, Matthew J. Jin, Song PY - 2009 SN - 0959-9428 SP - 934-940 ST - Epitaxial growth of hierarchical PbS nanowires T2 - Journal of Materials Chemistry TI - Epitaxial growth of hierarchical PbS nanowires UR - ://000263113500013 VL - 19 ID - 3783 ER - TY - JOUR AD - [Ledvina, Aaron R.; McAlister, Graeme C.; Coon, Joshua J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Gardner, Myles W.; Smith, Suncerae I.; Madsen, James A.; Brodbelt, Jennifer S.] Univ Texas Austin, Dept Chem, Austin, TX 78712 USA. [Schwartz, Jae C.; Stafford, George C., Jr.; Syka, John E. P.] Thermo Fisher Sci, San Jose, CA 95134 USA. AN - ISI:000271543800025 AU - Ledvina, Aaron R. AU - McAlister, Graeme C. AU - Gardner, Myles W. AU - Smith, Suncerae I. AU - Madsen, James A. AU - Schwartz, Jae C. AU - Stafford, George C., Jr. AU - Syka, John E. P. AU - Brodbelt, Jennifer S. AU - Coon, Joshua J. KW - ionization of gases mass spectrometry peptides photoactivation proteomics Electron-capture dissociation ion/ion reactions ions Chemistry, Multidisciplinary LB - ISI 2009 11 19 IS - 45 N1 - English Article NIH [R01 GM080149]; NSF [CHE-0747990, CHE-0718320] PY - 2009 SP - 8526-8528 ST - Infrared Photoactivation Reduces Peptide Folding and Hydrogen-Atom Migration following ETD Tandem Mass Spectrometry T2 - Angewandte Chemie-International Edition TI - Infrared Photoactivation Reduces Peptide Folding and Hydrogen-Atom Migration following ETD Tandem Mass Spectrometry VL - 48 ID - 4088 ER - TY - JOUR AB - CooA is a heme-dependent CO-sensing transcription factor that has three observable heme coordination states. There is some evidence that each CooA heme state has a distinct protein conformation; the goal of this study was to characterize these conformations by measuring their structural stabilities through guanidine hydrochloride (GuHCl) denaturation. By studying the denaturation processes of the Fe(Ill) state of WT CooA and several variants, we were able to characterize independent unfolding processes for each domain of CooA. This information was used to compare the unfolding profiles of various CooA heme activation states [Fe(III), Fe(II), and Fe(II)-CO] to show that the heme coordination state changes the stability of the effector binding domain. A mechanism consistent with the data predicts that all CooA coordination states and variants undergo unfolding of the DNA-binding domain between 2 and 3 M GuHCl with it free energy of unfolding of similar to 17 kJ/mol, while unfolding of the heme domain is variable and dependent on the heme coordination state. The Findings support it model in which changes in heme ligation alter the structural stability of the heme domain and dimer interface but do not alter the stability of the DNA-binding domain. These studies provide evidence that the domains of transcription factors are modular and that allosteric signaling occurs through changes in the relative positions of the protein domains without affecting the structure of the DNA-binding region. AD - [Lee, Andrea J.; Clark, Robert W.; Ponter, Sarah; Burstyn, Judith N.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Youn, Hwan] Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA. AN - ISI:000268137800004 AU - Lee, A. J. AU - Clark, R. W. AU - Youn, H. AU - Ponter, S. AU - Burstyn, J. N. DA - Jul KW - Camp receptor protein dna-binding domains rhodospirillum-rubrum escherichia-coli activator cooa crystal-structure conformational change allosteric regulation hinge reorientation circular-dichroism Biochemistry & Molecular Biology LB - ISI 2009 07 31 IS - 28 N1 - English Article NIH [HL-66147] PY - 2009 SP - 6585-6597 ST - Guanidine Hydrochloride-Induced Unfolding of the Three Heme Coordination States of the CO-Sensing Transcription Factor, CooA T2 - Biochemistry TI - Guanidine Hydrochloride-Induced Unfolding of the Three Heme Coordination States of the CO-Sensing Transcription Factor, CooA VL - 48 ID - 3974 ER - TY - JOUR AD - [Sadowsky, Jack D.; Peterson-Kaufman, Kimberly J.; Gellman, Samuel H.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Lee, Erinna F.; Smith, Brian J.; Czabotar, Peter E.; Colman, Peter M.; Fairlie, W. Douglas] Walter & Eliza Hall Inst Med Res, Struct Biol Div, Parkville, Vic 3052, Australia. AN - ISI:000267040000009 AU - Lee, E. F. AU - Sadowsky, J. D. AU - Smith, B. J. AU - Czabotar, P. E. AU - Peterson-Kaufman, K. J. AU - Colman, P. M. AU - Gellman, S. H. AU - Fairlie, W. D. KW - amino acids foldamers peptides protein-protein interactions X-ray diffraction Bcl-2 family crystallographic characterization bh3-recognition cleft crystal-structure beta-peptides inhibitors recognition antagonists sequence ligands Chemistry, Multidisciplinary LB - ISI 2009 07 03 IS - 24 N1 - English Article PY - 2009 SP - 4318-4322 ST - High-Resolution Structural Characterization of a Helical alpha/beta-Peptide Foldamer Bound to the Anti-Apoptotic Protein Bcl-x(L) T2 - Angewandte Chemie-International Edition TI - High-Resolution Structural Characterization of a Helical alpha/beta-Peptide Foldamer Bound to the Anti-Apoptotic Protein Bcl-x(L) VL - 48 ID - 3951 ER - TY - JOUR AB - When sufficient force is applied to a glassy polymer, it begins to deform through movement of the polymer chains. We used an optical photobleaching technique to quantitatively measure changes in molecular mobility during the active deformation of a polymer glass [ poly( methyl methacrylate)]. Segmental mobility increases by up to a factor of 1000 during uniaxial tensile creep. Although the Eyring model can describe the increase in mobility at low stress, it fails to describe mobility after flow onset. In this regime, mobility is strongly accelerated and the distribution of relaxation times narrows substantially, indicating a more homogeneous ensemble of local environments. At even larger stresses, in the strain- hardening regime, mobility decreases with increasing stress. Consistent with the view that stress- induced mobility allows plastic flow in polymer glasses, we observed a strong correlation between strain rate and segmental mobility during creep. AD - [Lee, Hau-Nan; Paeng, Keewook; Swallen, Stephen F.; Ediger, M. D.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000262290600032 AU - Lee, H. N. AU - Paeng, K. AU - Swallen, S. F. AU - Ediger, M. D. DA - Jan KW - Spatially heterogeneous dynamics constitutive model amorphous polymers deformation relaxation strain plasticity transition flow pmma Multidisciplinary Sciences LB - ISI 2009 01 22 IS - 5911 N1 - English Article 0036-8075 PY - 2009 SP - 231-234 ST - Direct Measurement of Molecular Mobility in Actively Deformed Polymer Glasses T2 - Science TI - Direct Measurement of Molecular Mobility in Actively Deformed Polymer Glasses VL - 323 ID - 3730 ER - TY - JOUR AB - An optical photobleaching method has been used to measure the segmental dynamics of a poly(methyl methacrylate) (PMMA) glass during uniaxial creep deformation at temperatures between T-g - 9 K and T-g - 20 K. Up to 1000-fold increases in mobility are observed during deformation, supporting the view that enhanced segmental mobility allows flow in polymer glasses. Although the Eyring model describes this mobility enhancement well at low stress, it fails to capture the dramatic mobility enhancement after flow onset, where in addition the shape of the relaxation time distribution narrows significantly. Regions of lower mobility accelerate their dynamics more in response to an external stress than do regions of high mobility. Thus, local environments in the sample become more dynamically homogeneous during flow. (C) 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 17131727, 2009 AD - [Lee, Hau-Nan; Paeng, Keewook; Swallen, Stephen F.; Ediger, M. D.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Stamm, Rebecca A.; Medvedev, Grigori A.; Caruthers, James M.] Purdue Univ, Sch Chem Engn, W Lafayette, IN 47907 USA. AN - ISI:000269090600008 AU - Lee, H. N. AU - Paeng, K. AU - Swallen, S. F. AU - Ediger, M. D. AU - Stamm, R. A. AU - Medvedev, G. A. AU - Caruthers, J. M. DA - Sep KW - fluorescence glassy polymers mechanical properties segmental dynamics yielding Nonlinearly viscoelastic behavior spatially heterogeneous dynamics enhanced translational diffusion polymer glasses amorphous polymers thermodynamically consistent temperature-dependence dielectric-relaxation model polycarbonate Polymer Science LB - ISI 2009 09 03 IS - 17 N1 - English Article National Science Foundation [NIRT 0506840, DMR 0907607] PY - 2009 SP - 1713-1727 ST - Molecular Mobility of Poly(methyl methacrylate) Glass During Uniaxial Tensile Creep Deformation T2 - Journal of Polymer Science Part B-Polymer Physics TI - Molecular Mobility of Poly(methyl methacrylate) Glass During Uniaxial Tensile Creep Deformation VL - 47 ID - 4007 ER - TY - JOUR AB - Optical photobleaching experiments and molecular dynamics computer simulations were used to investigate changes in segmental mobility during tensile creep deformation of polymer glasses. Experiments were performed on lightly cross-linked PMMA, and the simulations utilized a coarse-grained model. For both single-step and multistep creep deformations, the experiments and simulations show remarkably similar trends, with changes of mobility during deformation exceeding a factor of 100. Both experiment and simulation show a strong correlation between strain rate and mobility in single-step creep. However, in multistep creep, the correlation between strain rate and mobility is broken in both experiment and simulation; this emphasizes that no simple mechanical variable is likely to exhibit a simple relationship with molecular mobility universally. Both simulations and experiments show many features that are inconsistent with the Eyring model. AD - [Lee, Hau-Nan; Ediger, M. D.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Riggleman, Robert A.; de Pablo, Juan J.] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA. AN - ISI:000267048200070 AU - Lee, H. N. AU - Riggleman, R. A. AU - de Pablo, J. J. AU - Ediger, M. D. DA - Jun KW - Spatially heterogeneous dynamics amorphous polymers uniaxial deformation plastic-deformation active deformation constitutive model polystyrene transition diffusion behavior Polymer Science LB - ISI 2009 07 03 IS - 12 N1 - English Article National Science Foundation [0506840, DMR-0520527, DMR-0907607] PY - 2009 SP - 4328-4336 ST - Deformation-Induced Mobility in Polymer Glasses during Multistep Creep Experiments and Simulations T2 - Macromolecules TI - Deformation-Induced Mobility in Polymer Glasses during Multistep Creep Experiments and Simulations VL - 42 ID - 3949 ER - TY - JOUR AB - Polymers in the nylon-3 family contain subunits derived from beta-amino acids, which are linked to one another via amide bonds. Thus, the nylon-3 backbone is homologous to the CL-amino acid-based backbone of proteins. This molecular-level homology suggests that nylon-3 materials might be intrinsically protein-mimetic. The experiments described here explore this prospect in the context of cell adhesion, with tissue engineering as a long-range goal. We have evaluated a small library of sequence-random nylon-3 copolymers for the ability to render surfaces attractive to NIH 3T3 fibroblast adhesion and spreading. Library screening was accomplished in a high-throughput, parallel mode via attachment of the copolymers in a two-dimensional array to a modified glass surface. Significant variations in fibroblast adhesion and spreading were observed as a function of nylon-3 subunit identity and proportion. Several of the nylon-3 copolymers supported cell adhesion and morphology that was comparable, or even superior, to that achieved on positive control substrates such as tissue culture polystyrene and collagen-coated glass. Moreover, studies conducted under serum-free conditions demonstrated that specific nylon-3 derivatives supported cell adhesion independently of serum protein adsorption. Although cell adhesion was diminished in the absence of serum, particular copolymers demonstrated an ability to support substantially greater cell adhesion than any of the other conditions, including the positive controls. The nylon-3 copolymers that were most effective at promoting adhesion to a modified glass surface proved also to be effective at promoting adhesion when attached to a PEG-based hydrogel, demonstrating the potential for these copolymers to be used in tissue engineering applications. AD - [Lee, Myung-Ryul; Stahl, Shannon S.; Gellman, Samuel H.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Masters, Kristyn S.] Univ Wisconsin, Dept Biomed Engn, Madison, WI 53706 USA. AN - ISI:000272185400047 AU - Lee, Myung-Ryul AU - Stahl, Shannon S. AU - Gellman, Samuel H. AU - Masters, Kristyn S. DA - Nov KW - Ring-opening polymerization functionalized side-chains beta-lactams peptides biomaterials hydrogels nanofibers microenvironments mineralization proliferation Chemistry, Multidisciplinary LB - ISI 2009 12 11 IS - 46 N1 - English Article Nanoscale Science and Engineering Center at UW-Madison [DMR-0425880]; NSF Collaborative Research in Chemistry program [CHE-0404704]; National Institutes of Health [1R21-EB005440]; Korea Research Foundation ; Korean Government (MOEHRD) [KRF-2006-214-C00053] PY - 2009 SP - 16779-16789 ST - Nylon-3 Copolymers that Generate Cell-Adhesive Surfaces Identified by Library Screening T2 - Journal of the American Chemical Society TI - Nylon-3 Copolymers that Generate Cell-Adhesive Surfaces Identified by Library Screening VL - 131 ID - 4070 ER - TY - JOUR AB - TiO2 thin films are highly stable and can be deposited onto a wide variety of substrate materials under moderate conditions. We demonstrate that organic alkenes will graft to the surface of TiO2 when illuminated with UV light at 254 nm and that the resulting layers provide a starting point for the preparation of DNA-modified TiO2 thin films exhibiting excellent stability and biomolecular selectivity. By using alkenes with a protected amino group at the distal end, the grafted layers can be deprotected to yield molecular layers with exposed primary amino groups that can then be used to covalently link DNA oligonucleotides to the TiO2 surface. We demonstrate that the resulting DNA-modified surfaces exhibit excellent selectivity toward complementary versus noncomplementary target sequences in solution and that the surfaces can withstand 25 cycles of hybridization and denaturation in 8.3 M urea with little or no degradation. Furthermore, the use of simple masking methods provides a way to directly control the spatial location of the grafted layers, thereby providing a way to photopattern the spatial distribution of biologically active molecules to the TiO2 surfaces. Using Ti films ranging from 10 to 100 nm in thickness allows the preparation of TiO2 films that range from highly reflective to almost completely transparent; in both cases, the photochemical grafting of alkenes can be used as a starting point for stable surfaces with good biomolecular recognition properties. AD - [Li, Bo; Franking, Ryan; Landis, Elizabeth C.; Kim, Heesuk; Hamers, Robert J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000268665200007 AU - Li, B. AU - Franking, R. AU - Landis, E. C. AU - Kim, H. AU - Hamers, R. J. DA - May KW - metal oxide photochemistry surface functionalization titania DNA biointerfaces Self-assembled monolayers metal-oxide surfaces titanium-dioxide diamond surfaces protein adsorption elevated-temperatures reaction-mechanisms organic-molecules phosphonic acid functionalization LB - ISI 2009 08 13 IS - 5 N1 - English Article National Science Foundation [CHE-0613010, DMR-0425880]; U.S. Army Corp of Engineers PY - 2009 SP - 1013-1022 ST - Photochemical Grafting and Patterning of Biomolecular Layers onto TiO2 Thin Films T2 - ACS Applied Materials & Interfaces TI - Photochemical Grafting and Patterning of Biomolecular Layers onto TiO2 Thin Films VL - 1 ID - 3999 ER - TY - JOUR AB - iso-Migrastatin and related glutarimide-containing polyketides are potent inhibitors of tumor cell migration and their implied potential as antimetastatic agents for human cancers has garnered significant attention. Genome scanning of Streptomyces platensis NRRL 18993 unveiled two candidate gene clusters (088D and mgs); each encodes acyltransferase-less type I polyketide synthases commensurate with iso-migrastatin biosynthesis. Both clusters were inactivated by lambda-RED-mediated PCR-targeting mutagenesis in S. platensis; iso-migrastatin production was completely abolished in the Delta mgsF mutant SB11012 strain, whereas inactivation of 088D-orf7 yielded the SB11006 strain that exhibited no discernible change in iso-migrastatin biosynthesis. These data indicate that iso-migrastatin production is governed by the mgs cluster. Systematic gene inactivation allowed determination of the precise boundaries of the mgs cluster and the essentiality of the genes within the mgs cluster in iso-migrastatin production. The mgs cluster consists of 11 open reading frames that encode three acyltransferase-less type I polyketide synthases (MgsEFG), one discrete acyltransferase (MgsH), a type II thioesterase (MgsB), three post-PKS tailoring enzymes (MgsIJK), two glutarimide biosynthesis enzymes (MgsCD), and one regulatory protein (MgsA). A model for iso-migrastatin biosynthesis is proposed based on functional assignments derived from bioinformatics and is further supported by the results of in vivo gene inactivation experiments. AD - [Shen, Ben] Univ Wisconsin, Sch Pharm, Div Pharmaceut Sci, Madison, WI 53705 USA. [Shen, Ben] Univ Wisconsin, Natl Cooperat Drug Discovery Grp, Madison, WI 53705 USA. [Shen, Ben] Univ Wisconsin, Dept Chem, Madison, WI 53705 USA. [Zazopoulos, Emmanuel; Farnet, Chris M.] Thall Pharmaceut Inc, Montreal, PQ H4S 2C8, Canada. AN - ISI:000270896800056 AU - Lim, S. K. AU - Ju, J. H. AU - Zazopoulos, E. AU - Jiang, H. AU - Seo, J. W. AU - Chen, Y. H. AU - Feng, Z. Y. AU - Rajski, S. R. AU - Farnet, C. M. AU - Shen, B. DA - Oct KW - Cell-migration inhibitors gene-cluster molecular characterization biological-activity synthetase lactimidomycin congeners protein ketoreductase antibiotics Biochemistry & Molecular Biology LB - ISI 2009 10 29 IS - 43 N1 - English Article National Institutes of Health [CA106150, CA113297] PY - 2009 SP - 29746-29756 ST - iso-Migrastatin, Migrastatin, and Dorrigocin Production in Streptomyces platensis NRRL 18993 Is Governed by a Single Biosynthetic Machinery Featuring an Acyltransferase-less Type I Polyketide Synthase T2 - Journal of Biological Chemistry TI - iso-Migrastatin, Migrastatin, and Dorrigocin Production in Streptomyces platensis NRRL 18993 Is Governed by a Single Biosynthetic Machinery Featuring an Acyltransferase-less Type I Polyketide Synthase VL - 284 ID - 4060 ER - TY - JOUR AB - We study theoretically the steady-state and ultrafast vibrational spectroscopy, in the OD-stretch region, of dilute HOD in aqueous solutions of sodium bromide. Based on electronic-structure calculations on clusters containing salt ions and water, we develop new spectroscopic maps that enable us to undertake this study. We calculate OD-stretch absorption line shapes as a function of salt concentration, finding good agreement with experiment. We provide molecular-level understandings of the monotonic (as a function of concentration) blueshift, and nonmonotonic line width. We also calculate the frequency time-correlation function, as measured by spectral diffusion experiments. Here again we obtain good agreement with experiment, finding that at the highest salt concentration spectral diffusion slows down by a factor of 3 or 4 (compared to pure water). For longer times than can be accessed experimentally, we find that spectral diffusion is very complicated, with processes occurring on multiple time scales. We argue that from 6 to 40 ps, relaxation involves anionic solvation shell rearrangements. Finally, we consider our findings within the general context of the Hofmeister series, concluding that this series must reflect only local ordering of water molecules. (C) 2009 American Institute of Physics. [doi: 10.1063/1.3242083] AD - [Lin, Y. -S.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. Univ Wisconsin, Inst Theoret Chem, Madison, WI 53706 USA. AN - ISI:000270825600030 AU - Lin, Y. S. AU - Auer, B. M. AU - Skinner, J. L. DA - Oct DO - 144511 KW - Ultrafast infrared-spectroscopy hydrogen-bond dynamics aqueous solvation shells alkali-halide solutions liquid water molecular-dynamics ab-initio hydration shell hofmeister series line-shapes Physics, Atomic, Molecular & Chemical LB - ISI 2009 10 29 IS - 14 N1 - English Review National Science Foundation [CHE-0750307]; Department of Energy [DE-FG02-09ER16110] PY - 2009 ST - Water structure, dynamics, and vibrational spectroscopy in sodium bromide solutions T2 - Journal of Chemical Physics TI - Water structure, dynamics, and vibrational spectroscopy in sodium bromide solutions VL - 131 ID - 4059 ER - TY - JOUR AB - The amide I vibrational mode, primarily associated with peptide-bond carbonyl stretches, has long been used to probe the structures and dynamics of peptides and proteins by infrared (IR) spectroscopy. A number of ab initio-based amide I vibrational frequency maps have been developed for calculating IR line shapes. In this paper, a new empirical amide I vibrational frequency map is developed. To evaluate its performance, we applied this map to a system of isotope-edited CD3-zeta membrane peptide bundles in aqueous solution. The calculated 2D-IR diagonal line widths vary from residue to residue and show an asymmetric pattern as a function of position in the membrane. The theoretical results are in fair agreement with experiments on the same system. Through analysis of the computed frequency time-correlation functions, it is found that the 2D-IR diagonal widths are dominated by contributions from the inhomogeneous frequency distributions, from which it follows that these widths are a good probe of the extent of local structural fluctuations. Thus, the asymmetric pattern of line widths follows from the asymmetric structure of the bundle in the membrane. AN - ISI:000262522200002 AU - Lin, Y. S. AU - Shorb, J. M. AU - Mukherjee, P. AU - Zanni, M. T. AU - Skinner, J. L. DA - Jan DO - 10.1021/jp807528q LB - ISI 2009 02 05 IS - 3 N1 - Lin, Y. -S. Shorb, J. M. Mukherjee, P. Zanni, M. T. Skinner, J. L. PY - 2009 SN - 1520-6106 SP - 592-602 ST - Empirical Amide I Vibrational Frequency Map: Application to 2D-IR Line Shapes for Isotope-Edited Membrane Peptide Bundles T2 - Journal of Physical Chemistry B TI - Empirical Amide I Vibrational Frequency Map: Application to 2D-IR Line Shapes for Isotope-Edited Membrane Peptide Bundles UR - ://000262522200002 VL - 113 ID - 3795 ER - TY - JOUR AB - Islet amyloid polypeptide (IAPP, also known as amylin) is responsible for pancreatic amyloid deposits in type 2 diabetes. The deposits, as well as intermediates in their assembly, are cytotoxic to pancreatic beta-cells and contribute to the loss of beta-cell mass associated with type 2 diabetes. The factors that trigger islet amyloid deposition in vivo are not well understood, but peptide membrane interactions have been postulated to play an important role in islet amyloid formation. To better understand the role of membrane interactions in amyloid formation, two-dimensional infrared (2D IR) spectroscopy was used to compare the kinetics of amyloid formation for human IAPP both in the presence and in the absence of negatively charged lipid vesicles. Comparison of spectral features and kinetic traces from the two sets of experiments provides evidence for the formation of an ordered intermediate during the membrane-mediated assembly of IAPP amyloid. A characteristic transient spectral feature is detected during amyloid formation in the presence of vesicles that is not observed in the absence of vesicles. The spectral feature associated with the intermediate raises in intensity during the self-assembly process and subsequently decays in intensity in the classic manner of a kinetic intermediate. Studies with rat IAPP, a variant that is known to interact with membranes but does not form amyloid, confirm the presence of an intermediate. The analysis of 2D IR spectra in terms of specific structural features is discussed. The unique combination of time and secondary structure resolution of 2D IR spectroscopy has enabled the time-evolution of a hIAPP intermediate to be directly monitored for the first time. The data presented here demonstrates the utility of 2D IR spectroscopy for studying membrane-catalyzed amyloid formation. AD - [Raleigh, Daniel P.] SUNY Stony Brook, Grad Program Biochem & Struct Biol, Grad Program Biophys, Stony Brook, NY 11794 USA. [Raleigh, Daniel P.] SUNY Stony Brook, Dept Chem, Stony Brook, NY 11794 USA. [Ling, Yun L.; Strasfeld, David B.; Shim, Sang-Hee; Zanni, Martin T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000263529500036 AU - Ling, Y. L. AU - Strasfeld, D. B. AU - Shim, S. H. AU - Raleigh, D. P. AU - Zanni, M. T. KW - Chemistry, Physical LB - ISI 2009 03 05 N1 - English Article SOLID-STATE NMR; 2D IR; POLYPEPTIDE; PEPTIDE; AMYLIN; FIBRILS; MECHANISM; DYNAMICS; VIBRATIONS; TOXICITY FEB 26 8 PY - 2009 SP - 2498-2505 ST - Two-dimensional Infrared Spectroscopy Provides Evidence of an Intermediate in the Membrane-catalyzed Assembly of Diabetic Amyloid T2 - Journal of Physical Chemistry B TI - Two-dimensional Infrared Spectroscopy Provides Evidence of an Intermediate in the Membrane-catalyzed Assembly of Diabetic Amyloid ID - 3766 ER - TY - JOUR AB - Islet amyloid polypeptide (IAPP, also known as amylin) is responsible for pancreatic amyloid deposits in type 2 diabetes. The deposits, as well as intermediates in their assembly, are cytotoxic to pancreatic beta-cells and contribute to the loss of beta-cell mass associated with type 2 diabetes. The factors that trigger islet amyloid deposition in vivo are not well understood, but peptide membrane interactions have been postulated to play an important role in islet amyloid formation. To better understand the role of membrane interactions in amyloid formation, two-dimensional infrared (2D IR) spectroscopy was used to compare the kinetics of amyloid formation for human IAPP both in the presence and in the absence of negatively charged lipid vesicles. Comparison of spectral features and kinetic traces from the two sets of experiments provides evidence for the formation of an ordered intermediate during the membrane-mediated assembly of IAPP amyloid. A characteristic transient spectral feature is detected during amyloid formation in the presence of vesicles that is not observed in the absence of vesicles. The spectral feature associated with the intermediate raises in intensity during the self-assembly process and subsequently decays in intensity in the classic manner of a kinetic intermediate. Studies with rat IAPP, a variant that is known to interact with membranes but does not form amyloid, confirm the presence of an intermediate. The analysis of 2D IR spectra in terms of specific structural features is discussed. The unique combination of time and secondary structure resolution of 2D IR spectroscopy has enabled the time-evolution of a hIAPP intermediate to be directly monitored for the first time. The data presented here demonstrates the utility of 2D IR spectroscopy for studying membrane-catalyzed amyloid formation. AN - ISI:000263529500036 AU - Ling, Y. L. AU - Strasfeld, D. B. AU - Shim, S. H. AU - Raleigh, D. P. AU - Zanni, M. T. DA - Feb DO - 10.1021/jp810261x LB - ISI 2009 03 05 (Library clean-up) IS - 8 N1 - Ling, Yun L. Strasfeld, David B. Shim, Sang-Hee Raleigh, Daniel P. Zanni, Martin T. PY - 2009 SN - 1520-6106 SP - 2498-2505 ST - Two-dimensional Infrared Spectroscopy Provides Evidence of an Intermediate in the Membrane-catalyzed Assembly of Diabetic Amyloid T2 - Journal of Physical Chemistry B TI - Two-dimensional Infrared Spectroscopy Provides Evidence of an Intermediate in the Membrane-catalyzed Assembly of Diabetic Amyloid UR - ://000263529500036 VL - 113 ID - 3773 ER - TY - JOUR AB - Homopolymerizations and block copolymerizations of vinyl acetate (VAc), vinyl pivalate (VPv), and vinyl benzoate (VBz) by reversible addition-fragmentation chain transfer (RAFT) polymerization have been studied. Polymerizations of VAc initiated with 2,2'-azobis(isobutyronitrile) (AIBN) at 60 degrees C using two different xanthate RAFT agents C2H5OC(=S)SR (R = -CH(CH3)CO2C2H5 (1) and -CH(CH3)-O2CC(CH3)(3) (2)) were examined to elucidate the dependence of the polydispersities of the resulting polymers on the RAFT agent leaving group R. RAFT agent 2, in which the leaving R-group mimics a growing vinyl ester polymer chain, consistently yields poly(vinyl acetates) having broader polydispersities than those synthesized using 1 (M-n = 3.6-14 kg/mol and M-w/M-n = 1.15-1.33). While VPv exhibits similar controlled polymerization behavior to VAc, RAFT homopolymerizations of VBz mediated by 1 indicate this electron deficient vinyl ester requires higher temperatures to effect controlled polymerizations to yield polymers having M-n = 4-14 kg/mol and M-w/M-n = 1.29-1.53. Chain extension reactions from xanthate-terminated vinyl ester homopolymers with VAc, VPv, and VBz proceed with variable efficiencies to furnish block copolymers that microphase separate in the melt state as determined by small-angle X-ray scattering. AD - [Lipscomb, Corinne E.; Mahanthappa, Mahesh K.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000268138500037 AU - Lipscomb, C. E. AU - Mahanthappa, M. K. DA - Jul KW - Living radical polymerization vinyl-acetate polymerization raft process ab-initio degenerative transfer diblock copolymers phase polylactide transition stability Polymer Science LB - ISI 2009 07 31 IS - 13 N1 - English Article University of Wisconsin-Madison ; National Science Foundation [DMR-0748503]; NSF-MRSEC ; NSF-NSLC ; University of Wisconsin [DM R-0520527, DM R-0425880] PY - 2009 SP - 4571-4579 ST - Poly(vinyl ester) Block Copolymers Synthesized by Reversible Addition-Fragmentation Chain Transfer Polymerizations T2 - Macromolecules TI - Poly(vinyl ester) Block Copolymers Synthesized by Reversible Addition-Fragmentation Chain Transfer Polymerizations VL - 42 ID - 3964 ER - TY - JOUR AB - Amorphous carbon thin films are easily deposited at room temperature, readily functionalized with alkene-containing molecules through a UV photochemical reaction, and provide a robust surface capable of supporting array fabrication. Relatively few attachment chemistries for the fabrication of small organic molecule and/or biomolecule arrays on carbon substrates have been described to date. Here, acyl chloride-terminated amorphous carbon substrates were fabricated, characterized, and used to attach alcohol-, thiol-, and amine-containing small molecules. Oligonucleotide arrays of thiol- and amine-modified oligonucleotides were also prepared on these substrates. The hybridization density, average fluorescence signal of hybridized features, and average background fluorescence of oligonucleotide arrays prepared on acyl chloride-modified substrates were compared to the same parameters for oligonucleotide arrays prepared on maleimide- and aldehyde-modified substrates. AD - [Lockett, Matthew R.; Carlisle, Justin C.; Le, Dinh V.; Smith, Lloyd M.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Smith, Lloyd M.] Univ Wisconsin, Genome Ctr Wisconsin, Madison, WI 53706 USA. AN - ISI:000265528600042 AU - Lockett, M. R. AU - Carlisle, J. C. AU - Le, D. V. AU - Smith, L. M. DA - May KW - Diversity-oriented synthesis photochemical functionalization alkanethiol monolayers films surface arrays fabrication gold microarray chemistry Chemistry, Physical LB - ISI 2009 05 14 IS - 9 N1 - English Article NIH [R01HG002298, 5T32GM08349]; NSF [CHE-0809095]; MPS/CHE ; BIO/MCB Divisions ; University of Wisconsin Industrial and Economic Development Research ; GWC Technologies PY - 2009 SP - 5120-5126 ST - Acyl Chloride-Modified Amorphous Carbon Substrates for the Attachment of Alcohol-, Thiol-, and Amine-Containing Molecules T2 - Langmuir TI - Acyl Chloride-Modified Amorphous Carbon Substrates for the Attachment of Alcohol-, Thiol-, and Amine-Containing Molecules VL - 25 ID - 3980 ER - TY - JOUR AB - Amorphous carbon thin films are an attractive material because they provide a chemically robust surface that has been utilized in biomolecule array, biosensor, and bioelectronic applications. These thin films are particularly versatile because they are deposited at room temperature, making them readily integrated with other materials and devices. Here we present an alternative means of functionalizing carbon substrates based on Grignard chemistry. First, the amorphous carbon substrates are halogenated with a solution-based, radical-initiated halogenation reaction using PX5 (X = Br or Cl). Next, the halogenated surfaces are modified via the formation of a carbon-carbon bond between the surface and the Grignard reagents employed. Alkyl-, perfluoroalkyl-, and poly(ethylene glycol)-Grignard reagents were chosen to show the utility of this reaction scheme in functionalizing carbon surfaces to withstand oxidation and provide a hydrophobic and/or biocompatible substrate. AD - [Lockett, Matthew R.; Smith, Lloyd M.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000264145000005 AU - Lockett, M. R. AU - Smith, L. M. DA - Mar KW - Photochemical functionalization diamond surfaces thin-films halogenation monolayers arrays fabrication attachment black xps Chemistry, Physical LB - ISI 2009 03 26 IS - 6 N1 - English Article 0743-7463 PY - 2009 SP - 3340-3343 ST - Attaching Molecules to Chlorinated and Brominated Amorphous Carbon Substrates via Grignard Reactions T2 - Langmuir TI - Attaching Molecules to Chlorinated and Brominated Amorphous Carbon Substrates via Grignard Reactions VL - 25 ID - 3888 ER - TY - JOUR AB - Carbon-on-metal substrates consist of a surface plasmon-conducting metal substrate with a thin amorphous carbon overlayer. Recently, oligonucleotide arrays were in situ synthesized on carbon-on-gold substrates, and DNA hybridization experiments were monitored with surface plasmon resonance (SPR) imaging. We describe here the thorough characterization of these substrates and arrays as they progress through the fabrication process. Two surface plasmon-conducting metals, gold and silver, were utilized in the carbon-on-metal substrate preparation and their SPR responses compared. Oligonucleotide arrays synthesized on the carbon-on-metal substrates were analyzed with fluorescence- and SPR-based measurements. The stability of the carbon-on-metal substrates when exposed to prolonged incubations and/or serial hybridizations was also determined. AD - [Lockett, Matthew R.; Smith, Lloyd M.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Smith, Lloyd M.] Univ Wisconsin, Genome Ctr Wisconsin, Madison, WI 53706 USA. AN - ISI:000268455600060 AU - Lockett, M. R. AU - Smith, L. M. DA - Aug KW - Surface-plasmon resonance amorphous-carbon oligonucleotide arrays thin-films microarray hybridization alkenes chemistry density diamond Chemistry, Analytical LB - ISI 2009 08 13 IS - 15 N1 - English Article NIH [R01HG002298, 5T32GM08349]; University of Wisconsin Department of Chemistry PY - 2009 SP - 6429-6437 ST - Fabrication and Characterization of DNA Arrays Prepared on Carbon-on-Metal Substrates T2 - Analytical Chemistry TI - Fabrication and Characterization of DNA Arrays Prepared on Carbon-on-Metal Substrates VL - 81 ID - 3998 ER - TY - JOUR AB - Bacterial single-stranded (ss) DNA-binding proteins (SSBs) facilitate DNA replication, recombination, and repair processes in part by recruiting diverse genome maintenance enzymes to ssDNA. This function utilizes the C-terminus of SSB (SSB-Ct) as a common binding site for SSB's protein partners. The SSB-Ct is a highly conserved, amphipathic sequence comprising acidic and hydrophobic elements, A crystal structure of Escherichia coli exonuclease I (ExoI) bound to a peptide comprising the E. coli SSB-Ct sequence shows that the C-terminal-most SSB-Ct Pile anchors the peptide to a binding pocket oil Exol and implicates electrostatic binding roles for the acidic SSB-Ct residues. Here, we use SSB-Ct peptide variants in competition experiments to examine the roles of individual SSB-Ct residues in binding Exol in solution. Altering the C-terminal-most Pro or Phe residues in the SSB-Ct strongly impairs SSB-Ct binding to Exol, confirming a major role for the hydrophobic SSB-Ct residues in binding ExoI Alteration of N-termial SSB-Ct residues leads to changes that reflect cumulative electrostatic binding roles for the Asp residues in SSB-Ct. The SSB-Ct peptides also abrogate SSB stimulation of Exol activity through a competitive inhibition mechanism, indicating that the peptides call disrupt ExoI/SSB/ssDNA tertiary complexes. Differences in the potency of the SSB-Ct peptide variants in the binding and nuclease inhibition studies indicate that the acidic SSB-Ct residues play a more prominent role in the context of the tertiary complex than in the minimal ExoI/SSB-Ct interaction. Together, these data identify roles for residues in the SSB-Ct that are important for SSB complex formation with its protein partners. AD - [Lu, Duo; Keck, James L.] Univ Wisconsin, Dept Biomol Chem, Sch Med & Publ Hlth, Madison, WI 53706 USA. [Windsor, Matthew A.; Gellman, Samuel H.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000268175600007 AU - Lu, D. AU - Windsor, M. A. AU - Gellman, S. H. AU - Keck, J. L. DA - Jul KW - Dna-binding-protein directed mismatch repair escherichia-coli exonuclease-i polymerase processivity replication gene deoxyribonucleases sensitivity Biochemistry & Molecular Biology LB - ISI 2009 07 31 IS - 29 N1 - English Article NIH [GM068061, GM56414] PY - 2009 SP - 6764-6771 ST - Peptide Inhibitors Identify Roles for SSB C-Terminal Residues in SSB/Exonuclease I Complex Formation T2 - Biochemistry TI - Peptide Inhibitors Identify Roles for SSB C-Terminal Residues in SSB/Exonuclease I Complex Formation VL - 48 ID - 3975 ER - TY - JOUR AB - A computational framework is presented for studying the mechanical response of macromolecules. The method combines a continuum mechanics (CM) model for the mechanical properties of the macromolecule with a continuum electrostatic (CE) treatment of solvation. The molecules are represented by their shape and key physicochemical characteristics such as the distribution of materials properties and charge. As a test case, we apply the model to the effect of added salt on the bending of DNA. With a simple representation of DNA, the CM/CE framework using a Debye-Huckel model leads to results that are in good agreement with both analytical theories and recent experiments, including a modified Odijk-Skolnick-Fixman theory that takes the finite length of DNA into consideration. Calculations using a more sophisticated CE model (Poisson-Boltzmann), however, suffer from convergence problems, highlighting the importance of balancing numerical accuracy in the CM and CE models when dealing with very large systems, particularly those with a high degree of symmetry. AD - [Chen, Xi] Columbia Univ, Sch Engn & Appl Sci, Nanomech Res Ctr, New York, NY 10027 USA. [Ma, Liang; Cui, Qiang] Univ Wisconsin, Grad Program Biophys, Madison, WI USA. [Yethiraj, Arun; Cui, Qiang] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Yethiraj, Arun; Cui, Qiang] Univ Wisconsin, Inst Theoret Chem, Madison, WI 53706 USA. AN - ISI:000266397700008 AU - Ma, L. AU - Yethiraj, A. AU - Chen, X. AU - Cui, Q. DA - May KW - Electrostatic persistence length mechanosensitive channels nucleic-acids muscle-contraction gating mechanisms large-conductance bent dna molecules continuum models Biophysics LB - ISI 2009 06 12 IS - 9 N1 - English Article National Institutes of Health [R01-GM071429]; Alfred P. Sloan Foundation PY - 2009 SP - 3543-3554 ST - A Computational Framework for Mechanical Response of Macromolecules: Application to the Salt Concentration Dependence of DNA Bendability T2 - Biophysical Journal TI - A Computational Framework for Mechanical Response of Macromolecules: Application to the Salt Concentration Dependence of DNA Bendability VL - 96 ID - 3930 ER - TY - JOUR AB - The tetrapeptide, FMRFamide, was first discovered in 1977 in the molluscan nervous system and was found to affect the contractile force of molluscan cardiac muscle and other muscles [1]. Since then, numerous FMRFamide-related peptides (FaRPs) have been reported in both invertebrate and vertebrate species [2-9]. We have previously reported the detection and identification of numerous FaRPs in Cancer borealis pericardial organs (POs), one of the major neurosecretory structures in the crustaceans [2,3]. Here, we have developed two immunoaffinity-based methods, immunoprecipitation (IP) and immunodot blot screening assay, for the enrichment of FaRPs in C. borealis POs. A combined mass spectrometry (MS)-based approach involving both matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS) and nanoscale liquid chromatography Coupled to electrospray ionization quadrupole time-of-flight tandem mass spectrometry (nanoLC-ESI-QTOF MS/MS) is used for a more comprehensive characterization of the FaRP family by utilizing high mass accuracy measurement and efficient peptide sequencing. Overall, 17 FMRFamide-related pepticles were identified using these two complementary immuno-based approaches. Among them, three novel pepticles were reported for the first time in this study. (C) 2009 Elsevier Inc. All rights reserved. AD - [Li, Lingjun] Univ Wisconsin, Sch Pharm, Madison, WI 53705 USA. Univ Wisconsin, Dept Chem, Madison, WI 53705 USA. AN - ISI:000271552400028 AU - Ma, Mingming AU - Sturm, Robert M. AU - Kutz-Naber, Kimberly K. AU - Fu, Qiang AU - Li, Lingjun DA - Dec KW - FMRFamide-related peptide Neuropeptides Immuno-dot blot screening assay Immunoprecipitation MALDI-FTMS ESI-QTOF Caenorhabditis-elegans cardioactive peptides smooth-muscle gene families ascaris-suum neuropeptide rfamide helix Biochemistry & Molecular Biology Biophysics LB - ISI 2009 11 19 IS - 2 N1 - English Article School of Pharmacy and Wisconsin Alumni Research Foundation at the University of Wisconsin-Madison ; National Science Foundation CAREER [CHE-0449991]; National Institutes of Health [1RO1DK071801]; NIH [NIH T90 DK070079] PY - 2009 SP - 325-330 ST - Immunoaffinity-based mass spectrometric characterization of the FMRFamide-related peptide family in the pericardial organ of Cancer borealis T2 - Biochemical and Biophysical Research Communications TI - Immunoaffinity-based mass spectrometric characterization of the FMRFamide-related peptide family in the pericardial organ of Cancer borealis VL - 390 ID - 4087 ER - TY - JOUR AB - Carcinus maenas, commonly known as the European green crab, is one of the best-known and most successful marine invasive species. While a variety of natural and anthropogenic mechanisms are responsible for the geographic spread of this crab, its ability to adapt physiologically to a broad range of salinities, temperatures and other environmental factors has enabled its successful establishment in new habitats. To extend our understanding of hormonal control in C. maenas, including factors that allow for its extreme adaptability, we have undertaken a mass spectral/functional genomics investigation of the neuropeptides used by this organism. Via a strategy combining MALDI-based high resolution mass profiling, biochemical derivatization, and nanoscale separation coupled to tandem mass spectrometric sequencing, 122 peptide paracrines/hormones were identified from the C. maenas central nervous system and neuroendocrine organs. These peptides include 31 previously described Carcinus neuropeptides (e.g. NSELINSILGLPKVMNDAamide [beta-pigment dispersing hormone] and PFCNAFTGCamide [crustacean cardioactive peptide]), 49 peptides only described in species other than the green crab (e.g. pQTFQYSRGWTNamide [Arg(7)-corazonin]), and 42 new peptides de novo sequenced here for the first time (e.g. the pyrokinins TSFAFSPRLamide and DTGFAFSPRLamide). Of particular note are large collections of FMRFamide-like peptides (25, including nine new isoforms sequenced de novo) and A-type allatostatin peptides (25, including 10 new sequences reported here for the first time) in this study. Also of interest is the identification of two SIFamide isoforms, GYRKPPFNGSIFamide and VYRKPPFNGSIFamide, the latter peptide known previously only from members of the astacidean genus Homarus. Using transcriptome analyses, 15 additional peptides were characterized, including an isoform of bursicon beta and a neuroparsin-like peptide. Collectively, the data presented in this study not only greatly expand the number of identified C. maenas neuropeptides, but also provide a framework for future investigations of the physiological roles played by these molecules in this highly adaptable species. (C) 2009 Elsevier Inc. All rights reserved. AD - [Ma, Mingming; Li, Lingjun] Univ Wisconsin, Sch Pharm, Madison, WI 53705 USA. [Bors, Eleanor K.; Dickinson, Evelyn S.; Kwiatkowski, Molly A.; Sousa, Gregory L.; Smith, Christine M.; Towle, David W.; Christie, Andrew E.] Mt Desert Isl Biol Lab, Ctr Marine Funct Genom, Salsbury Cove, ME 04672 USA. [Henry, Raymond P.] Auburn Univ, Dept Biol Sci, Auburn, AL 36849 USA. [Li, Lingjun] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000265348500004 AU - Ma, M. M. AU - Bors, E. K. AU - Dickinson, E. S. AU - Kwiatkowski, M. A. AU - Sousa, G. L. AU - Henry, R. P. AU - Smith, C. M. AU - Towle, D. W. AU - Christie, A. E. AU - Li, L. J. DA - May KW - Carcinus maenas European green crab Matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS) Electrospray ionization quadrupole time-of-flight tandem mass spectrometry (ESI-Q-TOF MS/MS) Expressed sequence tag (EST) tblastn blastp Transcriptomics Neuropeptide Neurohormone Peptide sequencing Supraoesophageal ganglion Brain Thoracic ganglia Sinus gland (SG) Pericardial organ (PO) Pigment-concentrating hormone lobster homarus-americanus expressed sequence tags shore crab pericardial organs maldi-ftms allatostatin superfamily cardioactive peptide cancer-borealis nervous-system Endocrinology & Metabolism LB - ISI 2009 05 14 IS - 3 N1 - English Article University of Wisconsin School of Pharmacy ; Wisconsin Alumni Research Foundation ; National Science Foundation [CHE-0449991, NSF DBI-0453391, IBN 02-30005, EPS 04-47675]; National Institutes of Health [1R01DK071801]; Alfred P. Sloan Foundation ; National Center for Research Resources [NIH P20 RR-016463]; National Institute of Environmental Health Sciences [NIEHS R25 ES016254]; MDIBL High School Fellows Research Program ; Salisbury Cove Research Fund provided through the Thomas H. Maren Foundation ; MDIBL PY - 2009 SP - 320-334 ST - Characterization of the Carcinus maenas neuropeptidome by mass spectrometry and functional genomics T2 - General and Comparative Endocrinology TI - Characterization of the Carcinus maenas neuropeptidome by mass spectrometry and functional genomics VL - 161 ID - 3985 ER - TY - JOUR AB - The crustacean hyperglycemic hormone (CHH) is a 72-amino acid residue polypeptide with multiple physiological effects. The X-organ/sinus gland is the primary source for CHH and its family members. However, the amino acid sequence of CHH in Cancer borealis, a premier model system for neuromodulation, has not been characterized. In this study, a novel hybrid strategy combining "bottom-up" and "top-down" methodologies enabled direct sequencing of CHH peptide in the sinus gland of C. borealis. Multiple mass spectrometry (MS)-based techniques were employed to characterize the CHH peptide, including direct tissue analysis by MALDI-FT-ICR-MS, de novo sequencing of tryptic digested CHH by nano-LC/ESI-Q-TOF MS and intact CHH analysis by LC/FT-ICR-MS. In-trap cleaning removed the extensive matrix adducts of CHH in the direct tissue analysis by MALDI-FT-ICR-MS. Fragmentation efficiency of the intact CHH was drastically improved after the reduction-alkylation of the disulfide bonds. The sequence coverage was further enhanced by employing multiple complementary fragmentation techniques. Overall, this example is the largest neuropeptide de novo sequenced in C. borealis by mass spectrometric methods. AD - [Ma, Mingming; Li, Lingjun] Univ Wisconsin, Sch Pharm, Madison, WI 53705 USA. 53706 USA. Biochem, Tallahassee, FL 32306 USA. Madison, WI 53706 USA. Program, Natl High Magnet Field Lab, Tallahassee, FL 32310 USA. AN - ISI:000262113400034 AU - Ma, M. M. AU - Chen, R. B. AU - Ge, Y. AU - He, H. AU - Marshall, A. G. AU - Li, L. J. DA - Jan KW - Ion-cyclotron resonance electron-capture dissociation amino-acid-sequence infrared multiphoton dissociation crab pachygrapsus-marmoratus crayfish procambarus-clarkii lobster homarus-americanus precursor-related peptide inhibiting hormone decapod crustaceans Chemistry, Analytical LB - ISI 2009 01 22 IS - 1 N1 - English Article 0003-2700 PY - 2009 SP - 240-247 ST - Combining Bottom-Up and Top-Down Mass Spectrometric Strategies for De Novo Sequencing of the Crustacean Hyperglycemic Hormone from Cancer borealis T2 - Analytical Chemistry TI - Combining Bottom-Up and Top-Down Mass Spectrometric Strategies for De Novo Sequencing of the Crustacean Hyperglycemic Hormone from Cancer borealis VL - 81 ID - 3735 ER - TY - JOUR AB - The crustacean stomatogastric ganglion (STG) is modulated by numerous neuropeptides that are released locally in the neuropil or that reach the STG as neurohormones. Using 1,5-diaminonaphthalene (DAN) as a reductive screening matrix for matrix-assisted laser desorption/ionization (MALDI) mass spectrometric profiling of disulfide bond-containing C-type allatostatin peptides followed by electrospray ionization quadrupole time-of-flight (ESI-Q-TOF) tandem mass spectrometric (MS/MS) analysis, we identified and sequenced a novel C-type allatostatin peptide (CbAST-C1), pQIRYHQCYFN-PISCF-COOH, present in the pericardial organs of the crab, Cancer borealis. Another C-type allatostatin (CbAST-C2), SYWKQCAFNAVSCFamide, was discovered using the expressed sequence tag (EST) database search strategy in both C. borealis and the lobster, Homarus americanus, and further confirmed with de novo sequencing using ESI-Q-TOF tandem MS. Electrophysiological experiments demonstrated that both CbAST-C1 and CbAST-C2 inhibited the frequency of the pyloric rhythm of the STG, in a state-dependent manner. At 10(-6) M, both peptides were only modestly effective when initial frequencies of the pyloric rhythm were >0.8 Hz, but almost completely suppressed the pyloric rhythm when applied to preparations with starting frequencies <0.7 Hz. Surprisingly, these state-dependent actions are similar to those of the structurally unrelated allatostatin A and allatostatin B families of peptides. (C) 2009 Elsevier Inc. All rights reserved. AD - [Ma, Mingming; Jia, Chenxi; Li, Lingjun] Univ Wisconsin, Sch Pharm, Madison, WI 53705 USA. [Ma, Mingming; Jia, Chenxi; Li, Lingjun] Univ Wisconsin, Dept Chem, Madison, WI 53705 USA. [Szabo, Theresa M.; Marder, Eve] Brandeis Univ, Volen Ctr, Waltham AN - ISI:000269402500010 AU - Ma, M. M. AU - Szabo, T. M. AU - Jia, C. X. AU - Marder, E. AU - Li, L. J. DA - Sep KW - Allatostatin Crustaceans Neuromodulation Stomatogastric nervous system Neuropeptides Peptide sequencing Stomatogastric nervous-system juvenile-hormone biosynthesis lobster homarus-americanus central pattern generators cancer-borealis manduca-sexta drosophila-melanogaster molecular characterization genomic organization procambarus-clarkii Biochemistry & Molecular Biology Pharmacology & Pharmacy LB - ISI 2009 09 10 IS - 9 N1 - English Article National Institute of Neurological Disorders and Stroke [NS 17813]; National Institute of Diabetes and Digestive and Kidney Diseases [DK 071801]; National Science Foundation [CHE-0449991] PY - 2009 SP - 1660-1668 ST - Mass spectrometric characterization and physiological actions of novel crustacean C-type allatostatins T2 - Peptides TI - Mass spectrometric characterization and physiological actions of novel crustacean C-type allatostatins VL - 30 ID - 4010 ER - TY - JOUR AB - Infrared multiphoton dissociation (IRMPD) was implemented in a novel dual pressure linear ion trap for rapid top-down proteomics. The high pressure cell provided improved trapping and isolation efficiencies while the isotopic profiles of 10+ charged ions could be resolved by mass analysis in the low pressure cell that enabled effective top down protein identification. Striking differences between IRMPD in the low pressure cell and CID in the high pressure cell were observed for proteins ranging from 8.6 to 29 kDa. Because of secondary dissociation, IRMPD yielded product ions in significantly lower charge states as compared to CID, thus facilitating more accurate mass identification and streamlining product ion assignment. This outcome was especially useful for database searching of larger proteins (similar to 29 kDa) as IRMPD substantially improved protein identification and scoring confidence. Also, IRMPD showed an increased selectivity toward backbone cleavages N-terminal to proline and C-terminal to acidic residues (especially for the lowest charge states), which could be useful for a priori spectral predictions and enhanced database searching for protein identification. AD - [Madsen, James A.; Gardner, Myles W.; Smith, Suncerae I.; Brodbelt, Jennifer S.] Univ Texas Austin, Dept Chem & Biochem, Austin, TX 78712 USA. [Ledvina, Aaron R.; Coon, Joshua J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Coon, Joshua J.] Univ Wisconsin, Dept Biomol Chem, Madison, WI 53706 USA. [Schwartz, Jae C.; Stafford, George C., Jr.] Thermo Fisher Sci, San Jose, CA 95134 USA. AN - ISI:000276191900009 AU - Madsen, James A. AU - Gardner, Myles W. AU - Smith, Suncerae I. AU - Ledvina, Aaron R. AU - Coon, Joshua J. AU - Schwartz, Jae C. AU - Stafford, George C., Jr. AU - Brodbelt, Jennifer S. DA - Nov KW - Tandem mass-spectrometry collision-induced dissociation electron-capture dissociation multiply-charged ions esi-fticr-ms gas-phase ion/ion reactions activated dissociation whole proteins identification Chemistry, Analytical LB - ISI 2010 04 15 IS - 21 N1 - English Article NSF [CHE-0718320]; Welch Foundation [F1155] PY - 2009 SP - 8677-8686 ST - Top-Down Protein Fragmentation by Infrared Multiphoton Dissociation in a Dual Pressure Linear Ion Trap T2 - Analytical Chemistry TI - Top-Down Protein Fragmentation by Infrared Multiphoton Dissociation in a Dual Pressure Linear Ion Trap VL - 81 ID - 4225 ER - TY - JOUR AB - RNA accessible sites are the regions in an RNA molecule that are available for hybridization with cDNA or RNA molecules. The identification of these accessible sites is a critical first step in identifying antisense-mediated gene suppression sites, as well as in a variety of other RNA-based analysis methods. Here, we present a rapid, hybridization-based, label-free method of identifying RNA accessible sites with surface plasmon resonance imaging (SPRi) on in situ synthesized oligonucleotide arrays prepared on carbon-on-metal substrates. The accessible sites of three pre-miRNAs, miRNA precursors of similar to 75 nt in length, were determined by hybridizing the RNA molecules to RNA-specific tiling arrays. An array composed of all possible 6mer oligonucleotide sequences was also utilized in this work, offering a universal platform capable of studying RNA molecules in a high throughput manner. AD - [Mandir, Joshua B.; Lockett, Matthew R.; Phillips, Margaret F.; Smith, Lloyd M.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Allawi, Hatim T.; Lyamichev, Victor I.] Hologic Inc, Madison, WI 53719 USA. [Smith, Lloyd M.] Univ Wisconsin, Genome Ctr Wisconsin, Madison, WI 53706 USA. AN - ISI:000276191900043 AU - Mandir, Joshua B. AU - Lockett, Matthew R. AU - Phillips, Margaret F. AU - Allawi, Hatim T. AU - Lyamichev, Victor I. AU - Smith, Lloyd M. DA - Nov KW - Secondary structure oligonucleotide arrays chemical-modification imaging measurements prediction microarrays fabrication binding dependence protein Chemistry, Analytical LB - ISI 2010 04 15 IS - 21 N1 - English Article NIH [R01HG002298, R01HG003275]; NIH NHGRI [5T32HG002760]; University of Wisconsin ; GWC Technologies, Inc. PY - 2009 SP - 8949-8956 ST - Rapid Determination of RNA Accessible Sites by Surface Plasmon Resonance Detection of Hybridization to DNA Arrays T2 - Analytical Chemistry TI - Rapid Determination of RNA Accessible Sites by Surface Plasmon Resonance Detection of Hybridization to DNA Arrays VL - 81 ID - 4226 ER - TY - JOUR AB - The pH-controlled M2 protein from influenza A is a critical component of the virus and serves as a target for the aminoadamantane antiflu agents that block its H+ channel activity. To better understand its H+ gating mechanism, we investigated M2 in lipid bilayers with a new combination of IR spectroscopies and theory. Linear Fourier transform infrared (FTIR) spectroscopy was used to measure the precise orientation of the backbone carbonyl groups, and 2D infrared (IR) spectroscopy was used to identify channel-lining residues. At low pH (open state), our results match previously published solid-state NMR and X-ray structures remarkably well. However, at neutral pH when the channel is closed, our measurements indicate that a large conformational change occurs that is consistent with the transmembrane alpha-helices rotating by one amino acid register-a structural rearrangement not previously observed. The combination of simulations and isotope-labeled FTIR and 2D IR spectroscopies provides a noninvasive means of interrogating the structures of membrane proteins in general and ion channels in particular. AD - [Mukherjee, Prabuddha; Lin, Yu-Shan; Skinner, James L.; Zanni, Martin T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Manor, Joshua; Leonov, Hadas; Arkin, Isaiah T.] Hebrew Univ Jerusalem, Alexander Silberman Inst Life Sci, Dept Biol Chem, IL-91904 Jerusalem, Israel. AN - ISI:000263384800012 AU - Manor, J. AU - Mukherjee, P. AU - Lin, Y. S. AU - Leonov, H. AU - Skinner, J. L. AU - Zanni, M. T. AU - Arkin, I. T. KW - Biochemistry & Molecular Biology Biophysics Cell Biology LB - ISI 2009 03 05 N1 - English Article TRANSMEMBRANE DOMAIN; ION-CHANNEL; PROTON CHANNEL; MECHANOSENSITIVE CHANNEL; ACETYLCHOLINE-RECEPTOR; INFRARED-SPECTROSCOPY; SECONDARY STRUCTURE; ECHO SPECTROSCOPY; MEMBRANE-PROTEIN; LIPID-BILAYERS FEB 13 2 PY - 2009 SP - 247-254 ST - Gating Mechanism of the Influenza A M2 Channel Revealed by 1D and 2D IR Spectroscopies T2 - Structure TI - Gating Mechanism of the Influenza A M2 Channel Revealed by 1D and 2D IR Spectroscopies ID - 3762 ER - TY - JOUR AB - The pH-controlled M2 protein from influenza A is a critical component of the virus and serves as a target for the aminoadamantane antiflu agents that block its H+ channel activity. To better understand its H+ gating mechanism, we investigated M2 in lipid bilayers with a new combination of IR spectroscopies and theory. Linear Fourier transform infrared (FTIR) spectroscopy was used to measure the precise orientation of the backbone carbonyl groups, and 2D infrared (IR) spectroscopy was used to identify channel-lining residues. At low pH (open state), our results match previously published solid-state NMR and X-ray structures remarkably well. However, at neutral pH when the channel is closed, our measurements indicate that a large conformational change occurs that is consistent with the transmembrane alpha-helices rotating by one amino acid register-a structural rearrangement not previously observed. The combination of simulations and isotope-labeled FTIR and 2D IR spectroscopies provides a noninvasive means of interrogating the structures of membrane proteins in general and ion channels in particular. AN - ISI:000263384800012 AU - Manor, J. AU - Mukherjee, P. AU - Lin, Y. S. AU - Leonov, H. AU - Skinner, J. L. AU - Zanni, M. T. AU - Arkin, I. T. DA - Feb DO - 10.1016/j.str.2008.12.015 LB - ISI 2009 03 05 (Library clean-up) IS - 2 N1 - Manor, Joshua Mukherjee, Prabuddha Lin, Yu-Shan Leonov, Hadas Skinner, James L. Zanni, Martin T. Arkin, Isaiah T. PY - 2009 SN - 0969-2126 SP - 247-254 ST - Gating Mechanism of the Influenza A M2 Channel Revealed by 1D and 2D IR Spectroscopies T2 - Structure TI - Gating Mechanism of the Influenza A M2 Channel Revealed by 1D and 2D IR Spectroscopies UR - ://000263384800012 VL - 17 ID - 3769 ER - TY - JOUR AB - The successful growth of suspended carbon nanotubes is normally based on purely empirical results. Here we demonstrate the ability to predict the successful suspension of nanotubes across a range of trench widths by combining experimental growth data with a theoretical description of nanotube mechanics at the growth temperature. We show that rare thermal oscillations much larger than the rms amplitude combined with the large nanotube-substrate adhesion energy together are responsible for unsuccessful nanotube suspensions. We derive an upper limit on the number of deleterious nanotube-substrate interactions that can be tolerated before successful growth becomes impossible, and we are able to accurately explain literature reports of suspended nanotube growth. The methodology developed here should enable improved growth yields of suspended nanotubes, and it provides a framework in which to analyze the role of nanotube-substrate interactions during nanotube growth by chemical vapor deposition. AD - [Marcus, Matthew S.; Baker, Sarah E.; Hamers, Robert J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Marcus, Matthew S.; Simmons, Jason M.; Eriksson, Mark A.] Univ Wisconsin, Dept Phys, Madison, WI 53706 USA. AN - ISI:000266157100014 AU - Marcus, M. S. AU - Simmons, J. M. AU - Baker, S. E. AU - Hamers, R. J. AU - Eriksson, M. A. DA - May KW - Youngs modulus directed growth spectroscopy stiffness networks forces Chemistry, Multidisciplinary Nanoscience & Nanotechnology Materials Science, Multidisciplinary LB - ISI 2009 06 05 IS - 5 N1 - English Article NSF CAREER program [DMR-0094063]; NSF MRSEC program [DMR-0520527]; NSF NSEC [DMR-0425880] PY - 2009 SP - 1806-1811 ST - Predicting the Results of Chemical Vapor Deposition Growth of Suspended Carbon Nanotubes T2 - Nano Letters TI - Predicting the Results of Chemical Vapor Deposition Growth of Suspended Carbon Nanotubes VL - 9 ID - 3924 ER - TY - JOUR AB - Nuclear receptors E75, which regulates development in Drosophila melanogaster, and Rev-erb beta, which regulates circadian rhythm in humans, bind heme within their ligand binding, domains (LBD). The heme-bound ligand binding domains of E75 and Rev-erb beta Were studied using electronic absorption, MCD, resonance Raman, and EPR spectroscopies. Both proteins undergo redox-dependent ligand switching and CO- and NO-induced ligand displacement. In the Fe(I 11) oxidation state, the nuclear receptor hemes are low spin and 6-coordinate with cysteine(thiolate) as one of the two axial heme ligands. The sixth ligand is a neutral donor, presumably histidine. When the heme is reduced to the Fe(l 1) oxidation state, the cysteine(thiolate) is replaced by a different neutral donor ligand, whose identity is not known, CO binds to the Fe(II) heme in both E75(LBD) and Rev-erb beta(LBD) opposite a sixth neutral ligand, plausibly the same histidine that served as the sixth ligand in the Fe(III) state. NO binds to the heme of both proteins; however, the NO-heme is 5-coordinate in E75 and 6-coordinate in Rev-erb beta. These nuclear receptors exhibit coordination characteristics that are similar to other known redox and Gas sensors, suggesting that E75 and Rev-erb beta may function in heme-, redox-, or gas-regulated control of cellular function. AD - [Marvin, Katherine A.; Lee, Andrea J.; Burstyn, Judith N.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Reinking, Jeffrey L.; Pardee, Keith; Krause, Henry M.] Univ Toronto, Banting & Best Dept Mol Genet, Toronto, ON, Canada. [Reinking, Jeffrey L.; Pardee, Keith; Krause, Henry M.] Univ Toronto, Terrence Donnelly Ctr Cellular & Biomol Res, Toronto, ON, Canada. [Reinking, Jeffrey L.] SUNY Albany, Dept Biol, New Paltz, NY 12561 USA. AN - ISI:000268175600034 AU - Marvin, K. A. AU - Reinking, J. L. AU - Lee, A. J. AU - Pardee, K. AU - Krause, H. M. AU - Burstyn, J. N. DA - Jul KW - Magnetic-circular-dichroism resonance raman-spectra electron-paramagnetic-resonance nitric-oxide escherichia-coli carbon-monoxide circadian transcription hormone-receptors guanylate-cyclase alpha Biochemistry & Molecular Biology LB - ISI 2009 07 31 IS - 29 N1 - English Article NIH [HL-66147]; NCIC [010200] PY - 2009 SP - 7056-7071 ST - Nuclear Receptors Homo sapiens Rev-erb beta and Drosophila melanogaster E75 Are Thiolate-Ligated Heme Proteins Which Undergo Redox-Mediated Ligand Switching and Bind CO and NO T2 - Biochemistry TI - Nuclear Receptors Homo sapiens Rev-erb beta and Drosophila melanogaster E75 Are Thiolate-Ligated Heme Proteins Which Undergo Redox-Mediated Ligand Switching and Bind CO and NO VL - 48 ID - 3976 ER - TY - JOUR AB - A simple numerical model is proposed to compute the energy and momentum accommodation of molecules scattered from highly corrugated, disordered surfaces. The model is an extension of the "washboard model", which assumes that the component of the molecule's momentum parallel to the local surface tangent is conserved on impact and the normal component is altered by a hard, elastic collision with a moving surface "cube" with an adjustable effective mass. The surface is represented by Gaussian hills and valleys of random location and height. In contrast to the washboard model, the current model is fully three-dimensional and includes in-plane and out-of-plane scattering as well as trapping-desorption. In addition, it can be applied to highly corrugated surfaces and does not invoke a regular, periodic topography. This increased realism comes at the expense of an analytical solution; numerical simulations must be performed. We develop a very efficient procedure for carrying out the simulations. We test the model by comparing detailed angular and velocity scattering distributions for Xe scattering from a Pt(111) surface with those obtained by realistic molecular dynamics simulations of the same system. We then apply the model to the accommodation of H-2, N-2, CO, and CO2 on surface materials employed on vehicles in low Earth orbit. The model is capable of accurately reproducing the results of experimental measurements on these highly corrugated surfaces. AN - ISI:000263134700048 AU - Mateljevic, N. AU - Kerwin, J. AU - Roy, S. AU - Schmidt, J. R. AU - Tully, J. C. DA - Feb DO - 10.1021/jp8077634 LB - ISI 2009 02 20 IS - 6 N1 - Mateljevic, Natasa Kerwin, Jay Roy, Sharani Schmidt, J. R. Tully, John C. PY - 2009 SN - 1932-7447 SP - 2360-2367 ST - Accommodation of Gases at Rough Surfaces T2 - Journal of Physical Chemistry C TI - Accommodation of Gases at Rough Surfaces UR - ://000263134700048 VL - 113 ID - 3786 ER - TY - JOUR AB - Extending current coherent multidimensional spectroscopy (CMDS) methods to higher order multiwave mixing requires excitation intensities where dynamic Stark effects become important. This paper examines the dynamic Stark effects that occur in mixed frequency/time domain CMDS methods at high excitation intensities in a model system with an isolated vibrational state. The phase-matching restrictions in CMDS define the excitation beams that interact by nonlinear mixing while the dynamic Stark effects create vibrational ladders of increasingly more energetic overtone and combination band states. The excited guantum states form coherences that reemit the output beams. This paper uses the phase-matching conditions (k) over right arrow (out) = (k) over right arrow (1) - (k) over right arrow (2) + (k) over right arrow (2)' and (k) over right arrow (out) = -(k) over right arrow (1) + (k) over right arrow (2) + (k) over right arrow (2)', where the subscripts denote the excitation frequencies of each excitation pulse and the output pulse. The phase-matching condition constrains each pulse to have an odd number of interactions so the overall mixing process that creates the output coherence must also involve an odd number of interactions. Tuning the excitation frequencies and spectrally resolving the output intensity creates three-dimensional spectra that resolve the individual overtone states. Changing the excitation pulse time delays measures the dynamics of the coherences and populations created by the multiple excitations. The multidimensional spectra probe the highly excited states of a molecular potential energy surface. This paper uses tungsten hexacarbonyl (W(CO)(6)) as a model for observing how dynamic Stark effects change the multidimensional spectra of a simple system. The simplicity of the W(CO)(6) system provides the experimental data required to develop the nonperturbative theoretical methods that will be necessary to model this new approach to CMDS. AD - [Mathew, Nathan A.; Block, Stephen B.; Yurs, Lena A.; Kornau, Kathryn M.; Pakoulev, Andrei V.; Wright, John C.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000272038000016 AU - Mathew, Nathan A. AU - Block, Stephen B. AU - Yurs, Lena A. AU - Kornau, Kathryn M. AU - Pakoulev, Andrei V. AU - Wright, John C. DA - Dec KW - Vibrational echo experiments photon-echoes multidimensional nmr room-temperature dynamics liquids glass population anharmonicity excitation Chemistry, Physical Physics, Atomic, Molecular & Chemical LB - ISI 2009 11 26 IS - 48 N1 - English Article National Science Foundation [CHE-0650431] PY - 2009 SP - 13462-13469 ST - Multiply Enhanced Odd-Order Wave-Mixing Spectroscopy T2 - Journal of Physical Chemistry A TI - Multiply Enhanced Odd-Order Wave-Mixing Spectroscopy VL - 113 ID - 4090 ER - TY - JOUR AB - Mixed frequency/time domain, two color triply vibrationally enhanced (TRIVE) four wave mixing (FWM) spectroscopy is used to study the methyl and methylene modes in octane and dotriacontane. The experiments involve scanning different combinations of the two excitation frequencies, the monochromator frequency, and the two time delays between the three excitation pulses while the remaining variables are fixed. Two dimensional spectra of the methyl and methylene stretching region have weak, asymmetrical diagonal- and cross-peaks when the excitation pulses are temporally overlapped. As the time delays change, the spectra change as new peaks appear and their peak intensity and position change. Combined two-dimensional scans of the excitation frequency and time delay show the changes are caused by relaxation of the initially excited populations to other states that are coupled to the methyl and methylene stretching modes. Two dimensional time delay scans show that the coherence dephasing rates are very fast so fully coherent TRIVE FWM pathways involving multiple quantum coherences are not possible without shorter excitation pulses. Similar experiments involving the methyl and methylene bend and stretching modes identify cross-peaks between these modes and population transfer processes that create cross-peaks. The asymmetric methylene stretch/Fermi resonance band is observed to contain unresolved states that couple differently with the symmetric methylene stretching and scissor modes as well as with lower lying quantum states that are fed by population transfer. The TRIVE FWM data show that the multidimensional spectra are dominated by rapid population transfer within the methyl and methylene stretching modes and to lower quantum states that are coupled to the stretching modes. AD - [Mathew, Nathan A.; Rickard, Mark A.; Kornau, Kathryn M.; Pakoulev, Andrei V.; Block, Stephen B.; Yurs, Lena A.; Wright, John C.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000269655400005 AU - Mathew, N. A. AU - Rickard, M. A. AU - Kornau, K. M. AU - Pakoulev, A. V. AU - Block, S. B. AU - Yurs, L. A. AU - Wright, J. C. DA - Sep KW - Enhanced 4-wave-mixing spectroscopy 2-dimensional infrared-spectroscopy ch stretching modes energy redistribution algebraic description liquid methanol 1st overtone 2d ir relaxation molecules Chemistry, Physical Physics, Atomic, Molecular & Chemical LB - ISI 2009 09 17 IS - 36 N1 - English Article National Science Foundation [CHE-0650431] PY - 2009 SP - 9792-9803 ST - Coherent Multidimensional Vibrational Spectroscopy of Representative N-Alkanes T2 - Journal of Physical Chemistry A TI - Coherent Multidimensional Vibrational Spectroscopy of Representative N-Alkanes VL - 113 ID - 4019 ER - TY - JOUR AB - Multiple quantum coherences provide a powerful approach for studies of complex systems because increasing the number of quantum states in a quantum mechanical superposition state increases the selectivity of a spectroscopic measurement. We show that frequency domain multiple quantum coherence multidimensional spectroscopy can create these superposition states using different frequency excitation pulses. The superposition state is created using two excitation frequencies to excite the symmetric and asymmetric stretch modes in a rhodium dicarbonyl chelate and the dynamic Stark effect to climb the vibrational ladders involving different overtone and combination band states. A monochromator resolves the free induction decay of different coherences comprising the superposition state. The three spectral dimensions provide the selectivity required to observe 19 different spectral features associated with fully coherent nonlinear processes involving up to I I interactions with the excitation fields. The different features act as spectroscopic probes of the diagonal and off-diagonal parts of the molecular potential energy hypersurface. This approach can be considered as a coherent pump-probe spectroscopy where the pump is a series of excitation pulses that prepares a multiple quantum coherence and the probe is another series of pulses that creates the output coherence. AD - [Mathew, Nathan A.; Yurs, Lena A.; Block, Stephen B.; Pakoulev, Andrei V.; Kornau, Kathryn M.; Wright, John C.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000268796800001 AU - Mathew, N. A. AU - Yurs, L. A. AU - Block, S. B. AU - Pakoulev, A. V. AU - Kornau, K. M. AU - Wright, J. C. DA - Aug KW - 2d ir spectroscopy enhanced 4-wave-mixing spectroscopy excitation frequency dynamics analogs flames Chemistry, Physical Physics, Atomic, Molecular & Chemical LB - ISI 2009 08 20 IS - 33 N1 - English Letter PY - 2009 SP - 9261-9265 ST - Multiple Quantum Coherence Spectroscopy T2 - Journal of Physical Chemistry A TI - Multiple Quantum Coherence Spectroscopy VL - 113 ID - 4005 ER - TY - JOUR AB - Carbohydrate polymers are the most abundant organic substances on earth. Their degrees of polymerization range from tens to thousands of units, yet polymerases generate the relevant lengths without the aid of a template. To gain insight into template-independent length control, we investigated how the mycobacterial galactofuranosyl-transferase GlfT2 mediates formation of the galactan, a polymer of galactofuranose residues that is an integral part of the cell wall. We show that isolated recombinant GlfT2 can catalyze the synthesis of polymers with degrees of polymerization that are commensurate with values observed in mycobacteria, indicating that length control by GlfT2 is intrinsic. Investigations using synthetic substrates reveal that GlfT2 is processive. The data indicate that GlfT2 controls length by using a substrate tether, which is distal from the site of elongation. The strength of interaction of that tether with the polymerase influences the length of the resultant polymer. Thus, our data identify a mechanism for length control by a template-independent polymerase. AD - [May, John F.; Kiessling, Laura L.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. [Splain, Rebecca A.; Brotschi, Christine; Kiessling, Laura L.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000268178400009 AU - May, J. F. AU - Splain, R. A. AU - Brotschi, C. AU - Kiessling, L. L. DA - Jul KW - galactofuranose mycobacteria polymerase polysaccharide processivity Mycobacterial cell-wall escherichia-coli chain-length peptidoglycan glycosyltransferases spectrophotometric assay streptococcus-pneumoniae o-antigen biosynthesis cellulose lipopolysaccharide Multidisciplinary Sciences LB - ISI 2009 07 31 IS - 29 N1 - English Article National Institutes of Health [AI063596]; National Science Foundation [GM007215, S10 RR13790]; Swiss National Science Foundation [PBBE-108553]; National Institutes of Health, National Institute of Allergy and Infectious Diseases [N01 AI-75320] PY - 2009 SP - 11851-11856 ST - A tethering mechanism for length control in a processive carbohydrate polymerization T2 - Proceedings of the National Academy of Sciences of the United States of America TI - A tethering mechanism for length control in a processive carbohydrate polymerization VL - 106 ID - 3963 ER - TY - JOUR AB - Muoniated free radicals are formed by addition of muonium to unsaturated molecules. Successful detection by transverse-field muon spin rotation (mu SR) usually requires pure or highly concentrated samples and a muonium reaction rate in excess of 109 M(-1)s(-1) to ensure that the muon spin polarization is coherently transferred to the radical. For this reason muoniated radicals reported to date are all the primary radical products of Mu reaction. Thus, it was expected that Mu addition to a silylene would result in detection of a silyl radical. However, the muon hyperfine constant determined by experiment is much smaller than the value predicted by density functional calculations. instead, it is consistent with a disilanyl radical, the secondary radical formed by reaction of the initially formed silyl radical with a second silylene molecule. From an analysis of the signal amplitude it was deduced that the second-order rate constant for reaction of the muoniated silyl radical with the parent silylene is 5.7 x 10(-8) M(-1)s(-1). This work represents the first example of direct detection of a secondary radical product by transverse-field mu SR. (c) 2008 Elsevier B.V. All rights reserved. AD - [McCollum, Brett M.; Brodovitch, Jean-Claude; Percival, Paul W.] Simon Fraser Univ, TRIUMF, Burnaby, BC V5A 1S6, Canada. [McCollum, Brett M.; Brodovitch, Jean-Claude; Percival, Paul W.] Simon Fraser Univ, Dept Chem, Burnaby, BC V5A 1S6, Canada. [Clyburne, Jason A. C.] St Marys Univ, Dept Chem, Halifax, NS B3H 3C3, Canada. [West, Robert] Univ Wisconsin, Organosilicon Res Ctr, Madison, WI 53706 USA. AN - ISI:000265469800102 AU - McCollum, B. M. AU - Brodovitch, J. C. AU - Clyburne, J. A. C. AU - Percival, P. W. AU - West, R. DA - Apr KW - Muonium Radical Silylene Disilanyl Stable silylenes resonance Physics, Condensed Matter IS - 5-7 N1 - English Proceedings Paper 0921-4526 PY - 2009 SP - 940-942 ST - Detection of a secondary muoniated radical T2 - Physica B-Condensed Matter TI - Detection of a secondary muoniated radical VL - 404 ID - 3917 ER - TY - JOUR AB - Phosphorylation is universally used for controlling protein function, but knowledge of the phosphoproteome in vertebrate embryos has been limited. However, recent technical advances make it possible to define an organism's phosphoproteome at a more comprehensive level. Xenopus laevis offers established advantages for analyzing the regulation of protein function by phosphorylation. Functionally unbiased, comprehensive information about the Xenopus phosphoproteome would provide a powerful guide for future studies of phosphorylation in a developmental context. To this end, we performed a phosphoproteomic analysis of Xenopus oocytes, eggs, and embryos using recently developed mass spectrometry methods. We identified 1,441 phosphorylation sites present on 654 different Xenopus proteins, including hundreds of previously unknown phosphorylation sites. This approach identified several phosphorylation sites described in the literature and/or evolutionarily conserved in other organisms, validating the data's quality. These data will serve as a powerful resource for the exploration of phosphorylation and protein function within a developmental context. Developmental Dynamics 238: 1433-1443, 2009. (C) 2009 Wiley-Liss, Inc. AD - [McGivern, Jered V.; Coon, Joshua J.; Sheets, Michael D.] Univ Wisconsin, Dept Biomol Chem, Madison, WI 53706 USA. [Swaney, Danielle L.; Coon, Joshua J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000266678100018 AU - McGivern, J. V. AU - Swaney, D. L. AU - Coon, J. J. AU - Sheets, M. D. DA - Jun KW - phosphorylation Xenopus embryo proteomics mass spectrometry Electron-transfer dissociation tandem mass-spectrometry protein-sequence analysis dual-kinase mechanism ion/ion reactions beta-catenin cytoplasmic polyadenylation saccharomyces-cerevisiae phosphorylation analysis proteomics Anatomy & Morphology Developmental Biology LB - ISI 2009 06 19 IS - 6 N1 - English Article NIH PY - 2009 SP - 1433-1443 ST - Toward Defining the Phosphoproteome of Xenopus laevis Embryos T2 - Developmental Dynamics TI - Toward Defining the Phosphoproteome of Xenopus laevis Embryos VL - 238 ID - 3938 ER - TY - JOUR AD - [Mednikov, Evgueni G.; Dahl, Lawrence F.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000270520500007 AU - Mednikov, E. G. AU - Dahl, L. F. DA - Oct KW - Core pd-145(co)(x)(pet3)(30) Chemistry, Multidisciplinary Education, Scientific Disciplines LB - ISI 2009 10 23 IS - 10 N1 - English Editorial Material PY - 2009 SP - 1135-1135 ST - Palladium: It Forms Unique Nanosized Carbonyl Clusters T2 - Journal of Chemical Education TI - Palladium: It Forms Unique Nanosized Carbonyl Clusters VL - 86 ID - 4056 ER - TY - JOUR AB - Once released into the environment, engineered nanomaterials may be transformed by microbially mediated redox processes altering their toxicity and fate. Little information currently exists on engineered nanomaterial transformation under environmentally relevant conditions. Here, we report the development of an in vitro biomimetic assay for investigation of nanomaterial transformation under simulated oxidative environmental conditions. The assay is based on the extracellular hydroquinone-driven Fenton's reaction used by lignolytic fungi. We demonstrate the utility of the assay using CdSecore/ZnSshell quantum dots (QDs) functionalized with poly(ethylene glycol). GO transformation was assessed by UV-visible spectroscopy, inductively coupled plasma-optical emission spectroscopy, dynamic light scattering, transmission electron microscopy (TEM), and energy dispersive X-ray spectroscopy (EDX). ON were readily degraded under simulated oxidative environmental conditions: the ZnS shell eroded and cadmium was released from the CID core, TEM, electron diffraction analysis, and EDX of transformed QDs revealed formation of amorphous Se aggregates. The biomimetic hydroquinone-driven Fenton's reaction degraded QDs to a larger extent than did H2O2 and classical Fenton's reagent (H2O2 + Fe2+). This assay provides a new method to characterize transformations of nanoscale materials expected to occur under oxidative environmental conditions. AD - [Metz, Kevin M.; Pedersen, Joel A.] Univ Wisconsin, Environm Chem & Technol Program, Madison, WI 53706 USA. J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000263758600061 AU - Metz, K. M. AU - Mangham, A. N. AU - Bierman, M. J. AU - Jin, S. AU - Hamers, R. J. AU - Pedersen, J. A. DA - Mar J2 - N, S(1) KW - Basidiomycete gloeophyllum-trabeum semiconductor quantum dots brown-rot zinc-sulfide nanocrystals nanoparticles dissolution mechanism pathways reagent Engineering, Environmental Environmental Sciences LB - ISI 2009 03 13 IS - 5 N1 - English Article 0013-936X PY - 2009 SP - 1598-1604 ST - Engineered Nanomaterial Transformation under Oxidative Environmental Conditions: Development of an in vitro Biomimetic Assay T2 - Environmental Science & Technology TI - Engineered Nanomaterial Transformation under Oxidative Environmental Conditions: Development of an in vitro Biomimetic Assay VL - 43 ID - 3822 ER - TY - JOUR AB - We report an oxaziridine-mediated enantioselective aminohydroxylation of olefins catalyzed by a chiral copper(II) bis(oxazoline) complex. A variety of styrenic olefins undergo efficient aminohydroxylation with excellent regioselectivity and synthetically useful levels of enantioselectivity (up to 84% ee). The reaction can be conducted on multi-gram scale with as little as 2 mol % of the copper(II) catalyst. Hydrolysis of the resulting 1,3-oxazolines under acidic conditions produces N-sulfonyl amino alcohols that can be purified by recrystallization to afford very high levels of enantioselectivity. (C) 2009 Elsevier Ltd. All rights reserved. AD - [Michaelis, David J.; Williamson, Kevin S.; Yoon, Tehshik P.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000267506300021 AU - Michaelis, D. J. AU - Williamson, K. S. AU - Yoon, T. P. DA - Jun KW - Sharpless asymmetric aminohydroxylation chiral bis(oxazoline) vancomycin aglycon alkenes ligands aminoacetoxylation aminooxygenation rearrangement construction cyclization Chemistry, Organic LB - ISI 2009 07 17 IS - 26 N1 - English Article NIH [R01-GM084022, GM08505, S10-RR04981-01]; American Chemical Society ; NSF [CHE-9629688] PY - 2009 SP - 5118-5124 ST - Oxaziridine-mediated enantioselective aminohydroxylation of styrenes catalyzed by copper(II) bis(oxazoline) complexes T2 - Tetrahedron TI - Oxaziridine-mediated enantioselective aminohydroxylation of styrenes catalyzed by copper(II) bis(oxazoline) complexes VL - 65 ID - 3955 ER - TY - JOUR AB - We demonstrate amplitude, phase and polarization shaping of femtosecond mid-IR pulses using a germanium acousto-optical modulator by independently shaping the frequency-dependent amplitudes and phases of two orthogonally polarized pulses which are then collinearly overlapped using a wire-grid polarizer. We use a feedback loop to set and stabilize the relative phase of the orthogonal pulses. We have also used a wire-grid polarizer to implement polarization-based balanced heterodyne detection for improved signal-to-noise of 2D IR spectra collected in a pump-probe geometry. Applications include coherent control of molecular vibrations and improvements in multidimensional IR spectroscopy. (C) 2009 Optical Society of America AD - [Middleton, Chris T.; Strasfeld, David B.; Zanni, Martin T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000269232800008 AU - Middleton, C. T. AU - Strasfeld, D. B. AU - Zanni, M. T. DA - Aug KW - 2-dimensional infrared-spectroscopy islet amyloid polypeptide pulse-shaper 4-wave-mixing spectroscopy femtosecond pulses phase interferometer technology amplitude Optics LB - ISI 2009 09 10 IS - 17 N1 - English Article Packard Foundation ; National Institutes of Health [DK 79895] PY - 2009 SP - 14526-14533 ST - Polarization shaping in the mid-IR and polarization-based balanced heterodyne detection with application to 2D IR spectroscopy T2 - Optics Express TI - Polarization shaping in the mid-IR and polarization-based balanced heterodyne detection with application to 2D IR spectroscopy VL - 17 ID - 4011 ER - TY - JOUR AB - Helical beta-peptides have been shown to fold into well-defined structures. In aqueous solution, some beta-peptides self-assemble into nanoscale fibers, aggregates, and liquid crystalline phases. Molecular simulations, at an atomistic level, are used to examine, in a systematic manner, the interactions between distinct beta-peptide molecules. The relationship between side-chain chemistry (and position along the backbone) and, in particular, aggregation behaviors, is assessed by calculating the potential of mean force or dimerization free energy of two peptides in explicit water. The free energy profiles as a function of separation for helical, amphiphilic beta-peptides are consistent with experimental observations, and help explain the origins of aggregate or fiber formation in solution. Close examination of the energetic and entropic contributions to the free energy reveals that, depending on the position of certain side groups along the molecule, the tendency of two peptides to aggregate can be driven by entropy or by energy, respectively. In contrast to findings from previous works that employed a coarse representation of the solvent, it is shown that water-peptide interactions play key roles in the association behavior of beta-peptides. AD - [Miller, Clark A.; Abbott, Nicholas L.; de Pablo, Juan J.] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA. [Gellman, Samuel H.] Univ Wisconsin, Dept Chem, Madison, WI USA. AN - ISI:000266650400002 AU - Miller, C. A. AU - Gellman, S. H. AU - Abbott, N. L. AU - de Pablo, J. J. DA - Jun KW - Lyotropic liquid-crystals tempering monte-carlo molecular-dynamics secondary structure self-association aqueous-solution water simulations stability 14-helix Biophysics LB - ISI 2009 06 19 IS - 11 N1 - English Article National Science Foundation through the Nanoscale Science and Engineering Center PY - 2009 SP - 4349-4362 ST - Association of Helical beta-Peptides and their Aggregation Behavior from the Potential of Mean Force in Explicit Solvent T2 - Biophysical Journal TI - Association of Helical beta-Peptides and their Aggregation Behavior from the Potential of Mean Force in Explicit Solvent VL - 96 ID - 3939 ER - TY - JOUR AB - It has been previously proposed that nitric oxide (NO) is the only biologically relevant nitrogen oxide capable of activating the enzyme soluble guanylate cyclase (sGC). However, recent reports implicate HNO as another possible activator of sGC. Herein, we examine the affect of HNO donors on the activity of purified bovine lung sGC and find that, indeed, HNO is capable of activating this enzyme. Like NO, HNO activation appears to occur via interaction with the regulatory ferrous heme on sGC. Somewhat unexpectedly, HNO does not activate the ferric form of the enzyme. Finally, HNO-mediated cysteine thiol modification appears to also affect enzyme activity leading to inhibition. Thus, sGC activity can be regulated by HNO via interactions at both the regulatory heme and cysteine thiols. AD - [Miller, Thomas W.; Francoleon, Nestor E.] Univ Calif Los Angeles, Dept Chem & Biochem, Los Angeles, CA 90095 USA. [Cherney, Melisa M.; Lee, Andrea J.; Burstyn, Judith N.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Farmer, Patrick J.] Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA. [King, S. Bruce] Wake Forest Univ, Dept Chem, Winston Salem, NC 27109 USA. [Hobbs, Adrian J.] UCL, Dept Pharmacol, London WC1E 6BT, England. [Miranda, Katrina M.] Univ Arizona, Dept Chem, Tucson, AZ 85721 USA. [Fukuto, Jon M.] Sonoma State Univ, Dept Chem, Rohnert Pk, CA 94928 USA. AN - ISI:000268783700003 AU - Miller, T. W. AU - Cherney, M. M. AU - Lee, A. J. AU - Francoleon, N. E. AU - Farmer, P. J. AU - King, S. B. AU - Hobbs, A. J. AU - Miranda, K. M. AU - Burstyn, J. N. AU - Fukuto, J. M. DA - Aug KW - Nitric-oxide no ligand-binding properties smooth-muscle relaxation angelis salt bovine lung center-dot dioxygen complexes biological-systems protoporphyrin-ix aqueous-solution Biochemistry & Molecular Biology LB - ISI 2009 08 20 IS - 33 N1 - English Article PY - 2009 SP - 21788-21796 ST - The Effects of Nitroxyl (HNO) on Soluble Guanylate Cyclase Activity INTERACTIONS AT FERROUS HEME AND CYSTEINE THIOLS T2 - Journal of Biological Chemistry TI - The Effects of Nitroxyl (HNO) on Soluble Guanylate Cyclase Activity INTERACTIONS AT FERROUS HEME AND CYSTEINE THIOLS VL - 284 ID - 4006 ER - TY - JOUR AB - Proteome analysis has emerged as a powerful technology to decipher biological processes. One of the main goals is to discover biomarkers for diseases from tissues and body fluids. However, the complexity and wide dynamic range of protein expression present an enormous challenge to separation technologies and mass spectrometry (MS). In this review, we examine the limitations of proteomics, and aim towards the definition of the current key prerequisites. We focus on capillary electrophoresis coupled to mass spectrometry (CEMS), because this technique continues to show great promise. Me discuss CE-MS from an application point of view, and evaluate its merits and vices for biomarker discovery and clinical applications. Finally. we present several examples on the use of CE-MS to determine urinary biomarkers and implications for disease diagnosis, prognosis, and therapy evaluation. (C) 2008 Wiley Periodicals, Inc., Mass Spec Rev 28:703-724, 2009 AD - [Mischak, Harald] Mosaiques Diagnost & Therapeut AG, D-30625 Hannover, Germany. [Coon, Joshua J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Coon, Joshua J.] Univ Wisconsin, Dept Biochem, Madison, WI 53705 USA. [Novak, Jan] Univ Alabama, Dept Microbiol, Birmingham, AL 35294 USA. [Weissinger, Eva M.] Hannover Med Sch, Dept Hematol Hemostasis & Oncol, D-3000 Hannover, Germany. [Schanstra, Joost P.] INSERM, Dept Renal & Cardiac Remodelling, U858, I2MR, F-31432 Toulouse 4, France. [Schanstra, Joost P.] Univ Toulouse 3, Inst Med Mol Rangueil, F-31000 Toulouse, France. [Dominiczak, Anna F.] Univ Glasgow, BHF Glasgow Cardiovasc Res Ctr, Glasgow, Lanark, Scotland. AN - ISI:000268991700001 AU - Mischak, H. AU - Coon, J. J. AU - Novak, J. AU - Weissinger, E. M. AU - Schanstra, J. P. AU - Dominiczak, A. F. DA - Sep-Oct KW - capillary electrophoresis mass spectrometry biomarker urine clinical proteomics Assisted-laser-desorption/ionization ureteropelvic junction obstruction stem-cell transplantation urinary proteome analysis diabetic-nephropathy prostate-cancer iga nephropathy plasma proteome renal-diseases proteins Spectroscopy L1 - internal-pdf://Mischak-2009-Capillary Electropho-2846178816/Mischak-2009-Capillary Electropho.pdf LB - ISI 2009 08 27 IS - 5 N1 - English Review PY - 2009 SP - 703-724 ST - Capillary Electrophoresis-Mass Spectrometry as a Powerful Tool in Biomarker Discovery and Clinical Diagnosis: An Update of Recent Developments T2 - Mass Spectrometry Reviews TI - Capillary Electrophoresis-Mass Spectrometry as a Powerful Tool in Biomarker Discovery and Clinical Diagnosis: An Update of Recent Developments VL - 28 ID - 4001 ER - TY - JOUR AD - [Mueller, Thomas] Carl von Ossietzky Univ Oldenburg, Inst Reine & Angew Chem Carl von Ossietzky, D-26129 Oldenburg, Germany. [Mitra, Amitabha; Wojcik, Joseph P.; Lecoanet, Daniel; West, Robert] Univ Wisconsin, Dept Chem, Organosilicon Res Ctr, Madison, WI 53706 USA. AN - ISI:000266415400031 AU - Mitra, A. AU - Wojcik, J. P. AU - Lecoanet, D. AU - Muller, T. AU - West, R. KW - density functional calculations hydrolysis silicon selenium stereoconvergent reactions Stable silylene series te se Chemistry, Multidisciplinary LB - ISI 2009 06 12 IS - 22 N1 - English Article PY - 2009 SP - 4069-4072 ST - A Bis(silaselenone) with Two Donor-Stabilized Si=Se Bonds from an Unexpected Stereoconvergent Hydrolysis of a Diselenadisiletane T2 - Angewandte Chemie-International Edition TI - A Bis(silaselenone) with Two Donor-Stabilized Si=Se Bonds from an Unexpected Stereoconvergent Hydrolysis of a Diselenadisiletane VL - 48 ID - 3931 ER - TY - JOUR AN - ISI:000262718400029 AU - Mohrig, J. R. AU - Hammond, C. N. AU - Schatz, P. F. AU - Davidson, T. A. DA - Feb LB - ISI 2009 02 12 IS - 2 N1 - Mohrig, Jerry R. Hammond, Christina Noring Schatz, Paul F. Davidson, Tammy A. PY - 2009 SN - 0021-9584 SP - 234-239 ST - Synthesis and Hydrogenation of Disubstituted Chalcones A Guided-Inquiry Organic Chemistry Project T2 - Journal of Chemical Education TI - Synthesis and Hydrogenation of Disubstituted Chalcones A Guided-Inquiry Organic Chemistry Project UR - ://000262718400029 VL - 86 ID - 3792 ER - TY - JOUR AB - The sequence-directed organization of self-assembled monolayers of amphiphilic beta-peptides adsorbed on gold surfaces is studied using Monte Carlo simulations. A phenomenological model is presented in which each (helical) molecule is represented by a rigid nanorod; side groups are placed at appropriate locations. This model can distinguish between globally amphiphilic (GA) and nonglobally amphiphilic (iso-GA) sequence isomers. The simulations show that the GA isomers have a high degree of orientational order that is not exhibited by the iso-GA isomers, which is consistent with experiment (Pomerantz et al. Chem. Mater. 2007, 19, 4436). The effect of surface coverage and relative strength of electrostatic, hydrophilic, and hydrophobic interactions on the self-assembly of beta-peptides is quantified. AD - [Mondal, Jagannath; Yethiraj, Arun] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Sung, Bong June] Sogang Univ, Dept Chem, Seoul 121742, South Korea. AN - ISI:000268139000007 AU - Mondal, J. AU - Sung, B. J. AU - Yethiraj, A. DA - Jul KW - Monte-carlo-simulation nonselective solvent diblock copolymers folding behavior aqueous-solution acid oligomers adsorption surface amphiphiles foldamers Chemistry, Physical LB - ISI 2009 07 31 IS - 28 N1 - English Article UW-Madison Nanoscale Science and Engineering Center NSF [DMR-0425880] PY - 2009 SP - 9379-9385 ST - Sequence-Directed Organization of beta-Peptides in Self-Assembled Monolayers T2 - Journal of Physical Chemistry B TI - Sequence-Directed Organization of beta-Peptides in Self-Assembled Monolayers VL - 113 ID - 3966 ER - TY - JOUR AD - [Morin, Stephen A.; Streifer, Jeremy A.; Hamers, Robert J.; Jin, Song] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [La, Young-Hye; Liu, Chi-Chum; Nealey, Paul F.] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA. AN - ISI:000264411800017 AU - Morin, S. A. AU - La, Y. H. AU - Liu, C. C. AU - Streifer, J. A. AU - Hamers, R. J. AU - Nealey, P. F. AU - Jin, S. J2 - N, S(1) L5 *Order Full Text [ ] KW - block copolymers crystal growth nanocrystals nanostructures Fept nanoparticles thin-films superlattices organization nanoreactors lithography interfaces deposition templates chemistry Chemistry, Multidisciplinary LB - ISI 2009 04 03 IS - 12 N1 - English Article 1433-7851 PY - 2009 SP - 2135-2139 ST - Assembly of Nanocrystal Arrays by Block-Copolymer-Directed Nucleation T2 - Angewandte Chemie-International Edition TI - Assembly of Nanocrystal Arrays by Block-Copolymer-Directed Nucleation VL - 48 ID - 3895 ER - TY - JOUR AB - The interplay of short- and long-range interactions in protein structure and folding is poorly understood. This study focuses on the distribution of intramolecular contacts across different regions of the polypeptide chain in soluble single-domain proteins. We show that while the average number of intramolecular interactions per residue is similar across all regions of the sequence, the interaction counterparts are distributed nonrandomly. Two types of proteins are observed. The first class comprises structures that have the majority of their intramolecular contacts linking amino acids within the same region of the sequence (i.e., N-/C-terminal or intermediate portion of the chain). A second smaller class includes proteins that have extensive contacts between the N and C termini. Such extensive interactions involve primarily distal P-strands and are detected via the NCR parameter, a descriptor of the number of contacts with interaction counterparts in specific regions of the sequence. In summary, the majority of single-domain proteins (first class) is dominated by short-range interactions between contiguous elements of secondary structure and has only sparse contacts among the N and C termini. This finding defies the common assumption that the chain termini, often spatially close in folded proteins, have to participate in a large number of mutual interactions. Finally, our results suggest that the C-terminal region of Class 2 proteins may be particularly effective at promoting folding upon completion of protein biosynthesis in the cell. AD - [Mounce, Bryan C.; Kurt, Nese; Ellison, Paul A.; Cavagnero, Silvia] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000264169400013 AU - Mounce, B. C. AU - Kurt, N. AU - Ellison, P. A. AU - Cavagnero, S. DA - May KW - intramolecular interactions protein structure C terminus N terminus contact maps Chain elongation data-bank beta Biochemistry & Molecular Biology Biophysics LB - ISI 2009 03 26 IS - 2 N1 - English Article 0887-3585 PY - 2009 SP - 404-412 ST - Nonrandom distribution of intramolecular contacts in native single-domain proteins T2 - Proteins-Structure Function and Bioinformatics TI - Nonrandom distribution of intramolecular contacts in native single-domain proteins VL - 75 ID - 3887 ER - TY - JOUR AB - Host-defense peptides are natural antibiotics produced by multicellular organisms to ward off bacterial infection. Since the discovery of these molecules, in the 1980s, a great deal of effort has been devoted to elucidating their mechanisms of action and to developing analogues with improved properties for possible therapeutic use. The vast majority of this effort has focused on materials composed of a single type of molecule, most commonly a peptide with a specific sequence of alpha-amino acid residues. We have recently shown that sequence-random nylon-3 copolymers can mimic favorable properties of host-defense peptides, and here we document structure-activity relationships in this polymer family. Although the polymers are heterogeneous in terms of subunit order and stereochemistry, these materials display structure-activity relationships comparable to those that have been documented among host-defense peptides and analogous synthetic peptides. Previously such relationships have been interpreted in terms of a specific and regular folding pattern (usually an alpha-helix), but our findings show that these correlations between covalent structure and biological activity do not require the adoption of a specific or regular conformation. In some cases our observations suggest alternative interpretations of results obtained with discrete peptides. AD - [Mowery, Brendan P.; Lindner, Alexandra H.; Stahl, Shannon S.; Gellman, Samuel H.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Weisblum, Bernard] Univ Wisconsin, Dept Pharmacol, Madison, WI 53706 USA. AN - ISI:000268399800035 AU - Mowery, B. P. AU - Lindner, A. H. AU - Weisblum, B. AU - Stahl, S. S. AU - Gellman, S. H. DA - Jul KW - Helical antimicrobial peptides signal-transduction pathway ring-opening polymerization functionalized side-chains pyridinium-type polymers de-novo design beta-peptides hemolytic activities bacillus-subtilis rational design Chemistry, Multidisciplinary LB - ISI 2009 08 06 IS - 28 N1 - English Article NSF [CHE-0404704]; UW-Madison Nanoscale Science and Engineering Center [NSF DMR-0425880]; NSF Award [CHE-9520868]; UW-Madison Department of Chemistry PY - 2009 SP - 9735-9745 ST - Structure-activity Relationships among Random Nylon-3 Copolymers That Mimic Antibacterial Host-Defense Peptides T2 - Journal of the American Chemical Society TI - Structure-activity Relationships among Random Nylon-3 Copolymers That Mimic Antibacterial Host-Defense Peptides VL - 131 ID - 3987 ER - TY - JOUR AN - ISI:000263082200012 AU - Muller, M. M. AU - Windsor, M. A. AU - Pomerantz, W. C. AU - Gellman, S. H. AU - Hilvert, D. DO - 10.1002/anie.200804996 LB - ISI 2009 02 20 IS - 5 N1 - Mueller, Manuel M. Windsor, Matthew A. Pomerantz, William C. Gellman, Samuel H. Hilvert, Donald PY - 2009 SN - 1433-7851 SP - 922-925 ST - A Rationally Designed Aldolase Foldamer T2 - Angewandte Chemie-International Edition TI - A Rationally Designed Aldolase Foldamer UR - ://000263082200012 VL - 48 ID - 3790 ER - TY - JOUR AD - [Myers, Eddie L.; Raines, Ronald T.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. [Raines, Ronald T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000264784400020 AU - Myers, E. L. AU - Raines, R. T. KW - azides heterocycles phosphines Staudinger reaction synthetic methods Staudinger ligation organic-synthesis n-acyltriazenes decomposition diazoalkanes antibiotics phosphazide carbenoids oxidation kinamycin Chemistry, Multidisciplinary LB - ISI 2009 04 17 IS - 13 N1 - English Article 1433-7851 PY - 2009 SP - 2359-2363 ST - A Phosphine-Mediated Conversion of Azides into Diazo Compounds T2 - Angewandte Chemie-International Edition TI - A Phosphine-Mediated Conversion of Azides into Diazo Compounds VL - 48 ID - 3886 ER - TY - JOUR AB - Kinetics for intramolecular charge transfer between two diarylhydrazine Units, Measured by ESR, are reported for six charge-localized mixed valence compounds having 9, 11, 13, and 16 bonds between the nitrogen atoms. A 17-bond bridged Compound had too slow electron transfer to measure the rate constant by ESR. The optical spectra of these radical cations are compared with tert-butyl,aryl-substituted hydrazines', and rate constants calculated using parameters derived from the optical spectra ire compared with the experimental values where possible. The chai-e-transfer band overlapped too badly with bridge-centered absorption for the 16-bond bridged compound to allow the comparison to be made. The 13-bond bridged compound gave worse agreement than the other Compounds. Its optical rate constant was about 5.4 times the ESR rate constant at a temperature between the ranges in which the data were collected. AD - [Nelsen, Stephen F.; Schultz, Kevin P.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000265887700012 AU - Nelsen, S. F. AU - Schultz, K. P. DA - May KW - Intervalence compounds am1 calculations optical-spectra exchange anions oligo(p-phenyleneethynylene)s systems model esr Chemistry, Physical Physics, Atomic, Molecular & Chemical LB - ISI 2009 05 29 IS - 19 N1 - English Article NSF [CHE-0204197, -0647719] PY - 2009 SP - 5577-5584 ST - Electron Transfer within Charge-Localized Arylhydrazine-Centered Mixed Valence Radical Cations Having Larger Bridges T2 - Journal of Physical Chemistry A TI - Electron Transfer within Charge-Localized Arylhydrazine-Centered Mixed Valence Radical Cations Having Larger Bridges VL - 113 ID - 3922 ER - TY - JOUR AB - Charge distribution in six aromatic-bridged, aryldialkylhydrazine-centered mixed valence radical cations is discussed through consideration of their optical spectra. The compounds considered have two 2-phenyl-2,3-diazabicyclo-[2,2,2]octane-3-yl (HyPh) charge-bearing units linked by a 1,4-phenylene bridge and its p-methoxyphenyl (HyAn) analogue, is well as the (HyPh)(2)-substituted 1,4-naphthalene, 2,6-naphthalene, 9, 10-anthracene, and 4,4'-biphenyl compounds in methylene chloride and acetonitrile. Consideration of band shape and position leads us to assign the 1,4-phenylene- and 2,6-naphthalene-bridged compounds as charge-delocalized (class III) in both solvents, but the 1,4-naphthalene-bridged one lies closer to the borderline, and appears to be charge-localized (class II) in acetonitrile. The 4,4'-biphenyl-bridged compound is clearly class II in acetonitrile, and possibly also in methylene chloride. The lowest energy absorption band for the 9,10-anthracene-bridged compound is assigned as a bridge-to-HyPh band, and its charge distribution is not clear. Problems with the often-used relationship that the electronic coupling is half the transition energy for the lowest energy band of class III mixed valence compounds are discussed, as is interpretation of the vertical reorganization energy near the class II, class III borderline. AD - [Nelsen, Stephen F.; Schultz, Kevin P.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000265631000009 AU - Nelsen, S. F. AU - Schultz, K. P. DA - May KW - Dinitroaromatic radical-anions electron-transfer reactions intervalence compounds optical-spectra matrix-elements transfer rates mulliken-hush cations systems localization Chemistry, Physical Physics, Atomic, Molecular & Chemical LB - ISI 2009 05 14 IS - 18 N1 - English Article NSF [CHE-0204197, -0647719] PY - 2009 SP - 5324-5332 ST - Charge Distribution in Arylhydrazine-Centered Mixed Valence Compounds with Smaller Bridges (Five to Nine Bonds between Closest Nitrogens) T2 - Journal of Physical Chemistry A TI - Charge Distribution in Arylhydrazine-Centered Mixed Valence Compounds with Smaller Bridges (Five to Nine Bonds between Closest Nitrogens) VL - 113 ID - 3982 ER - TY - JOUR AB - This work represents the first use of mesoporous zirconium oxide nanomaterials for highly effective and selective enrichment of phosphorylated peptides. AD - [Nelson, Cory A.; Szczech, Jeannine R.; Jin, Song] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Nelson, Cory A.; Xu, Qingge; Lawrence, Mathew J.; Ge, Ying] Univ Wisconsin, Sch Med & Publ Hlth, Human Prote Program, Madison, WI 53706 USA. AN - ISI:000271506600025 AU - Nelson, Cory A. AU - Szczech, Jeannine R. AU - Xu, Qingge AU - Lawrence, Mathew J. AU - Jin, Song AU - Ge, Ying KW - Electron-capture dissociation tof ms analysis phosphorylated peptides metal-oxides affinity-chromatography femtomole level proteins nanoparticles chemistry Chemistry, Multidisciplinary LB - ISI 2009 11 19 IS - 43 N1 - English Article US National Institutes of Health (NIH) [CA126701]; UW-Madison IEDR ; Draper TIF PY - 2009 SP - 6607-6609 ST - Mesoporous zirconium oxide nanomaterials effectively enrich phosphopeptides for mass spectrometry-based phosphoproteomics T2 - Chemical Communications TI - Mesoporous zirconium oxide nanomaterials effectively enrich phosphopeptides for mass spectrometry-based phosphoproteomics ID - 4086 ER - TY - JOUR AB - Addition of CrCl2 to the dinuclear synthon MoW(dpa)(4) yields a regioselectively formed heterotrimetallic Mo W center dot center dot center dot Cr chain; computational studies suggest that the polarization of the Mo W quadruple bond partially accounts for this unexpected selectivity. AD - [Nippe, Michael; Timmer, George H.; Berry, John F.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000268081300004 AU - Nippe, M. AU - Timmer, G. H. AU - Berry, J. F. KW - Metal-metal bonds quadruple bond theoretical-analysis linear trinuclear complexes tungsten molybdenum chromium design ligand Chemistry, Multidisciplinary LB - ISI 2009 07 31 IS - 29 N1 - English Article National Science Foundation [CHE-0745500] PY - 2009 SP - 4357-4359 ST - Remarkable regioselectivity in the preparation of the first heterotrimetallic Mo W center dot center dot center dot Cr chain T2 - Chemical Communications TI - Remarkable regioselectivity in the preparation of the first heterotrimetallic Mo W center dot center dot center dot Cr chain ID - 3973 ER - TY - JOUR AB - Reported is a facile, high-yielding one-pot synthesis of the quadruply bonded ditungsten (II,II) compound W-2(dpa)(4) (1) (dpa=2,2'-dipyridylamide), which was obtained from W(CO)(6) at high temperature in naphthalene. A similar reaction in 1,2-dichlorobenzene furnished a ditungsten (III, III) species as the major product that was crystallized as [W-2(dpa)(3)Cl-2][BPh4] (3). The [W-2(dpa)(3)Cl-2](+) cation is better prepared by oxidation of 1 with SO2Cl2 Compound 1 was characterized by X-ray crystallography and cyclic-voltammetry, and is compared with its earlier reported molybdenum analogue, Mo-2(dpa)(4) (2). One-electron oxidation products of 1 and 2, [W-2(dpa)(4)][BPh4] (1BPh(4)) and [Mo-2(dpa)(4)][BPh4] (2BPh(4)), respectively, have also been synthesized. The crystallographically determined metal-metal distances of 2.23 angstrom and 2.14 angstrom in 1BPh(4) and 2BPh(4), respectively, are in agreement with metal-metal bond orders of 3.5. Unlike most previously reported Mo-2(5+) and W-2(5+) compounds, the primary coordination spheres around the M-2-units in 1/1BPh(4) and 2/2BPh(4) remain unchanged upon one-electron oxidation, because the tridentate dpa ligand hinders axial coordination of exogenous ligands AD - [Nippe, Michael; Victor, Eric; Berry, John F.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000272556700054 AU - Nippe, Michael AU - Victor, Eric AU - Berry, John F. DA - Dec KW - Metal-metal dinuclear compound ligand complexes ditungsten(ii) dimolybdenum(ii) coordination molybdenum activation cations Chemistry, Inorganic & Nuclear LB - ISI 2009 12 24 IS - 24 N1 - English Article National Science Foundation [CHE-0745500, CHE-0741901, CHE-9208463] PY - 2009 SP - 11889-11895 ST - Oxidation Chemistry of Axially Protected Mo-2 and W-2 Quadruply Bonded Compounds T2 - Inorganic Chemistry TI - Oxidation Chemistry of Axially Protected Mo-2 and W-2 Quadruply Bonded Compounds VL - 48 ID - 4112 ER - TY - JOUR AB - Reactions of 2-(3,5-dimethylpyrazol-1-ylmethyl)pyridine (L1) and 2-(3,5-di-tert-butylpyrazol-1-ylmethyl)pyridine (L2) with either [PdClMe(COD)] or [PdCl2(COD)] gave the mononuclear palladium complexes [PdCl2(L1)] (1), [PdClMe(L1)] (2) [PdCl2(L2)] (3) and [PdClMe(L2)] (4) in good yields. All compounds were characterized by NMR spectrometry, mass spectrometry, elemental analyses and also by single crystal X-ray crystallography for complexes 1, 3, and 4. The reaction of 2 with NaBAr4 in NCMe gave the salt, [[PdMeNCMe(L3)] BAr4 (5), in good yield. This salt was used as a catalyst to oligomerize ethylene at high pressures to branched polyethylene, but catalytic activity was low. The reaction of 2 with SO2 and CO formed the respective insertion products [PdClS(O)(2)Me(L1)] (6) and [PdClC(O) Me(L1)] (7). (C) 2008 Elsevier B.V. All rights reserved. AD - [Ojwach, Stephen O.; Darkwa, J.] Univ Johannesburg, Dept Chem AN - ISI:000264637400022 AU - Ojwach, S. O. AU - Guzei, I. A. AU - Darkwa, J. DA - Apr KW - Synthesis Molecular structures (Pyrazol-1-yl)pyridine palladium complexes Ethylene polymerization Insertion sulfur dioxide and carbon monoxide Pyridine-imidazoline ligands metal-carbon bonds co/styrene copolymerization alternating copolymerization polymerization catalysts diimine ligand alpha-olefins ethylene insertion monoxide Chemistry, Inorganic & Nuclear Chemistry, Organic LB - ISI 2009 04 17 IS - 9-10 N1 - English Article 0022-328X PY - 2009 SP - 1393-1399 ST - (Pyrazol-1-ylmethyl)pyridine palladium complexes: Synthesis, molecular structures, and activation of small molecules T2 - Journal of Organometallic Chemistry TI - (Pyrazol-1-ylmethyl)pyridine palladium complexes: Synthesis, molecular structures, and activation of small molecules VL - 694 ID - 3882 ER - TY - JOUR AB - Coherent multidimensional spectroscopy (CMDS) is now the optical analogue of nuclear magnetic resonance (NMR). Just as NMR heteronuclear multiple-quantum coherence (HMQC) methods rely on multiple quantum coherences, achieving widespread application requires that CMDS also excites multiple quantum coherences over a wide range of quantum state energies. This Account focuses on frequency-domain CMDS because these methods tune the excitation frequencies to resonance with the desired quantum states and can form multiple quantum coherences between states with very different energies. CMDS methods use multiple excitation pulses to excite multiple quantum states within their dephasing time, so their quantum mechanical phase is maintained. Coherences formed from pairs of the excited states emit coherent beams of light The temporal ordering of the excitation pulses defines a sequence of coherences that can result in zero, single, double, or higher order coherences as required for multiple quantum coherence CMDS. Defining the temporal ordering and the excitation frequencies and spectrally resolving the output frequency also defines a particular temporal pathway for the coherences, just as an NMR pulse sequence defines an NMR method. Two dimensional contour plots through this multidimensional parameter space allow visualization of the state energies and dynamics. This Account uses nickel and rhodium chelates as models for understanding mixed frequency-/time-domain CMDS. Mixed frequency-/time-domain methods use excitation pulse widths that are comparable to the dephasing times, so multidimensional spectra are obtained by scanning the excitation frequencies, while the coherence and population dynamics are obtained by scanning the time delays. Changing the time delays changes the peaks in the 2D excitation spectra depending upon whether the pulse sequence excites zero, single, or double quantum coherences. In addition, peaks split as a result of the frequency-domain manifestation of quantum beating. Similarly, changing the excitation and monochromator frequencies changes the dependence on the excitation delay times depending upon whether the frequencies match the resonances involved in the different time-ordered pathways. Contour plots that change a time delay and frequency visualize the temporal changes of specific spectral features. Frequency-domain methods are resonant with specific states, so the sequence of coherences and populations is defined. Coherence transfer, however, can cause output beams at unexpected frequencies. Coherence transfer occurs when the thermal bath induces a coherence between two states (a and g) to evolve to a new coherence (b and g). Since the two coherences have different frequencies and since there are different time orderings for the occurrence of coherence transfer, the delay time dependence develops modulations that depend on the coherences' frequency difference. Higher order coherences can also be generated by raising the excitation intensities. New features appear in the 2D spectra and dynamic Stark splittings occur. These effects will form the basis for the higher order multiple quantum coherence methods and also provide a method for probing molecular potential energy surfaces. AD - [Pakoulev, Andrei V.; Rickard, Mark A.; Kornau, Kathryn M.; Mathew, Nathan A.; Yurs, Lena A.; Block, Stephen B.; Wright, John C.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000269861400012 AU - Pakoulev, A. V. AU - Rickard, M. A. AU - Kornau, K. M. AU - Mathew, N. A. AU - Yurs, L. A. AU - Block, S. B. AU - Wright, J. C. DA - Sep KW - Enhanced 4-wave-mixing spectroscopy 2-dimensional infrared-spectroscopy vibrational spectroscopy photon-echoes ir spectroscopy resonance peptides nmr spectra analogs Chemistry, Multidisciplinary LB - ISI 2009 10 01 IS - 9 N1 - English Review National Science Foundation [CHE-0650431] Sp. Iss. SI PY - 2009 SP - 1310-1321 ST - Mixed Frequency-/Time-Domain Coherent Multidimensional Spectroscopy: Research Tool or Potential Analytical Method? T2 - Accounts of Chemical Research TI - Mixed Frequency-/Time-Domain Coherent Multidimensional Spectroscopy: Research Tool or Potential Analytical Method? VL - 42 ID - 4030 ER - TY - JOUR AB - The reaction of Ru-2(OAc)(4)Cl with N,N'N ''-triphenylguanidine (HTPG) produces one of two different compounds depending on the reaction conditions. In acetone in the presence of triethyl amine, the reaction produces tri-substituted Ru-2(TPG)(3)(OAc)Cl, and in refluxing xylene, the tetra-substituted Ru-2(TPG)(4)Cl is produced. Both of these new complexes can be cleanly converted into their corresponding azido analogues by reaction with sodium azide in methanol. The X-ray crystal structures of Ru-2(TPG)(3)(OAc)Cl, Ru-2(TPG)(3)(OAc)N-3, and Ru-2(TPG)(4)Cl are presented, along with magnetic, electrochemical, and spectral measurements for each compound. Studies in solution show that, in contrast to Ru-2(TPG)(3)(OAc)Cl, Ru-2(TPG)(4)Cl is sterically hindered at the axial positions, and readily dissociates a chloride ion at high ionic strength. Equilibrium constants for chloride association and dissociation have been estimated. Mass spectrometric data suggest that the two azido complexes are precursors to new diruthenium nitrido species. AD - [Pap, Jozsef S.; Snyder, Jamie L.; Piccoli, Paula M. B.; Berry, John F.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000270561400029 AU - Pap, J. S. AU - Snyder, J. L. AU - Piccoli, P. M. B. AU - Berry, J. F. DA - Oct KW - Free-energy relationships molecule-based magnets crystal-structures carboxylate compounds building-blocks metal-metal tetracarboxylates electrochemistry oxygenation monocation Chemistry, Inorganic & Nuclear LB - ISI 2009 10 23 IS - 20 N1 - English Article University of Wisconsin ; National Science Foundation [CHE-0741901] PY - 2009 SP - 9846-9852 ST - Chloro and Azido Diruthenium complexes Bearing Electron-Rich N,N ',N ''-Triphenylguanidinate Ligands T2 - Inorganic Chemistry TI - Chloro and Azido Diruthenium complexes Bearing Electron-Rich N,N ',N ''-Triphenylguanidinate Ligands VL - 48 ID - 4057 ER - TY - JOUR AB - A C-60-terminated self-assembled monolayer can be used to place molecular acceptor states at the interface between the semiconductor and gate insulator of an organic field effect transistor. The time dependence of the photoinduced charge transfer between pentacene and C-60 has a fast component with a characteristic time of 1.9 s and slower component with a time constant of 32 and 48 s at the beginning and end of a transient increase in illumination, respectively. Variation in the threshold voltage shift with the thickness of the pentacene results from the competing length scales for light absorption and exciton diffusion. AD - [Park, Byoungnam; Paoprasert, Peerasak; Gopalan, Padma; Kuech, T. F.; Evans, Paul G.] Univ Wisconsin, Madison, WI 53706 USA. AN - ISI:000263599200077 AU - Park, B. AU - Paoprasert, P. AU - Gopalan, P. AU - Kuech, T. F. AU - Evans, P. G. DA - Feb DO - 073302 KW - charge exchange diffusion excitons fullerenes interface states organic field effect transistors organic semiconductors self-assembly semiconductor-insulator boundaries silicon compounds Field-effect transistors solar-cells films Physics, Applied LB - ISI 2009 03 13 IS - 7 N1 - English Article 0003-6951 PY - 2009 ST - Dynamics of photoinduced charge transfer between pentacene and a C-60-terminated self-assembled monolayer T2 - Applied Physics Letters TI - Dynamics of photoinduced charge transfer between pentacene and a C-60-terminated self-assembled monolayer VL - 94 ID - 3823 ER - TY - JOUR AB - Aerosol particles in the atmosphere are tiny chemical reactors that catalyze numerous reactions, including the conversion of benign gases Into ozone-destroying ones. In the lower stratosphere, these particles are often supercooled mixtures of water and Sulfuric acid. The different species present at the surface of these droplets (H2O, H3O+, HSO4, H2SO4, and SO42-) stand at the "gas-liquid frontier"; as the first to be struck by Impinging molecules, these species provide the initial environment for solvation and reaction. Furthermore, aerosol particles may contain a wide range of organic molecules, some of which migrate to the surface and coat the droplet. How do ambient gases dissolve In the droplet If it Is coated with an organic layer? At one extreme, monolayer films of insoluble, long-chain alcohols can dramatically reduce gas transport, packing so tightly at the surface of water that they Impede water evaporation by factors of 10 000 or more. Shorter chain surfactants are expected to pack less tightly, but we wondered whether these incomplete monolayers also block gas transport and whether this system could serve as a model for Understanding the surfaces of atmospheric aerosol particles. To address these questions, our research focuses on small, soluble surfactants such as butanol and hexanol dissolved in supercooled sulfuric acid. These amphiphilic molecules spontaneously segregate to the surface and coat the acid but only to a degree. Cas-liquid scattering experiments reveal that these porous films behave in surprisingly diverse ways: they can impose a barrier (to N2O5 hydrolysis), be "invisible" (to water evaporation), or even enhance gas uptake (of HCl). The transition from obstacle to catalyst can be traced to specific Interactions between the surfactant and each gas. For example, the hydrolysis of N2O5 may be Impeded because of Its large size and because alcohol molecules that straddle the interface limit contact between N2O5 and its H3O+ and H2O reaction partners. However, these same alcohol molecules assist HCl dissociation because the alcohol OH groups provide extra interfacial protonation sites. Interestingly, butanol does not impede water evaporation, In part because the butyl chains pack much more loosely than insoluble, long-chain surfactants. Through these Investigations, we hope to gain Insight into the mechanisms by which surfactants on sulfuric acid and other aqueous solutions affect transport and reactivity at the gas-liquid interface. AD - [Park, Seong-Chan; Burden, Daniel K.; Nathanson, Gilbert M.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000263428300016 AU - Park, S. C. AU - Burden, D. K. AU - Nathanson, G. M. KW - Chemistry, Multidisciplinary LB - ISI 2009 03 05 N1 - English Review HETEROGENEOUS REACTIONS; ORGANIC FILMS; TROPOSPHERIC AEROSOLS; OZONE DEPLETION; MOLECULAR-BEAM; BUTANOL FILMS; N2O5; HCL; MONOLAYERS; EVAPORATION FEB 2 PY - 2009 SP - 379-387 ST - Surfactant Control of Gas Transport and Reactions at the Surface of Sulfuric Acid T2 - Accounts of Chemical Research TI - Surfactant Control of Gas Transport and Reactions at the Surface of Sulfuric Acid ID - 3768 ER - TY - JOUR AB - Aerosol particles in the atmosphere are tiny chemical reactors that catalyze numerous reactions, including the conversion of benign gases Into ozone-destroying ones. In the lower stratosphere, these particles are often supercooled mixtures of water and Sulfuric acid. The different species present at the surface of these droplets (H2O, H3O+, HSO4, H2SO4, and SO42-) stand at the "gas-liquid frontier"; as the first to be struck by Impinging molecules, these species provide the initial environment for solvation and reaction. Furthermore, aerosol particles may contain a wide range of organic molecules, some of which migrate to the surface and coat the droplet. How do ambient gases dissolve In the droplet If it Is coated with an organic layer? At one extreme, monolayer films of insoluble, long-chain alcohols can dramatically reduce gas transport, packing so tightly at the surface of water that they Impede water evaporation by factors of 10 000 or more. Shorter chain surfactants are expected to pack less tightly, but we wondered whether these incomplete monolayers also block gas transport and whether this system could serve as a model for Understanding the surfaces of atmospheric aerosol particles. To address these questions, our research focuses on small, soluble surfactants such as butanol and hexanol dissolved in supercooled sulfuric acid. These amphiphilic molecules spontaneously segregate to the surface and coat the acid but only to a degree. Cas-liquid scattering experiments reveal that these porous films behave in surprisingly diverse ways: they can impose a barrier (to N2O5 hydrolysis), be "invisible" (to water evaporation), or even enhance gas uptake (of HCl). The transition from obstacle to catalyst can be traced to specific Interactions between the surfactant and each gas. For example, the hydrolysis of N2O5 may be Impeded because of Its large size and because alcohol molecules that straddle the interface limit contact between N2O5 and its H3O+ and H2O reaction partners. However, these same alcohol molecules assist HCl dissociation because the alcohol OH groups provide extra interfacial protonation sites. Interestingly, butanol does not impede water evaporation, In part because the butyl chains pack much more loosely than insoluble, long-chain surfactants. Through these Investigations, we hope to gain Insight into the mechanisms by which surfactants on sulfuric acid and other aqueous solutions affect transport and reactivity at the gas-liquid interface. AN - ISI:000263428300016 AU - Park, S. C. AU - Burden, D. K. AU - Nathanson, G. M. DA - Feb DO - 10.1021/ar800172m LB - ISI 2009 03 05 (Library clean-up) IS - 2 N1 - Park, Seong-Chan Burden, Daniel K. Nathanson, Gilbert M. PY - 2009 SN - 0001-4842 SP - 379-387 ST - Surfactant Control of Gas Transport and Reactions at the Surface of Sulfuric Acid T2 - Accounts of Chemical Research TI - Surfactant Control of Gas Transport and Reactions at the Surface of Sulfuric Acid UR - ://000263428300016 VL - 42 ID - 3775 ER - TY - JOUR AB - Recently, we developed a quantitative interpretation of surface tension increments (STI) of salts, acids, and bases in terms of the solute (or salt ion) partitioning model (SPM). Here, we obtain an analogous SPM-based interpretation of surface tension increments of nonelectrolytes,. which yields local-bulk partition coefficients (K-p) quantifying the accumulation or exclusion of these solutes in the local region near the air-water surface, and the amount of water per unit area of that region (b(1)(0)). Sucrose exhibits the largest positive STI (approximately 1.4 ergs cm(-2) Osm(-1)). Assuming that K-p = 0 for sucrose (i.e., that it is completely excluded from the surface of water), these STI provide a minimum estimate of b(1)(0) of 0.20 H-2 O/angstrom(2), or a minimum thickness of the surface region of approximately two layers of water at bulk density. This is the same value as obtained previously from analysis of surface tension and hydrocarbon solubility increments of Na2SO4 and also for the interaction of glycine betaine with anionic carboxylate surface, indicating that this quantity is not a function of the type of solute or surface investigated and therefore that it may represent the molecular thickness of the region. Partition coefficients of other nonelectrolytes investigated range from moderately excluded (e.g., urea) to moderately accumulated (e.g., glycerol, ethylene glycol); strongly accumulated surface active solutes (e.g., monosubstituted alcohols) were not included in this analysis. Partition coefficients for many salt ions obtained from STI and hydrocarbon solubility increments fall in a rank order which corresponds to the Hofmeister series for protein folding and protein solubility, indicating a common pattern of accumulation or exclusion of salt ions at the air-water surface and nonpolar surfaces of dissolved hydrocarbons and proteins; no such patterns are observed for nonelectrolytes. AN - ISI:000263134700019 AU - Pegram, L. M. AU - Record, M. T. DA - Feb DO - 10.1021/jp8073305 LB - ISI 2009 02 20 IS - 6 N1 - Pegram, Laurel M. Record, M. Thomas, Jr. PY - 2009 SN - 1932-7447 SP - 2171-2174 ST - Using Surface Tension Data to Predict Differences in Surface and Bulk Concentrations of Nonelectrolytes in Water T2 - Journal of Physical Chemistry C TI - Using Surface Tension Data to Predict Differences in Surface and Bulk Concentrations of Nonelectrolytes in Water UR - ://000263134700019 VL - 113 ID - 3785 ER - TY - JOUR AD - [Phanstiel, D.; Brumbaugh, J.; McAlister, G. C.; Wenger, C. D.; Coon, J. J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Stewart, R.; Tian, S.; Thomson, J. A.] Univ Wisconsin, Morgridge Inst Res, Madison, WI 53706 USA. AN - ISI:000268939000002 AU - Phanstiel, D. AU - Brumbaugh, J. AU - McAlister, G. C. AU - Wenger, C. D. AU - Stewart, R. AU - Tian, S. AU - Thomson, J. A. AU - Coon, J. J. DA - Aug KW - Biochemical Research Methods LB - ISI 2009 08 27 N1 - English Meeting Abstract Suppl. S PY - 2009 SP - S11-S11 ST - New Technology for the Large-scale Proteomic Comparison of Human Embryonic Stem Cells, Induced Pluripotent Stem Cells, and Somatic Cells T2 - Molecular & Cellular Proteomics TI - New Technology for the Large-scale Proteomic Comparison of Human Embryonic Stem Cells, Induced Pluripotent Stem Cells, and Somatic Cells ID - 4000 ER - TY - JOUR AB - Isobaric tags for absolute and relative quantitation (iTRAQ) allow for simultaneous relative quantification of peptides from up to eight different samples. Typically peptides labeled with 8-plex iTRAQ tags are pooled and fragmented using beam-type collision activated dissociation (CAD) which, in addition to cleaving the peptide backbone bonds, cleaves the tag to produce reporter ions. The relative intensities of the reporters are directly proportional to the relative abundances of each peptide in the solution phase. Recently, studies using the 4-plex iTRAQ tagging reagent demonstrated that electron transfer dissociation (EM) of 4-plex iTRAQ labeled peptides cleaves at the N-C alpha bond in the tag and allows for up to three channels of quantification. In this paper we investigate the ETD fragmentation patterns of peptides labeled with 8-plex iTRAQ tags. We demonstrate that upon ETD, peptides labeled with 8-plex iTRAQ tags fragment to produce unique reporter ions that allow for five channels of quantification. ETD-MS/MS of these labeled peptides also produces a peak at 322 m/z which, upon resonant excitation (CAD), gives rise to all eight iTRAQ reporter ions and allows for eight channels of quantification. Comparison of this method to beam-type CAD quantification shows a good correlation (y = 0.91x + 0.01, R-2 = 0.9383). AN - ISI:000263319000054 AU - Phanstiel, D. AU - Unwin, R. AU - McAlister, G. C. AU - Coon, J. J. DA - Feb DO - 10.1021/ac8019202 LB - ISI 2009 02 26 IS - 4 N1 - Phanstiel, Doug Unwin, Richard McAlister, Graeme C. Coon, Joshua J. PY - 2009 SN - 0003-2700 SP - 1693-1698 ST - Peptide Quantification Using 8-Plex Isobaric Tags and Electron Transfer Dissociation Tandem Mass Spectrometry T2 - Analytical Chemistry TI - Peptide Quantification Using 8-Plex Isobaric Tags and Electron Transfer Dissociation Tandem Mass Spectrometry UR - ://000263319000054 VL - 81 ID - 3778 ER - TY - JOUR AB - In this work, we combine atomistic molecular dynamics simulations with theoretical vibrational spectroscopy to study the properties of water confined inside bis(2-ethylhexyl)sulfosuccinate (AOT) reverse micelles. This approach is found to successfully reproduce the experimental spectra, rotational anisotropy decays, and spectral diffusion time-correlation functions as a function of micelle size. These results are interpreted in terms of water molecules in different hydrogen bonding environments. One interesting result from our simulation, not directly accessible experimentally, involves the distance from the surfactant headgroup/water interface over which the dynamical properties of water become bulk-like. We find that this distance varies with micelle size, casting doubt on the core/shell model. In particular, the distance increases with decreasing micelle size, and hence decreasing radius of curvature of the interface. We suggest that this arises from curvature-induced frustration. We also find that the dynamics in the smallest micelle studied is extremely slow-relaxation is still incomplete by 1 ns. As in other glassy systems with collective relaxation, our time-correlation functions can be fit to stretched exponentials, in this case with very small exponents. AD - [Pieniazek, Piotr A.; Lin, Yu-Shan; Skinner, J. L.] Univ Wisconsin, Inst Theoret Chem, Madison, WI 53706 USA. [Pieniazek, Piotr A.; Lin, Yu-Shan; Skinner, J. L.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Chowdhary, Janamejaya; Ladanyi, Branka M.] Colorado State Univ, Dept Chem, Ft Collins, CO 80523 USA. AN - ISI:000271428200024 AU - Pieniazek, Piotr A. AU - Lin, Yu-Shan AU - Chowdhary, Janamejaya AU - Ladanyi, Branka M. AU - Skinner, J. L. DA - Nov KW - Ultrafast infrared-spectroscopy hydrogen-bond dynamics protein hydration water molecular-dynamics solvation dynamics liquid water computer-simulation neutron-scattering spectral diffusion nmr-spectroscopy Chemistry, Physical LB - ISI 2009 12 11 IS - 45 N1 - English Review DOE [DE-FG03-0ZER15376, DE-FG02-09ER16110]; NSF [CHE-0608640, CHE-0750307] PY - 2009 SP - 15017-15028 ST - Vibrational Spectroscopy and Dynamics of Water Confined inside Reverse Micelles T2 - Journal of Physical Chemistry B TI - Vibrational Spectroscopy and Dynamics of Water Confined inside Reverse Micelles VL - 113 ID - 4071 ER - TY - JOUR AB - BACKGROUND: Carcinoids are neuroendocrine (NE) tumors with limited treatment options. Raf-1 pathway activation has been shown to suppress hormone production in carcinoid cells. We investigated a novel treatment for carcinoid cell growth based on pharmacologic Raf-1 activation using the compound tautomycin (TTY). METHODS: Human carcinoid cells were treated with TTY for 48 hours. Western blot analysis was used to demonstrate Raf-1 pathway activation by phosphorylation of ERK1/2 and to determine the effect on NE tumor markers. Cellular growth was measured by methylthiazolyldiphenyl-tetrazolium bromide (MTT) assay. RESULTS: Treatment with TTY resulted in dose-dependent activation of the Raf-1 pathway. Furthermore, a significant decrease in NE tumor markers was seen. Importantly, TTY inhibited carcinoid cellular growth and induced the cell-cycle inhibitors p21 and p27. CONCLUSION: TTY activates the Raf-1 pathway, limits carcinoid cell growth, and suppresses NE market production in vitro. This new Compound warrants further investigation in animal models of carcinoid cancer. (C) 2009 Published by Elsevier Inc. AD - [Pinchot, Scott N.; Adler, Joel T.; Kunnimalaiyaan, Muthusamy; Chen, Herbert] Univ Wisconsin, Dept Surg, Endocrine Surg Res Labs, Madison, WI 53706 USA. [Luo, Yinggang; Ju, Jianhua; Li, Wenli; Shen, Ben] Univ Wisconsin, Div Pharmaceut Sci, Madison, WI USA. [Shen, Ben] Univ Wisconsin, Dept Chem, Drug Discovery Grp, Univ Wisconsin Natl Cooperat, Madison, WI 53706 USA. AN - ISI:000264277400015 AU - Pinchot, S. N. AU - Adler, J. T. AU - Luo, Y. G. AU - Ju, J. H. AU - Li, W. L. AU - Shen, B. AU - Kunnimalaiyaan, M. AU - Chen, H. DA - Mar KW - Carcinoid tumor Extracellular-regulated kinase pathway Ref 1 Targeted therapies Tautomycin Medullary-thyroid cancer inhibits growth heart-disease cycle arrest tumors mutations induction p21(cip1) targets Surgery LB - ISI 2009 04 03 IS - 3 N1 - English Proceedings Paper 0002-9610 PY - 2009 SP - 313-318 ST - Tautomycin suppresses growth and neuroendocrine hormone markers in carcinoid cells through activation of the Raf-1 pathway T2 - American Journal of Surgery TI - Tautomycin suppresses growth and neuroendocrine hormone markers in carcinoid cells through activation of the Raf-1 pathway VL - 197 ID - 3896 ER - TY - JOUR AD - [Pomerantz, William C.; Hadley, Erik B.; Fry, Charles G.; Gellman, Samuel H.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000269831900010 AU - Pomerantz, W. C. AU - Hadley, E. B. AU - Fry, C. G. AU - Gellman, S. H. DA - Sep KW - backbone thioester exchange coiled coil fluorine NMR spectroscopy protein folding Acid-binding protein coiled-coil secondary structure stability design spectroscopy domain probe Biochemistry & Molecular Biology Chemistry, Medicinal LB - ISI 2009 10 01 IS - 13 N1 - English Article NIH [GM061238]; Nanoscale Science and Engineering Center at UW-Madison [NSF DMR-0425880] PY - 2009 SP - 2177-2181 ST - In Situ Monitoring of Backbone Thioester Exchange by F-19 NMR T2 - Chembiochem TI - In Situ Monitoring of Backbone Thioester Exchange by F-19 NMR VL - 10 ID - 4028 ER - TY - JOUR AB - The mechanism of catalyst oxidation by O-2 in Pd-catalyzed aerobic oxidation reactions has been the subject of considerable debate, particularly with respect to the reactivity of Pd-II-hydride species. Here. we describe the use of unrestricted DFT computational methods to investigate the mechanism of catalyst reoxidation with the Pd(OAc)(2)/pyridine catalyst system, one of the most widely used catalysts. These Studies probe four different pathways for the formation of a Pd-II-hydroperoxide species from the reaction of 0, from the corresponding Pd-II-hydride [(py)(n)Pd-II(H)OAc]: 1) a homolytic pathway involving hydrogen-atom abstraction by O-2: 2) AcOH reductive elimination to yield a Pd-0 species that subsequently reacts with O-2; 3) migratory insertion of O-2 into a Pd-H bond: and 4) oxidative addition of O-2 to Pd-II to yield a Pd-IV(eta(2)-peroxo) species. In conlrast to previous Studies of reactions between O-2 and Pd-hydride species, the reductive-elimination pathway (mechanism 2) is significantly more favorable than ant of the other pathways. This outcome is traced to the presence of labile ligands (pyridine) that can readily dissociate from Pd to enable the hydride and acetate ligands to Occupy cis-coordination sites. These results strongly support the involvement of Pd-0 as an intermediate in the catalytic cycle. Investigations of the mechanism of the reaction of O-2 with the Pd-0 intermediate revealed a novel. previously unrecognized mechanism that yields a Pd-OOH product Without proceeding through the intermediacy of a Pd-II(eta(2)-peroxo) species. This mechanism resembles pathways commonly observed in biological O-2 activation and suggests that noble-inetal and biological oxidation mechanisms may be more similar than previously appreciated. AD - [Popp, Brian V.; Stahl, Shannon S.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000264511500019 AU - Popp, B. V. AU - Stahl, S. S. KW - homogeneous catalysis density functional calculations dioxygen ligands oxidation palladium Aerobic alcohol oxidation continuum solvation models coupled electron-transfer pd-mediated activation molecular-oxygen palladium(ii)-catalyzed oxidation coordinated palladium(0) anisotropic dielectrics organic-chemicals oxidase catalysis Chemistry, Multidisciplinary LB - ISI 2009 04 09 IS - 12 N1 - English Article 0947-6539 PY - 2009 SP - 2915-2922 ST - Mechanism of Pd(OAc)(2)/Pyridine Catalyst Reoxidation by O-2: Influence of Labile Monodentate Ligands and Identification of a Biomimetic Mechanism for O-2 Activation T2 - Chemistry-A European Journal TI - Mechanism of Pd(OAc)(2)/Pyridine Catalyst Reoxidation by O-2: Influence of Labile Monodentate Ligands and Identification of a Biomimetic Mechanism for O-2 Activation VL - 15 ID - 3898 ER - TY - JOUR AB - A method for the synthesis of small molecule macroarrays of N-acylated L-homoserine lactones (AHLs) is reported. A focused library of AHLs was constructed, and the macroarray platform was found to be compatible with both solution and agar-overlay assays using quorum-sensing (QS) reporter strains. Several QS antagonists were discovered and serve to showcase the macroarray as a straightforward technique for QS research. AD - [Praneenararat, Thanit; Geske, Grant D.; Blackwell, Helen E.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000270461300030 AU - Praneenararat, T. AU - Geske, G. D. AU - Blackwell, H. E. DA - Oct KW - Gram-negative bacteria acylated homoserine lactones chromobacterium-violaceum cell communication spot-synthesis identification autoinducers mechanisms Chemistry, Organic LB - ISI 2009 10 15 IS - 20 N1 - English Article NIH [AI063326-01]; Greater Milwaukee Foundation ; Burroughs Welcome Fund ; Johnson Johnson ; Alfred P. Sloan Foundation ; Anandamahidol Foundation (Thailand) PY - 2009 SP - 4600-4603 ST - Efficient Synthesis and Evaluation of Quorum-Sensing Modulators Using Small Molecule Macroarrays T2 - Organic Letters TI - Efficient Synthesis and Evaluation of Quorum-Sensing Modulators Using Small Molecule Macroarrays VL - 11 ID - 4035 ER - TY - JOUR AB - (Me2N)(4)Ta-(SiBuPh2)-Ph-t (1) reacts with O-2 to give (Me2N)(4)Ta((OSiBuPh2)-Ph-t) (2), (Me2N)(3)Ta(ONMe2)((OSiBuPh2)-Ph-t) (3), and the unusualy-oxo amino (Me2N)(2)((Ph2BuSiO)-Si-t)(2)(mu,eta(2)-Me2NCH2NMe)(2)Ta-2(mu-O)(2) (4) containing two bridging chelating (aminomethyl)am ides -N(Me)CH2NMe2. The dimer 4 was characterized by X-ray crystallography. 2 also reacts with 02 to give both 3 and 4. Reaction pathways in the formation of these complexes are discussed. In reactions of O-2 with d(0) 1 and 2, oxidation of the ligands is the prevailing pathway. AD - [Qiu, He; Chen, Shu-Jian; Xue, Zi-Ling] Univ Tennessee, Dept Chem, Knoxville, TN 37996 USA. [Wang, Chang-Sheng; Wu, Yun-Dong] Hong Kong Univ Sci & Technol, Dept Chem, Hong Kong, Hong Kong, Peoples R China. [Wang, Chang-Sheng] Liaoning Normal Univ, Dept Chem, Dalian 116029, Peoples R China. [Guzei, Ilia A.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Chen, Xue-Tai] Nanjing Univ, Sch Chem & Chem Engn, Nanjing Natl Lab Microstruct, State Key Lab Coordinat Chem, Nanjing 210093, Peoples R China. AN - ISI:000264759500044 AU - Qiu, H. AU - Chen, S. J. AU - Wang, C. S. AU - Wu, Y. D. AU - Guzei, I. A. AU - Chen, X. T. AU - Xue, Z. L. DA - Apr KW - Chemical-vapor-deposition anionic pi-ligands high-k dielectrics crystal-structure group-4 amides atom transfer dioxygen alkyl zirconium si Chemistry, Inorganic & Nuclear LB - ISI 2009 04 17 IS - 7 N1 - English Article 0020-1669 PY - 2009 SP - 3073-3079 ST - Synthesis and Characterization of Siloxy, Aminoxy, and Oxo Complexes from the Reaction of a Tantalum Amide Silyl Complex with Oxygen T2 - Inorganic Chemistry TI - Synthesis and Characterization of Siloxy, Aminoxy, and Oxo Complexes from the Reaction of a Tantalum Amide Silyl Complex with Oxygen VL - 48 ID - 3884 ER - TY - JOUR AB - The extreme steric bulk of tris(trimethylsilyl)methyl derivatives (1-X) provides interesting structural and dynamic behavior for study. Dynamic NMR studies on 1-SePh and 1-I showed restricted rotation around the C-Si bonds of each trimethylsilyl groups. An extensive multinuclear NMR study of natural abundance and Li-6 and C-13 enriched 1-Li revealed three species in THF-containing solvents, a dimer 1T, and two monomers, the contact ion pair 1C, and solvent separated ion pair 1S. Observed barriers for interconversion of 1-Li aggregates were unusually high (Delta G(double dagger) ca. 9 kcal/mol for exchange of 1S and 1C, Delta G(41)(double dagger) = 16.4 kcal/mol for exchange of 1T with 1C and 1S), allowing For study of reactivity of each aggregate individually. We call show that 1S is at least 50 times as, reactive as 1C and at least 5 x 10(10) times as reactive as 1T toward MeI. The large difference in reactivity allowed further study on the mechanism of the lithium-iodine exchange of 1-I with 1-Li and characterization of the intermediate iodine ate complex 4. Additional calibrations are presented for the sensitive yet. chemically inert C-13 NMR chemical shift thermometer 1-H. AD - [Reich, Hans J.; Sikorski, William H.; Sanders, Aaron W.; Jones, Amanda C.; Plessel, Kristin N.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000262338700027 AU - Reich, H. J. AU - Sikorski, W. H. AU - Sanders, A. W. AU - Jones, A. C. AU - Plessel, K. N. DA - Jan KW - Nuclear magnetic-resonance organometallic compounds crystal-structure organolithium compounds lithium ion solid-state tetrahydrofuran mechanism kinetics relaxation Chemistry, Organic LB - ISI 2009 01 22 IS - 2 N1 - English Article 0022-3263 PY - 2009 SP - 719-729 ST - Multinuclear NMR Study of the Solution Structure and Reactivity of Tris(trimethylsilyl)methyllithium and its Iodine Ate Complex T2 - Journal of Organic Chemistry TI - Multinuclear NMR Study of the Solution Structure and Reactivity of Tris(trimethylsilyl)methyllithium and its Iodine Ate Complex VL - 74 ID - 3734 ER - TY - JOUR AB - Normal mode analysis using elastic network models has grown popular for probing the low-frequency collective dynamics of proteins and other biomolecular assemblies. In most previous studies, these models were validated by comparing calculated atomic fluctuations for isolated proteins with experimental temperature factors determined in the crystalline state, although there were also hints that including crystal contacts in the calculations has an impact on the comparison. In this study, a set of 83 ultra-high resolution crystal structures with experimentally determined anisotropic displacement parameters is used to evaluate several C-alpha-based elastic network models that either ignore or treat the crystal environment in different ways; the latter include using periodic boundary conditions defined with respect to the asymmetric unit or the primitive unit cell as well as using the Born-von Karman boundary condition that accounts for lattice vibrations. For all elastic network models, treating the crystal environment leads to better agreement with experimental anisotropic displacement parameters with the Born-von Karman boundary condition giving the best agreement. Atomic correlations over the entire protein are clearly affected by the presence of the crystal contacts and fairly sensitive to the way that the crystal environment is treated. These observations highlight the importance of properly treating the protein system in an environment consistent with experiment when either evaluating approximate protein models or using approximate dynamic models in structural refinement application types. Finally, investigation of the scaling behaviors of the cumulative density of states and the heat capacity indicates that there are still gaps between simplified elastic models and all-atom models for proteins. AD - [Phillips, George N., Jr.] Univ Wisconsin, Dept Biochem, Madison, WI 53705 USA. [Phillips, George N., Jr.] Univ Wisconsin, Dept Comp Sci, Madison, WI 53706 USA. [Riccardi, Demian] Univ Wisconsin, Program Computat & Informat Biol & Med, Madison, WI USA. [Cui, Qiang] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Cui, Qiang] Univ Wisconsin, Inst Theoret Chem, Madison, WI USA. AN - ISI:000266377200018 AU - Riccardi, D. AU - Cui, Q. AU - Phillips, G. N. DA - Jan KW - Grained biomolecular simulation pancreatic trypsin-inhibitor frequency normal-modes x-ray crystallography diffuse-scattering molecular-dynamics folded proteins motions refinement fluctuations Biophysics LB - ISI 2009 06 12 IS - 2 N1 - English Article National Library of Medicine [5T15LM007359] PY - 2009 SP - 464-475 ST - Application of Elastic Network Models to Proteins in the Crystalline State T2 - Biophysical Journal TI - Application of Elastic Network Models to Proteins in the Crystalline State VL - 96 ID - 3927 ER - TY - JOUR AD - [Rich, Daniel H.] Univ Wisconsin, Sch Pharm, Madison, WI 53705 USA. [Rich, Daniel H.] Univ Wisconsin, Dept Chem, Madison, WI 53705 USA. AN - ISI:000269988300002 AU - Rich, D. H. DA - Sep KW - Biochemistry & Molecular Biology LB - ISI 2009 10 01 IS - 9 N1 - English Biographical-Item PY - 2009 SP - 695-697 ST - Ralph F. Hirschmann, 1922-2009. A Perspective T2 - ACS Chemical Biology TI - Ralph F. Hirschmann, 1922-2009. A Perspective VL - 4 ID - 4029 ER - TY - JOUR AB - Since the initial discovery of poly(ethylene glycol) (PEG) as a good lithium ion conductor at elevated temperatures, efforts have been made to find ways of incorporating this biocompatible polymer into lithium ion batteries. In areas of research involving implantable medical devices, consumer electronics and automotive power sources, there is a need to develop a 'safe' alternative to the solvent-based, flammable and toxic electrolytes currently employed. However, PEG has been shown to be electrochemically unstable and crystalline at room temperature. In order to overcome these problems, polysiloxanes have been conjugated to PEG in order to improve its conductivity and physical properties. Over the last few years, the group at the University of Wisconsin-Madison has been involved in collaborations with scientists at Argonne National Laboratories, Grinnell College and Quallion LLC to develop commercially viable silicon-containing polymer electrolytes. This mini-review discusses the electrochemical, thermal and physical properties of these electrolytes, and highlights the progress from high molecular weight polysiloxane-based electrolytes to low-viscosity, highly conducting oligosiloxane and silane electrolytes. (C) 2009 Society of Chemical Industry AD - [West, Robert] Univ Wisconsin, Dept Chem, Organosilicon Res Ctr, Madison, WI 53706 USA. Vancouver, BC V6T 1Z3, Canada. Vancouver, BC V6T 1Z3, Canada. Vancouver, BC V6T 1Z3, Canada. AN - ISI:000263771500007 AU - Rossi, N. A. A. AU - West, R. DA - Mar KW - polymer electrolyte lithium ion battery polysiloxane poly(ethylene oxide) silane Side-chains siloxane oxide) conductivity complexes oligo(oxyethylene) polysiloxanes solvents salts Polymer Science LB - ISI 2009 03 13 IS - 3 N1 - English Review 0959-8103 Sp. Iss. SI PY - 2009 SP - 267-272 ST - Silicon-containing liquid polymer electrolytes for application in lithium ion batteries T2 - Polymer International TI - Silicon-containing liquid polymer electrolytes for application in lithium ion batteries VL - 58 ID - 3818 ER - TY - JOUR AB - Peptide characterization using electron transfer dissociation (ETD) is an important analytical tool for protein identification. The fragmentation observed in ETD spectra is complementary to that seen when using the traditional dissociation method, collision activated dissociation (CAD). Applications of ETD enhance the scope and complexity of the peptides that can be studied by mass spectrometry-based methods. For example, ETD is shown to be particularly useful for the study of post-translationally modified peptides. To take advantage of the power provided by ETD, it is important to have an ETD-specific database search engine, an integral tool of mass spectrometry-based analytical proteomics. In this paper, we report on our development of a database search engine using ETD spectra and protein sequence databases to identify peptides. The search engine is based on the probabilistic modeling of shared peaks count and shared peaks intensity between the spectra and the peptide sequences. The shared peaks count accounts for the cumulative variations from amino acid sequences, while shared peaks intensity models the variations between the candidate sequence and product ion intensities. To demonstrate the utility of this algorithm for searching real-world data, we present the results of applications of this model to two high-throughput data sets. Both data sets were obtained from yeast whole cell lysates. The first data set was obtained from a sample digested by Lys-C, and the second data set was obtained by a digestion using trypsin. We searched the data sets against a combined forward and reversed yeast protein database to estimate false discovery rates. We compare the search results from the new methods with the results from a search engine often employed for ETD spectra, OMSSA. Our findings show that overall the new model performs comparably to OMSSA for low false discovery rates. At the same time, we demonstrate that there are substantial differences with OMSSA for results on subsets of data. Therefore, we conclude the new model can be considered as being complementary to previously developed models. AD - [Sadygov, Rovshan G.] Univ Texas Med Branch, Dept Biochem & Mol Biol, Galveston, TX 77555 USA. [Good, David M.; Swaney, Danielle L.; Coon, Joshua J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Coon, Joshua J.] Univ Wisconsin, Dept Biomol Chem, Madison, WI 53706 USA. AN - ISI:000266719400056 AU - Sadygov, R. G. AU - Good, D. M. AU - Swaney, D. L. AU - Coon, J. J. DA - Jun KW - tandem mass spectrometry electron transfer dissociation probabilistic model for peptide identification compound distribution Electron-transfer dissociation tandem mass-spectrometry amino-acid-sequences protein identification peptide identification capture dissociation ms-ms proteomics phosphorylation activation Biochemical Research Methods LB - ISI 2009 06 26 IS - 6 N1 - ON, JJ(1) L5 *Order Full Text [ ] English Article NIH [5T32GM08349, 5T32HG002706, 1R01GM080148]; University of Wisconsin ; Beckman Foundation ; Eli Lilly PY - 2009 SP - 3198-3205 ST - A New Probabilistic Database Search Algorithm for ETD Spectra T2 - Journal of Proteome Research TI - A New Probabilistic Database Search Algorithm for ETD Spectra VL - 8 ID - 3945 ER - TY - JOUR AB - A mesoscale model of DNA is presented (3SPN.1), extending the scheme previously developed by our group. Each nucleotide is mapped onto three interaction sites. Solvent is accounted for implicitly through a medium-effective dielectric constant and electrostatic interactions are treated at the level of Debye-Huckel theory. The force field includes a weak, solvent-induced attraction, which helps mediate the renaturation of DNA. Model parameterization is accomplished through replica exchange molecular dynamics simulations of short oligonucleotide sequences over a range of composition and chain length. The model describes the melting temperature of DNA as a function of composition as well as ionic strength, and is consistent with heat capacity profiles from experiments. The dependence of persistence length on ionic strength is also captured by the force field. The proposed model is used to examine the renaturation of DNA. It is found that a typical renaturation event occurs through a nucleation step, whereby an interplay between repulsive electrostatic interactions and colloidal-like attractions allows the system to undergo a series of rearrangements before complete molecular reassociation occurs. AD - [Sambriski, E. J.; de Pablo, J. J.] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA. [Schwartz, D. C.] Univ Wisconsin, Dept Chem, Genet Lab, Lab Mol & Computat Genom, Madison, WI 53706 USA. AN - ISI:000266376500003 AU - Sambriski, E. J. AU - Schwartz, D. C. AU - de Pablo, J. J. DA - Mar KW - Brownian dynamics simulations monte-carlo-simulation heat-capacity changes molecular-dynamics shear-flow b-dna translational diffusion supercoiled dna double helices nucleic-acids Biophysics LB - ISI 2009 06 12 IS - 5 N1 - English Article National Human Genome Research Institute [5T32HG002760, R01HG000225]; National Science Foundation through the University of Wisconsin-Madison Nanoscale Science and Engineering Center PY - 2009 SP - 1675-1690 ST - A Mesoscale Model of DNA and Its Renaturation T2 - Biophysical Journal TI - A Mesoscale Model of DNA and Its Renaturation VL - 96 ID - 3929 ER - TY - JOUR AB - DNA hybridization plays a central role in biology and, increasingly, in materials science. Yet, there is no precedent for examining the pathways by which specific single-stranded DNA sequences interact to assemble into a double helix. A detailed model of DNA is adopted in this work to examine such pathways and to determine the role of sequence, if any, on DNA hybridization. Transition path sampling simulations reveal that DNA rehybridization is prompted by a distinct nucleation event involving molecular sites with approximately four bases pairing with partners slightly offset from those involved in ideal duplexation. Nucleation is promoted in regions with repetitive base pair sequence motifs, which yield multiple possibilities for finding complementary base partners. Repetitive sequences follow a nonspecific pathway to renaturation consistent with a molecular "slithering'' mechanism, whereas random sequences favor a restrictive pathway involving the formation of key base pairs before renaturation fully ensues. AD - [Sambriski, E. J.; de Pablo, J. J.] Delaware Valley Coll, Dept Chem & Biol Engn, Doylestown, PA 18901 USA. [Sambriski, E. J.] Delaware Valley Coll, Dept Chem & Biochem, Doylestown, PA 18901 USA. [Schwartz, D. C.] Univ Wisconsin, Lab Mol & Computat Genom, Dept Chem, Madison, WI 53706 USA. [Schwartz, D. C.] Univ Wisconsin, Genet Lab, Madison, WI 53706 USA. AN - ISI:000271222500018 AU - Sambriski, E. J. AU - Schwartz, D. C. AU - de Pablo, J. J. DA - Oct KW - mesoscale modeling nucleic acids self-assembly Model denaturation landscape oligomers Multidisciplinary Sciences LB - ISI 2009 11 12 IS - 43 N1 - English Article PY - 2009 SP - 18125-18130 ST - Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis T2 - Proceedings of the National Academy of Sciences of the United States of America TI - Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis VL - 106 ID - 4066 ER - TY - JOUR AD - [Sambriski, E. J.; de Pablo, J. J.] Univ Wisconsin, Dept Biol & Chem [Schwartz, D. C.] Univ Wisconsin, Dept Chem, Lab Mol & Computat Gen, [Schwartz, D. C.] Univ Wisconsin, Genet Lab, Madison, WI 53706 USA. [Sambriski, E. J.] Delaware Valley Coll, Dept Chem & Biochem Sambriski, EJ, Univ Wisconsin, Dept Biol & Chem Engn, Madison, WI 53706 USA. AN - ISI:000272553000081 AU - Sambriski, E. J. AU - Schwartz, D. C. AU - de Pablo, J. J. DA - Dec DO - 10.1073/pnas.0912578106 LA - English LB - ISI 2010 02 02 IS - 49 M3 - Correction N1 - Sambriski, E. J. Schwartz, D. C. de Pablo, J. J. 1 Natl acad sciences; 2101 constitution ave nw, washington, dc 20418 usa 529xp PY - 2009 SN - 0027-8424 SP - 21007-21007 ST - Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis (vol 106, pg 18125, 2009) T2 - Proceedings of the National Academy of Sciences of the United States of America TI - Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis (vol 106, pg 18125, 2009) VL - 106 ID - 4164 ER - TY - JOUR AB - P>Protein ubiquitylation is a central regulatory mechanism that controls numerous processes in plants, including hormone signaling, developmental progression, responses to biotic and abiotic challenges, protein trafficking and chromatin structure. Despite data implicating thousands of plant proteins as targets, so far only a few have been conclusively shown to be ubiquitylated in planta. Here we describe a method to isolate ubiquitin-protein conjugates from Arabidopsis that exploits a stable transgenic line expressing a synthetic poly-UBQ gene encoding ubiquitin (Ub) monomers N-terminally tagged with hexahistidine. Following sequential enrichment by Ub-affinity and nickel chelate-affinity chromatography, the ubiquitylated proteins were trypsinized, separated by two-dimensional liquid chromatography, and analyzed by mass spectrometry. Our list of 54 non-redundant targets, expressed by as many as 90 possible isoforms, included those predicted by genetic studies to be ubiquitylated in plants (EIN3 and JAZ6) or shown to be ubiquitylated in other eukaryotes (ribosomal subunits, elongation factor 1 alpha, histone H1, HSP70 and CDC48), as well as candidates whose control by the Ub/26S proteasome system is not yet appreciated. Ub attachment site(s) were resolved for a subset of these proteins, but surprisingly little sequence consensus was detected, implying that specific residues surrounding the modified lysine are not important determinants for ubiquitylation. We also identified six of the seven available lysine residues on Ub itself as Ub attachment sites, together with evidence for a branched mixed-linkage chain, suggesting that the topologies of Ub chains can be highly complex in plants. Taken together, our method provides a widely applicable strategy to define ubiquitylation in any tissue of intact plants exposed to a wide range of conditions. AD - [Saracco, Scott A.; Hansson, Maria; Walker, Joseph M.; Vierstra, Richard D.] Univ Wisconsin, Dept Genet, Madison, WI 53706 USA. [Scalf, Mark; Smith, Lloyd M.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000267540600013 AU - Saracco, S. A. AU - Hansson, M. AU - Scalf, M. AU - Walker, J. M. AU - Smith, L. M. AU - Vierstra, R. D. DA - Jul KW - ubiquitin post-translation modification mass spectrometry Arabidopsis Large-scale analysis ubiquitinated proteins 26s proteasome identification technology in-vivo saccharomyces-cerevisiae polyubiquitin chains proteolytic pathway tagged ubiquitin reveals Plant Sciences LB - ISI 2009 07 17 IS - 2 N1 - English Article National Science Foundation Arabidopsis 2010 Program [MCB-0115870]; University of Wisconsin College of Agricultural and Life Sciences ; National Heart, Lung, and Blood Institute Proteomics Center [N01-HV-28182]; WennerGren Foundation, Sweden PY - 2009 SP - 344-358 ST - Tandem affinity purification and mass spectrometric analysis of ubiquitylated proteins in Arabidopsis T2 - Plant Journal TI - Tandem affinity purification and mass spectrometric analysis of ubiquitylated proteins in Arabidopsis VL - 59 ID - 3957 ER - TY - JOUR AB - We report a layer-by-layer approach to the assembly of ultrathin and erodible DNA-containing films on the surfaces of polymer microparticles. DNA-containing multilayered films were fabricated layer-by-layer on the surfaces of polystyrene microspheres (similar to 6 mu m) by iterative and alternating cycles of particle suspension, centrifugation and resuspension in solutions of plasmid DNA and a hydrolytically degradable polyamine. Film growth occurred in a stepwise manner, as demonstrated by characterization of the zeta potentials and fluorescence intensities of film-coated particles during film assembly. Characterization of film-coated particles by confocal fluorescence microscopy and scanning electron microscopy revealed the multilayered particle coatings to be smooth, uniform and free of large-scale physical defects. Film-coated microparticles sustained the release of transcriptionally active DNA into solution for approximately three days when incubated in physiologically relevant media. Previous studies have demonstrated that the adsorption of DNA onto the surfaces of cationic microparticles can be used to target the delivery of DNA to antigen-presenting cells. As a first step toward the application of this layer-by-layer approach to the development of methods for the delivery of DNA to antigen-presenting cells, we demonstrated that film-coated microparticles could be used to transport DNA into macrophage cells in vitro using a model mouse macrophage cell line. Our results suggest the basis of a general approach that could, with further development, prove useful for the delivery of DNA-encoded antigens to macrophages, or other antigen-presenting cells, and provide new materials-based methods for the formulation and delivery of DNA vaccines. (c) 2008 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. AD - [Saurer, Eric M.; Jewell, Christopher M.; Kuchenreuther, Jon M.; Lynn, David M.] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA. AN - ISI:000264622100012 AU - Saurer, E. M. AU - Jewell, C. M. AU - Kuchenreuther, J. M. AU - Lynn, D. M. DA - Mar KW - Thin films Layer-by-layer DNA Polyelectrolytes Microparticles Multilayered polyelectrolyte films co-glycolide microparticles plasmid dna cationic microparticles immune-responses gene delivery anionic polyelectrolytes biomedical applications poly(d,l-lactic acid) degradable polyamines Materials Science, Biomaterials LB - ISI 2009 04 09 IS - 3 N1 - English Article 1742-7061 PY - 2009 SP - 913-924 ST - Assembly of erodible, DNA-containing thin films on the surfaces of polymer microparticles: Toward a layer-by-layer approach to the delivery of DNA to antigen-presenting cells T2 - Acta Biomaterialia TI - Assembly of erodible, DNA-containing thin films on the surfaces of polymer microparticles: Toward a layer-by-layer approach to the delivery of DNA to antigen-presenting cells VL - 5 ID - 3899 ER - TY - JOUR AB - We describe here the Harvard integrated cavity output spectroscopy (ICOS) isotope instrument, a mid-IR infrared spectrometer using ICOS to make in situ measurements of the primary isotopologues of water vapor (H2O, HDO, and (H2O)-O-18) in the upper troposphere and lower stratosphere (UTLS). The long path length provided by ICOS provides the sensitivity and accuracy necessary to measure these or other trace atmospheric species at concentrations in the ppbv range. The Harvard ICOS isotope instrument has been integrated onto NASA's WB-57 high-altitude research aircraft and to date has flown successfully in four field campaigns from winter 2004-2005 to the present. Off-axis alignment and a fully passive cavity ensure maximum robustness against the vibrationally hostile aircraft environment. The very simple instrument design permitted by off-axis ICOS is also helpful in minimizing contamination necessary for accurate measurements in the dry UTLS region. The instrument is calibrated in the laboratory via two separate water addition systems and crosscalibrated against other instruments. Calibrations have established an accuracy of 5% for all species. The instrument has demonstrated measurement precision of 0.14 ppmv, 0.10 ppbv, and 0.16 ppbv in 4 s averages for H2O, HDO, and (H2O)-O-18, respectively. At a water vapor mixing ratio of 5 ppmv the isotopologue ratio precision is 50% and 30% for delta D and delta O-18, respectively. AD - [Sayres, David S.] Harvard Univ, Dept Earth & Planetary Sci, Cambridge, MA 02138 USA. Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA. AN - ISI:000266597100033 AU - Sayres, D. S. AU - Moyer, E. J. AU - Hanisco, T. F. AU - Clair, J. M. AU - Keutsch, F. N. AU - O'Brien, A. AU - Allen, N. T. AU - Lapson, L. AU - Demusz, J. N. AU - Rivero, M. AU - Martin, T. AU - Greenberg, M. AU - Tuozzolo, C. AU - Engel, G. S. AU - Kroll, J. H. AU - Paul, J. B. AU - Anderson, J. G. DA - Apr DO - 044102 KW - atmospheric humidity atmospheric measuring apparatus infrared spectrometers isotopes stratosphere troposphere water Output spectroscopy vapor transport sensitivity temperatures humidity exchange feedback climate clouds Instruments & Instrumentation Physics, Applied LB - ISI 2009 06 19 IS - 4 N1 - English Article PY - 2009 ST - A new cavity based absorption instrument for detection of water isotopologues in the upper troposphere and lower stratosphere T2 - Review of Scientific Instruments TI - A new cavity based absorption instrument for detection of water isotopologues in the upper troposphere and lower stratosphere VL - 80 ID - 3933 ER - TY - JOUR AB - The development of enantiomerically resolved, axially-chiral seven-membered N-heterocyclic carbene ((NHC)-N-7) ligands for palladium is described. These (NHC)-N-7 ligands are derived from enatiomerically pure 2,2'-diamino-6,6'-dimethylbiphenyl, which is transformed via a synthetic sequence consisting of ortho-arylation, N-alkylation, and cyclization to afford seven-membered-ring amidinium salts. Synthesis of the seven-membered amidinium salts benefits from microwave irradiation, and in-situ metalation of the amidinium salts yields (NHC)-N-7-Pd-II complexes. The chiral (NHC)-N-7-Pd complexes were examined as chiral catalysts under aerobic conditions in two intramolecular oxidative amination reactions of alkenes. In one case, enantioselectivities up to 63% ee were obtained, while the other substrate underwent cyclization to afford essentially racemic products. The catalytic data compare favorably to results obtained with a Pd-II catalyst bearing a chiral five-membered-ring NHC ligand and, thereby, highlight the potential significance of this new class of chiral NHC ligands. (C) 2009 Elsevier Ltd. All rights reserved. AD - [Scarborough, Christopher C.; Bergant, Ana; Sazama, Graham T.; Guzei, Ilia A.; Spencer, Lara C.; Stahl, Shannon S.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000267506300017 AU - Scarborough, C. C. AU - Bergant, A. AU - Sazama, G. T. AU - Guzei, I. A. AU - Spencer, L. C. AU - Stahl, S. S. DA - Jun KW - N-Heterocyclic carbene Palladium Organometallic chemistry Wacker oxidation Catalyzed allylic alkylation ring-opening/cross-metathesis chiral ruthenium catalysts anilide ortho-arylation olefin metathesis stereodirecting ligands alpha-arylation metal-complexes reagents efficient Chemistry, Organic LB - ISI 2009 07 17 IS - 26 N1 - English Article American Chemical Society Division of Organic Chemistry ; National Institutes of Health [R01 GM67173]; UW-Madison Graduate School Technology PY - 2009 SP - 5084-5092 ST - Synthesis of Pd-II complexes bearing an enantiomerically resolved seven-membered N-heterocyclic carbene ligand and initial studies of their use in asymmetric Wacker-type oxidative cyclization reactions T2 - Tetrahedron TI - Synthesis of Pd-II complexes bearing an enantiomerically resolved seven-membered N-heterocyclic carbene ligand and initial studies of their use in asymmetric Wacker-type oxidative cyclization reactions VL - 65 ID - 3954 ER - TY - JOUR AB - Palladium-catalyzed directed arylation of 2,2'-diacetamidobiaryls with aryl iodides provides efficient access to chiral ortho-substituted biaryl diamines. Aryl iodides with para and meta-substituents are tolerated. Deprotection of the acetyl groups under basic conditions furnishes the free diamines, which should find broad utility in asymmetric catalysis. AD - [Scarborough, Christopher C.; McDonald, Richard I.; Hartmann, Caroline; Sazama, Graham T.; Bergant, Ana; Stahl, Shannon S.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000264111400055 AU - Scarborough, C. C. AU - McDonald, R. I. AU - Hartmann, C. AU - Sazama, G. T. AU - Bergant, A. AU - Stahl, S. S. DA - Mar KW - Anilide ortho-arylation schiff-base complexes diels-alder reaction enantioselective hydroamination/cyclisation asymmetric catalysis alkene aziridination amidate complexes copper-complexes ligands hydrogenation Chemistry, Organic LB - ISI 2009 03 26 IS - 6 N1 - English Article 0022-3263 PY - 2009 SP - 2613-2615 ST - Steric Modulation of Chiral Biaryl Diamines via Pd-Catalyzed Directed C-H Arylation T2 - Journal of Organic Chemistry TI - Steric Modulation of Chiral Biaryl Diamines via Pd-Catalyzed Directed C-H Arylation VL - 74 ID - 3889 ER - TY - JOUR AB - We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize. AD - [Wilson, Richard K.] Washington Univ, Genome Ctr, St Louis, MO 63108 USA. Iowa State Univ, Ctr Plant Genom, Ames, IA 50011 USA. Iowa State Univ, Dept Agron, Ames, IA 50011 USA. Iowa State Univ, Dept Genet Dev & Cell Biol, Ames, IA 50011 USA. Iowa State Univ, Ctr Carbon Capturing Crops, Ames, IA 50011 USA. Robert Holley Ctr Agr & Hlth, N Atlantic Area, USDA, Ithaca, NY 14853 USA. Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA. Univ Arizona, Arizona Genom Inst, Sch Plant Sci, Tucson, AZ 85721 USA. Univ Arizona, Dept Ecol & Evolutionary Biol, BIO5 Inst Collaborat Res, Tucson, AZ 85721 USA. Iowa State Univ, Dept Elect & Comp Engn, Ames, IA 50011 USA. Univ Notre Dame, Dept Comp Sci & Engn, Notre Dame, IN 46556 USA. Washington State Univ, Sch Elect Engn & Comp Sci, Pullman, WA 99164 USA. Univ Florida, Dept Bot, Gainesville, FL 32611 USA. Univ Georgia, Dept Genet, Athens, GA 30602 USA. Cornell Univ, Boyce Thompson Inst, Ithaca, NY 14853 USA. Purdue Univ, Dept Bot & Plant Pathol, W Lafayette, IN 47907 USA. Univ Perpignan, CNRS, F-66025 Perpignan, France. Univ Georgia, Dept Plant Pathol, Athens, GA 30602 USA. NimbleGen, Madison, WI 53711 USA. Univ Wisconsin, Dept Hort, Madison, WI 53706 USA. Univ Calif Berkeley, Dept Plant Biol, Berkeley, CA 94720 USA. Purdue Univ, Dept Biol Sci, W Lafayette, IN 47907 USA. Purdue Univ, Dept Hort & Landscape Architecture, W Lafayette, IN 47907 USA. Iowa State Univ, Dept Biochem Biophys & Mol Biol, Ames, IA 50011 USA. Iowa State Univ, Dept Stat, Ames, IA 50011 USA. Univ So Calif, Dept Math, Los Angeles, CA 90089 USA. Univ So Calif, Dept Biol, Los Angeles, CA 90089 USA. Univ So Calif, Dept Comp Sci, Los Angeles, CA 90089 USA. Cornell Univ, Computat Biol Serv Unit, Ithaca, NY 14850 USA. Univ Hawaii, Honolulu, HI 96822 USA. Univ Wisconsin, Lab Mol & Computat Genom, Dept Chem, Genet Lab, Madison, WI 53706 USA. Univ Arizona, BIO5 Inst Collaborat Res, Tucson, AZ 85721 USA. Univ Minnesota, Dept Plant Biol, St Paul, MN 55108 USA. Michigan State Univ, Dept Hort, E Lansing, MI 48824 USA. Indian Inst Technol, Bombay 400076, Maharashtra, India. Washington Univ, Sch Med, Dept Genet, St Louis, MO 63110 USA. AN - ISI:000271951000044 AU - Schnable, Patrick S. AU - Ware, Doreen AU - Fulton, Robert S. AU - Stein, Joshua C. AU - Wei, Fusheng AU - Pasternak, Shiran AU - Liang, Chengzhi AU - Zhang, Jianwei AU - Fulton, Lucinda AU - Graves, Tina A. AU - Minx, Patrick AU - Reily, Amy Denise AU - Courtney, Laura AU - Kruchowski, Scott S. AU - Tomlinson, Chad AU - Strong, Cindy AU - Delehaunty, Kim AU - Fronick, Catrina AU - Courtney, Bill AU - Rock, Susan M. AU - Belter, Eddie AU - Du, Feiyu AU - Kim, Kyung AU - Abbott, Rachel M. AU - Cotton, Marc AU - Levy, Andy AU - Marchetto, Pamela AU - Ochoa, Kerri AU - Jackson, Stephanie M. AU - Gillam, Barbara AU - Chen, Weizu AU - Yan, Le AU - Higginbotham, Jamey AU - Cardenas, Marco AU - Waligorski, Jason AU - Applebaum, Elizabeth AU - Phelps, Lindsey AU - Falcone, Jason AU - Kanchi, Krishna AU - Thane, Thynn AU - Scimone, Adam AU - Thane, Nay AU - Henke, Jessica AU - Wang, Tom AU - Ruppert, Jessica AU - Shah, Neha AU - Rotter, Kelsi AU - Hodges, Jennifer AU - Ingenthron, Elizabeth AU - Cordes, Matt AU - Kohlberg, Sara AU - Sgro, Jennifer AU - Delgado, Brandon AU - Mead, Kelly AU - Chinwalla, Asif AU - Leonard, Shawn AU - Crouse, Kevin AU - Collura, Kristi AU - Kudrna, Dave AU - Currie, Jennifer AU - He, Ruifeng AU - Angelova, Angelina AU - Rajasekar, Shanmugam AU - Mueller, Teri AU - Lomeli, Rene AU - Scara, Gabriel AU - Ko, Ara AU - Delaney, Krista AU - Wissotski, Marina AU - Lopez, Georgina AU - Campos, David AU - Braidotti, Michele AU - Ashley, Elizabeth AU - Golser, Wolfgang AU - Kim, HyeRan AU - Lee, Seunghee AU - Lin, Jinke AU - Dujmic, Zeljko AU - Kim, Woojin AU - Talag, Jayson AU - Zuccolo, Andrea AU - Fan, Chuanzhu AU - Sebastian, Aswathy AU - Kramer, Melissa AU - Spiegel, Lori AU - Nascimento, Lidia AU - Zutavern, Theresa AU - Miller, Beth AU - Ambroise, Claude AU - Muller, Stephanie AU - Spooner, Will AU - Narechania, Apurva AU - Ren, Liya AU - Wei, Sharon AU - Kumari, Sunita AU - Faga, Ben AU - Levy, Michael J. AU - McMahan, Linda AU - Van Buren, Peter AU - Vaughn, Matthew W., et al. DA - Nov KW - Transposable elements arabidopsis-thaliana zea-mays genes plant retrotransposons methylation divergence evolution genetics Multidisciplinary Sciences LB - ISI 2009 11 26 IS - 5956 N1 - English Article NSF [DBI-0527192, DBI-0607123, DBI-0421671, DBI-0321467, DBI-0321711, DBI-0333074, DBI-0501818, DBI-0501857, DBI-0701736, DBI-0703273, DBI-0703908]; USDA Cooperative State Research, Education, and Extension Service [2005-35301-15715, 2007-35301-18372]; USDA-ARS [408934, 413089]; Office of Science (Biological and Environmental Research) ; U. S. Department of Energy [DE-FG02-08ER64702] PY - 2009 SP - 1112-1115 ST - The B73 Maize Genome: Complexity, Diversity, and Dynamics T2 - Science TI - The B73 Maize Genome: Complexity, Diversity, and Dynamics VL - 326 ID - 4089 ER - TY - JOUR AB - The utility of cobalt dinitrosyl complexes for the [3 + 2] annulation of alkenes with unsaturated enones and ketimines has been demonstrated. Reaction of a series of cobalt dinitrosyl/alkene adducts with conjugate acceptors in the presence of Sc(OTf)(3)/LHMDS formed two new C-C bonds at the carbons alpha to the nitrosyl groups of the substrate, leading to unusual tri- and tetracycles. Retrocycloaddition of these products in the presence of norbornadiene yielded functionalized tetrasubstituted bicyclic olefins. AD - [Schomaker, Jennifer M.; Toste, F. Dean; Bergman, Robert G.] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. AN - ISI:000268796700045 AU - Schomaker, J. M. AU - Toste, F. D. AU - Bergman, R. G. DA - Aug KW - Nitrosyl metal-complexes c-h bond organocobalt compounds nitric-oxide olefins Chemistry, Organic LB - ISI 2009 08 20 IS - 16 N1 - English Article NIH [GM 25459, GM F32GM080059]; Director, Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231] PY - 2009 SP - 3698-3700 ST - Cobalt-Mediated [3+2]-Annulation Reaction of Alkenes with alpha,beta-Unsaturated Ketones and Imines T2 - Organic Letters TI - Cobalt-Mediated [3+2]-Annulation Reaction of Alkenes with alpha,beta-Unsaturated Ketones and Imines VL - 11 ID - 4003 ER - TY - JOUR AB - Bacterial RNA polymerase and a "sigma" transcription factor form an initiation-competent "open" complex at a promoter by disruption of about 14 base pairs. Strand separation is likely initiated at the highly conserved -11 A-T base pair. Amino acids in conserved region 2.3 of the main Escherichia coli sigma factor, sigma(70), are involved in this process, but their roles are unclear. To monitor the fates of particular bases upon addition of RNA polymerase, promoters bearing single substitutions of the fluorescent A-analog 2-aminopurine (2-AP) at -11 and two other positions in promoter DNA were examined. Evidence was obtained for an open intermediate on the pathway to open complex formation, in which these 2-APs are no longer stacked onto their neighboring bases. The tyrosine at residue 430 in region 2.3 of sigma(70) was shown to be involved in quenching the fluorescence of a 2-AP substituted at -11, presumably through a stacking interaction. These data refine the structural model for open complex formation and reveal a novel interaction involved in DNA melting by RNA polymerase. (C) 2008 Elsevier Ltd. All rights reserved. AN - ISI:000262916900002 AU - Schroeder, L. A. AU - Gries, T. J. AU - Saecker, R. M. AU - Record, M. T. AU - Harris, M. E. AU - deHaseth, P. L. DA - Jan DO - 10.1016/j.jmb.2008.10.023 LB - ISI 2009 02 20 IS - 2 N1 - Schroeder, Lisa A. Gries, Theodore J. Saecker, Ruth M. Record, M. Thomas, Jr. Harris, Michael E. deHaseth, Pieter L. PY - 2009 SN - 0022-2836 SP - 339-349 ST - Evidence for a Tyrosine-Adenine Stacking Interaction and for a Short-lived Open Intermediate Subsequent to Initial Binding of Escherichia coli RNA Polymerase to Promoter DNA T2 - Journal of Molecular Biology TI - Evidence for a Tyrosine-Adenine Stacking Interaction and for a Short-lived Open Intermediate Subsequent to Initial Binding of Escherichia coli RNA Polymerase to Promoter DNA UR - ://000262916900002 VL - 385 ID - 3782 ER - TY - JOUR AB - Mechanistic and spectroscopic investigations of reactive C3H2 hydrocarbons necessitated the preparation of diazopropyne isotopomers bearing mono-C-13 substitution at each of the three unique positions. The diazo compounds and their tosylhydrazone precursors were prepared from the mono-C-13 isotopomers of propynal (in the form of either the aldehyde or the diethyl acetal). The introduction of C-13-labeling at either alkyne position in propynal utilized the Corey-Fuchs procedure for chain homologation. AD - [Seburg, Randal A.; Hodges, Jonathan A.; McMahon, Robert J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000269515500020 AU - Seburg, R. A. AU - Hodges, J. A. AU - McMahon, R. J. KW - Interstellar space c3h2 isomers carbon bond reactivity acetals alkynyl route automerizations isomerizations identification Chemistry, Multidisciplinary LB - ISI 2009 09 10 IS - 8 N1 - English Article U.S. National Science Foundation ; NSF ; Lubrizol Corporation PY - 2009 SP - 1626-1643 ST - Propynal Equivalents and Diazopropyne: Synthesis of All Mono-C-13 Isotopomers T2 - Helvetica Chimica Acta TI - Propynal Equivalents and Diazopropyne: Synthesis of All Mono-C-13 Isotopomers VL - 92 ID - 4014 ER - TY - JOUR AB - Spectroscopic data for triplet isotopomers H-C-C-C-H, H-C-13-C-C-H, and H-C-C-13-C-H are consistent with computational predictions for a symmetric structure in which the terminal carbons are equivalent (C or C-2v) and are inconsistent with a planar (C-s) structure in which they are not. Experimentally observed C-13 isotope shifts in the IR spectra and C-13 hyperfine coupling constants in the EPR spectra exhibit good agreement with values predicted by theory for a C-2 structure. The C-13 hyperfine coupling constants also provide an independent experimental estimate for the bond angles in the molecule. The isotope-dependence of the zero-field splitting parameters reveals the influence of molecular motion in modulating the values of these parameters. The interpretation of motional effects provides a basis for rationalizing the anomalously low E value, which had previously been interpreted in terms of an axially symmetric (D-infinity h) structure. Computational studies involving Natural Bond Orbital and Natural Resonance Theory analyses provide insight into the spin densities and the complex electronic structure of this reactive intermediate. AD - [Seburg, Randal A.; McMahon, Robert J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Patterson, Eric V.] Truman State Univ, Dept Chem, Kirksville, MO 63501 USA. AN - ISI:000267633300061 AU - Seburg, R. A. AU - Patterson, E. V. AU - McMahon, R. J. DA - Jul KW - Electron-paramagnetic resonance ground-state triplet ab-initio interstellar space quantum monodromy molecules cco c3h2 isomers propargylene methylene carbenes Chemistry, Multidisciplinary LB - ISI 2009 07 17 IS - 26 N1 - English Article National Science Foundation ; Lubrizol Corporation PY - 2009 SP - 9442-9455 ST - Structure of Triplet Propynylidene (HCCCH) as Probed by IR, UV/vis, and EPR Spectroscopy of Isotopomers T2 - Journal of the American Chemical Society TI - Structure of Triplet Propynylidene (HCCCH) as Probed by IR, UV/vis, and EPR Spectroscopy of Isotopomers VL - 131 ID - 3960 ER - TY - JOUR AB - The considerable progress in high-throughput proteomics analysis via liquid chromatography-electrospray ionization-tandem mass spectrometry over the past decade has been fueled to a large degree by continuous improvements in instrumentation. High-throughput identification experiments are based on peptide sequencing and are largely accomplished through the use of tandem mass spectrometry, with ion trap and trap-based instruments having become broadly adopted analytical platforms. To satisfy increasingly demanding requirements for depth of characterization and throughput, we present a newly developed dual-pressure linear ion trap mass spectrometer (LTQ Velos) that features increased sensitivity, afforded by a new source design, and demonstrates practical cycle times 2 times shorter than that of an LTQ XL, while improving or maintaining spectral quality for MS/MS fragmentation spectra. These improvements, resulted in a substantial increase in the detection and identification of both proteins and unique peptides from the complex proteome of Caenorhabditis elegans, as compared to existing platforms. The greatly increased ion flux into the mass spectrometer in combination with improved isolation of low-abundance precursor ions resulted in increased detection of low-abundance peptides. These improvements cumulatively resulted in a substantially greater penetration into the baker's yeast (Saccharomyces cerevisiae) proteome compared to LTQ XL. Alternatively, faster cycle times on the new instrument allowed for higher throughput for a given depth of proteome analysis, with more peptides and proteins identified in 60 min using an LTQ Velos than in 180 min using an LTQ XL. When mass analysis was carried out with resolution in excess of 25 000 full width at half-maximum (fwhm), it became possible to isotopically resolve a small intact protein and its fragments, opening possibilities for top down experiments. AD - [Second, Tonya Pekar; Blethrow, Justin D.; Schwartz, Jae C.; Zabrouskov, Vlad] Thermo Fisher Sci, San Jose, CA 95134 USA. [Merrihew, Gennifer E.; MacCoss, Michael J.] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA. [Swaney, Danielle L.; Russell, Jason D.; Coon, Joshua J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Swaney, Danielle L.; Russell, Jason D.; Coon, Joshua J.] Univ Wisconsin, Dept Biomol Chem, Madison, WI 53706 USA. AN - ISI:000269656700030 AU - Second, T. P. AU - Blethrow, J. D. AU - Schwartz, J. C. AU - Merrihew, G. E. AU - MacCoss, M. J. AU - Swaney, D. L. AU - Russell, J. D. AU - Coon, J. J. AU - Zabrouskov, V. DA - Sep KW - Shotgun proteomics c. elegans phosphorylation identification accuracy Chemistry, Analytical LB - ISI 2009 09 17 IS - 18 N1 - English Article National Institutes of Health [P41 RR011823, R01 DK069386, R01 GM080148, P01 GM081629]; NIH predoctoral fellowship ; Genomic Sciences Training Program [5T32 HG002760] PY - 2009 SP - 7757-7765 ST - Dual-Pressure Linear Ion Trap Mass Spectrometer Improving the Analysis of Complex Protein Mixtures T2 - Analytical Chemistry TI - Dual-Pressure Linear Ion Trap Mass Spectrometer Improving the Analysis of Complex Protein Mixtures VL - 81 ID - 4021 ER - TY - JOUR AB - Reactions of 2-(3,5-dimethylpyrazol-1-ylmethyl)pyridine (L1), 2-(3,5-diphenylpyrazol-1-ylmethyl)pyridine (L2), 2-(3,5-di-tert-butylpyrazol-1-ylmethyl)pyridine (L3) and 2-(3-p-tolylpyrazol-1-ylmethyl)pyridine (L4) with K-2[PtCl4] in a mixture of ethanol and water formed the dichloro platinum complexes [PtCl2(L1)] (1), [PtCl2(L2)] (2), [PtCl2(L3)] (3) and [PtCl2(L4)] (4). Complex 1, [PtCl2(L1)], could also be prepared in a mixture of acetone and water. Performing the reactions of L2 and L3 in a mixture of acetone and water, however, led to C-H activation of acetone under mild conditions to form the neutral acetonyl complexes [Pt(CH2COCH3) Cl(L2)] (2a) and [Pt(CH2COCH3) Cl(L3)] (3a). The same ligands reacted with HAuCl4 center dot 4H(2)O in a mixture of ethanol and water to form the gold salts [AuCl2(L1)][AuCl4] (5) [AuCl2(L2)][Cl] (6) [AuCl2(L3)][Cl] (7) and [AuCl2(L4)][AuCl4] (8); however, with the pyrazolyl unit in the para position of the pyridinyl ring in 4-(3,5-dimethylpyrazol-1-ylmethyl)pyridine (L5), 4-(3,5-diphenylpyrazol-1-ylmethyl)pyridine (L6) neutral gold complexes [AuCl3(L5)] (9) and [AuCl2(L6)] (10) were formed; signifying the role the position of the pyrazolyl group plays in product formation in the gold reactions. X-ray crystallographic structural determination of L6, 2, 3 3a, 8 and 10 were very important in confirming the structures of these compounds; particularly for 3a and 8 where the presence of the acetonyl group confirmed C-H activation and for 8 where the counter ion is AuCl4-. Cytotoxicity studies of L2, L4 and complexes 1-10 against HeLa cells showed the Au complexes were much less active than the Pt complexes. (C) 2009 Elsevier B. V. All rights reserved. AD - [Segapelo, Tebogo V.; Van Zyl, Werner E.; Darkwa, James] Univ Johannesburg, Dept Chem, ZA-2006 Johannesburg, South Africa. [Guzei, Ilia A.; Spencer, Lara C.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000265659900054 AU - Segapelo, T. V. AU - Guzei, I. A. AU - Spencer, L. C. AU - Van Zyl, W. E. AU - Darkwa, J. DA - Jul KW - (Pyrazol-1-ylmethyl)pyridine ligands Platinum complexes Gold complexes C-H activation Antitumor activity Tumor-cell lines x-ray structures solution chemistry molecular-structure crystal-structure dna-binding in-vitro dithiocarbamate derivatives copper(ii) complexes bipyridyl ligands Chemistry, Inorganic & Nuclear LB - ISI 2009 05 14 IS - 9 N1 - English Article AuTek (Mintek and Harmony gold, South Africa) ; University of Johannesburg PY - 2009 SP - 3314-3324 ST - (Pyrazolylmethyl)pyridine platinum(II) and gold(III) complexes: Synthesis, structures and evaluation as anticancer agents T2 - Inorganica Chimica Acta TI - (Pyrazolylmethyl)pyridine platinum(II) and gold(III) complexes: Synthesis, structures and evaluation as anticancer agents VL - 362 ID - 3984 ER - TY - JOUR AB - Photochemically induced dynamic nuclear polarization (photo-CIDNP) is usually employed as a probe of solvent exposure in biomolecular NMR. The potential of the photo-CIDNP effect for sensitivity enhancement, however, remains poorly explored. Here, we introduce H-1-photo-CIDNP in heteronuclear correlation spectroscopy at low laser irradiation power (1 W), and compare the sensitivity of various H-1-photo-CIDNP-enhanced- (HPE) H-1-N-15 heteronuclear correlation pulse sequences, including HSQC, HMQC, and SOFAST-HMQC, in terms of their ability to detect the Trp indole H-epsilon 1 resonance. Both Trp and the Trp-containing protein apoHmpH were analyzed using flavin mononucleotide as photosensitizer in aqueous solutions either containing or lacking urea. We find that H-1-N-15 photo-CIDNP-SOFAST-HMQC, denoted here as HPESOFAST-HMQC, yields a 2-fold higher signal-to-noise per unit time than the parent SOFAST-HMQC, for the solvent-exposed Trp of urea-unfolded apoHmpH. Thus, HPE-SOFAST-HMQC is the most sensitive heteronuclear correlation pulse sequence-for the detection of solvent-exposed Trp. AD - [Sekhar, Ashok; Cavagnero, Silvia] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000266930200016 AU - Sekhar, A. AU - Cavagnero, S. DA - Jun KW - Nuclear-polarization spectroscopy amino-acids multidimensional nmr aqueous-solutions surface probe proteins relaxation gradient spectra illumination Chemistry, Physical LB - ISI 2009 07 03 IS - 24 N1 - English Article National Institutes of Health [GM068538] PY - 2009 SP - 8310-8318 ST - H-1 Photo-CIDNP Enhancements in Heteronuclear Correlation NMR Spectroscopy T2 - Journal of Physical Chemistry B TI - H-1 Photo-CIDNP Enhancements in Heteronuclear Correlation NMR Spectroscopy VL - 113 ID - 3950 ER - TY - JOUR AB - Photochemically induced dynamic nuclear polarization (photo-CIDNP) of nuclei other than H-1 offers a tremendous potential for sensitivity enhancement in liquid state NMR under mild, physiologically relevant conditions. Photo-CIDNP enhancements of N-15 magnetization are much larger than those typically observed for H-1. However, the low gyromagnetic ratio of N-15 prevents a full fruition of the potential signal-to-noise gains attainable via N-15 photo-CIDNP. Here, we propose two novel pulse sequences, EPIC-and CHANCE-HSQC, tailored to overcome the above limitation. EPIC-HSQC exploits the strong H-1 polarization and its subsequent transfer to non-equilibrium N-z magnetization prior to N-15 photo-CIDNP laser irradiation. CHANCE-HSQC synergistically combines H-1 and N-15 photo-CIDNP. The above pulse sequences, tested on tryptophan (Trp) and the Trp-containing protein apoHmpH, were found to display up to 2-fold higher sensitivity than the reference NPE-SE-HSQC pulse train (based on simple N-15 photo-CIDNP followed by N-H polarization transfer), and up to a ca. 3-fold increase in sensitivity over the corresponding dark pulse schemes (lacking laser irradiation). The observed effects are consistent with the predictions from a theoretical model of photo-CIDNP and prove the potential of N-15 and H-1 photo-CIDNP in liquid state heteronuclear correlation NMR. (C) 2009 Elsevier Inc. All rights reserved. AD - [Sekhar, Ashok; Cavagnero, Silvia] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000272260900005 AU - Sekhar, Ashok AU - Cavagnero, Silvia DA - Oct KW - Photo-CIDNP EPIC-HSQC CHANCE-HSQC Sensitivity enhancement Dynamic nuclear-polarization nmr relaxation data photo-cidnp nmr unfolded proteins surface probe amino-acids density state spectroscopy absorption Biochemical Research Methods Physics, Atomic, Molecular & Chemical Spectroscopy LB - ISI 2009 12 11 IS - 2 N1 - English Article National Institutes of Health [GM068535] PY - 2009 SP - 207-213 ST - EPIC- and CHANCE-HSQC: Two N-15-photo-CIDNP-enhanced pulse sequences for the sensitive detection of solvent-exposed tryptophan T2 - Journal of Magnetic Resonance TI - EPIC- and CHANCE-HSQC: Two N-15-photo-CIDNP-enhanced pulse sequences for the sensitive detection of solvent-exposed tryptophan VL - 200 ID - 4073 ER - TY - JOUR AB - A soft x-ray absorption and x-ray magnetic circular dichroism (XMCD) study of the ferromagnetism in solution-grown EuS nanocrystals (NCs) is reported. The absorption edges of Eu M-5 and M-4, S K, O K, and P K were probed to determine elementally specific contributions to the magnetism of EuS NCs. Differential spin absorption was observed by XMCD at the Eu M-5,M-4 edges confirming the presence of a magnetic moment on the Eu2+ 4f shell. No dichroic signal was observed for S, O, or P. Vibrating sample magnetometry of ensembles of NCs shows ferromagnetic properties consistent with the XMCD studies. AD - [Selinsky, Rachel S.; Bierman, Matthew J.; Jin, Song] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Keavney, David J.] Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA. AN - ISI:000272052200037 AU - Selinsky, Rachel S. AU - Keavney, David J. AU - Bierman, Matthew J. AU - Jin, Song DA - Nov DO - 202501 KW - europium compounds ferromagnetic materials magnetic circular dichroism magnetic moments magnetic semiconductors magnetometers nanofabrication nanostructured materials wide band gap semiconductors X-ray absorption spectra Magnetic-properties nanoparticles semiconductors spintronics electronics gds Physics, Applied LB - ISI 2009 11 26 IS - 20 N1 - English Article NSF [DMR-0548232]; NIH [CA126701]; U. S. Department of Energy ; Office of Science ; Office of Basic Energy Sciences [DE-AC0206CH11357] PY - 2009 ST - Element-specific magnetometry of EuS nanocrystals T2 - Applied Physics Letters TI - Element-specific magnetometry of EuS nanocrystals VL - 95 ID - 4091 ER - TY - JOUR AB - There is considerable interest in uncovering the pathway of amyloid formation because the toxic properties of amyloid likely stems from prefibril intermediates and not the fully formed fibrils. Using a recently invented method of collecting 2-dimensional infrared spectra and site-specific isotope labeling, we have measured the development of secondary structures for 6 residues during the aggregation process of the 37-residue polypeptide associated with type 2 diabetes, the human islet amyloid polypeptide (hIAPP). By monitoring the kinetics at 6 different labeled sites, we find that the peptides initially develop well-ordered structure in the region of the chain that is close to the ordered loop of the fibrils, followed by formation of the 2 parallel beta-sheets with the N-terminal beta-sheet likely forming before the C-terminal sheet. This experimental approach provides a detailed view of the aggregation pathway of hIAPP fibril formation as well as a general methodology for studying other amyloid forming proteins without the use of structure-perturbing labels. AD - [Gupta, Ruchi; Raleigh, Daniel P.] SUNY Stony Brook, Dept Chem, Stony Brook, NY 11794 USA. [Raleigh, Daniel P.] SUNY Stony Brook, Grad Program Biochem & Struct Biol, Stony Brook, NY 11794 USA. [Raleigh, Daniel P.] SUNY Stony Brook, Grad Program Biophys, Stony Brook, NY 11794 USA. [Shim, Sang-Hee; Ling, Yun L.; Strasfeld, David B.; Zanni, Martin T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000265506800036 AU - Shim, S. H. AU - Gupta, R. AU - Ling, Y. L. AU - Strasfeld, D. B. AU - Raleigh, D. P. AU - Zanni, M. T. DA - Apr KW - aggregation amylin fibers human islet amyloid polypeptide nucleation Fibril formation beta-hairpin polypeptide amylin protein fibrillogenesis nucleation inhibitor mechanism membrane Multidisciplinary Sciences LB - ISI 2009 05 14 IS - 16 N1 - English Article National Institutes of Health [GM 070941, GM 078114, DK 79895]; Sloan Foundation PY - 2009 SP - 6614-6619 ST - Two-dimensional IR spectroscopy and isotope labeling defines the pathway of amyloid formation with residue-specific resolution T2 - Proceedings of the National Academy of Sciences of the United States of America TI - Two-dimensional IR spectroscopy and isotope labeling defines the pathway of amyloid formation with residue-specific resolution VL - 106 ID - 3979 ER - TY - JOUR AB - We have recently developed a new and simple way of collecting 2D infrared and visible spectra that utilizes a pulse shaper and a partly collinear beam geometry. 2D IR and Vis spectroscopies are powerful tools for studying molecular structures and their dynamics. They can be used to correlate vibrational or electronic eigenstates, measure energy transfer rates, and quantify the dynamics of lineshapes, for instance, all with femtosecond time-resolution. As a result, they are finding use in systems that exhibit fast dynamics, such as sub-millisecond chemical and biological dynamics, and in hard-to-study environments, such as in membranes. While powerful, these techniques have been difficult to implement because they require a series of femtosecond pulses to be spatially and temporally overlapped with precise time-resolution and interferometric phase stability. However, many of the difficulties associated with implementing 2D spectroscopies are eliminated by using a pulse shaper and a simple beam geometry, which substantially lowers the technical barriers required for researchers to enter this exciting field while simultaneously providing many new capabilities. The aim of this paper is to provide an overview of the methods for collecting 2D spectra so that an outsider considering using 2D spectroscopy in their own research can judge which approach would be most suitable for their research aims. This paper focuses primarily on 2D IR spectroscopy, but also includes our recent work on adapting this technology to collecting 2D Vis spectra. We review work that has already been published as well as cover several topics that we have not reported previously, including phase cycling methods to remove background signals, eliminate unwanted scatter, and shift data collection into the rotating frame. AN - ISI:000262649300001 AU - Shim, S. H. AU - Zanni, M. T. DO - 10.1039/b813817f LB - ISI 2009 02 05 IS - 5 N1 - Shim, Sang-Hee Zanni, Martin T. PY - 2009 SN - 1463-9076 SP - 748-761 ST - How to turn your pump-probe instrument into a multidimensional spectrometer: 2D IR and Vis spectroscopies via pulse shaping T2 - Physical Chemistry Chemical Physics TI - How to turn your pump-probe instrument into a multidimensional spectrometer: 2D IR and Vis spectroscopies via pulse shaping UR - ://000262649300001 VL - 11 ID - 3794 ER - TY - JOUR AB - According to a prevailing theory, (2S, 4R)-4-hydroxyproline (Hyp) residues stabilize the collagen triple helix via a stereoelectronic effect that preorganizes appropriate backbone torsion angles for triple-helix formation. This theory is consistent with the marked stability that results from replacing the hydroxyl group with the more electron-withdrawing fluoro group, as in (2S, 4R)-4-fluoroproline (Flp). Nonetheless, the hyperstability of triple helices containing Flp has been attributed by others to the hydrophobic effect rather than a stereoelectronic effect. We tested this hypothesis by replacing Hyp with 4,4-difluoroproline (Dfp) in collagen-related peptides. Dfp retains the hydrophobicity of Flp, but lacks the ability of Flp to pre-organize backbone torsion angles. Unlike Flp, Dfp does not endow triple helices with elevated stability, indicating that the hyperstability conferred by Flp is not due to the hydrophobic effect. (C) 2009 Elsevier Ltd. All rights reserved. AD - [Shoulders, Matthew D.; Raines, Ronald T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Kamer, Kimberli J.] Univ Wisconsin, Dept Biomed Engn, Madison, WI 53706 USA. [Raines, Ronald T.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. AN - ISI:000267762600038 AU - Shoulders, M. D. AU - Kamer, K. J. AU - Raines, R. T. DA - Jul KW - Collagen 4,4-Difluoroproline 4-Fluoroproline Hydrophobic effect Peptide Preorganization Protein stability Stereoelectronic effect Triple helix Triple-helix coiled-coil host-guest hydroxyproline stabilization peptides proteins residues proline design Chemistry, Medicinal Chemistry, Organic LB - ISI 2009 07 24 IS - 14 N1 - English Article PY - 2009 SP - 3859-3862 ST - Origin of the stability conferred upon collagen by fluorination T2 - Bioorganic & Medicinal Chemistry Letters TI - Origin of the stability conferred upon collagen by fluorination VL - 19 ID - 3962 ER - TY - JOUR AD - [Shoulders, Matthew D.; Raines, Ronald T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Raines, Ronald T.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. AN - ISI:000265773200115 AU - Shoulders, M. D. AU - Raines, R. T. KW - Conformational stability code LB - ISI 2009 05 29 N1 - ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY English Proceedings Paper NIH [AR44276]; Department of Homeland Security. PY - 2009 SP - 251-252 ST - Modulating Collagen Triple-Helix Stability with 4-Chloro, 4-Fluoro, and 4-Methylprolines T2 - Peptides for Youth TI - Modulating Collagen Triple-Helix Stability with 4-Chloro, 4-Fluoro, and 4-Methylprolines VL - 611 ID - 3920 ER - TY - JOUR AB - Collagen is the most abundant protein in animals. This fibrous, structural protein comprises a right-handed bundle of three parallel, left-handed polyproline II-type helices. Much progress has been made in elucidating the structure of collagen triple helices and the physicochemical basis for their stability. New evidence demonstrates that stereoelectronic effects and preorganization play a key role in that stability. The fibrillar structure of type I collagen-the prototypical collagen fibril has been revealed in detail. Artificial collagen fibrils that display some properties of natural collagen fibrils are now accessible using chemical synthesis and self-assembly. A rapidly emerging understanding of the mechanical and structural properties of native collagen fibrils will guide further development of artificial collagenous materials for biomedicine and nanotechnology. AD - [Shoulders, Matthew D.; Raines, Ronald T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Raines, Ronald T.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. AN - ISI:000268069200033 AU - Shoulders, M. D. AU - Raines, R. T. KW - biomaterials extracellullar matrix fibrillogenesis proline stereoelectronic effects triple helix Triple-helix formation hydroxylation-induced stabilization basement-membrane collagen higher-order structures amino-acid-sequence i collagen osteogenesis imperfecta crystal-structure molecular-structure model peptides Biochemistry & Molecular Biology LB - ISI 2009 07 31 N1 - English Review Department of Homeland Security ; Division of Medicinal Chemistry, American Chemical Society ; NIH [AR044276] PY - 2009 SP - 929-958 ST - Collagen Structure and Stability T2 - Annual Review of Biochemistry TI - Collagen Structure and Stability VL - 78 ID - 3977 ER - TY - JOUR AB - Single molecule-based protocols have been gaining popularity as a way to visualize DNA replication at the global genomic-and locus-specific levels. These protocols take advantage of the ability of many organisms to incorporate nucleoside analogs during DNA replication, together with a method to display stretched DNA on glass for immunostaining and microscopy. We describe here a microfluidic platform that can be used to stretch and to capture labeled DNA molecules for replication analyses. This platform consists of parallel arrays of three-sided, 3- or 4-mu m high, variable-width capillary channels fabricated from polydimethylsiloxane by conventional soft lithography, and of silane-modified glass coverslips to reversibly seal the open side of the channels. Capillary tension in these microchannels facilitates DNA loading, stretching and glass coverslip deposition from microliter-scale DNA samples. The simplicity and extensibility of this platform should facilitate DNA replication analyses using small samples from a variety of biological and clinical sources. AD - [Sidorova, Julia M.; Monnat, Raymond J., Jr.] Univ Washington, Dept Pathol, Seattle, WA 98195 USA. [Li, Nianzhen; Folch, Albert] Univ Washington, Dept Bioengn, Seattle AN - ISI:000266546200005 AU - Sidorova, J. M. AU - Li, N. Z. AU - Schwartz, D. C. AU - Folch, A. AU - Monnat, R. J. KW - S-phase polymerases chromosome damage cells Biochemical Research Methods LB - ISI 2009 06 19 IS - 6 N1 - English Article NIH [P20 CA103728Subaward 000618167]; NHGRI [R01 (HG000225), R21/R33 EB0003307]; NCI [PO1 CA88752] PY - 2009 SP - 849-861 ST - Microfluidic-assisted analysis of replicating DNA molecules T2 - Nature Protocols TI - Microfluidic-assisted analysis of replicating DNA molecules VL - 4 ID - 3934 ER - TY - JOUR AD - [Skinner, James L.; Auer, Benjamin M.; Lin, Yu-Shan] Univ Wisconsin, Inst Theoret Chem, Madison, WI 53706 USA. [Skinner, James L.; Auer, Benjamin M.; Lin, Yu-Shan] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000266543800002 AU - Skinner, J. L. AU - Auer, B. M. AU - Lin, Y. S. KW - Molecular-dynamics simulations ultrafast infrared-spectroscopy time-correlation function oh stretching band frequency generation spectroscopy echo correlation spectroscopy instantaneous normal-mode pump-probe spectroscopy 3-pulse photon-echoes ab-initio LB - ISI 2009 06 19 N1 - ADVANCES IN CHEMICAL PHYSICS English Review National Science Foundation [CHE-0446666, CHE0750307] PY - 2009 SP - 59-103 ST - Vibrational Line Shapes, Spectral Diffusion, and Hydrogen Bonding in Liquid Water T2 - Advances in Chemical Physics, Vol 142 TI - Vibrational Line Shapes, Spectral Diffusion, and Hydrogen Bonding in Liquid Water VL - 142 ID - 3941 ER - TY - JOUR AB - The analysis of single-stranded DNA attached to a polycrystalline diamond surface by reflection anisotropy spectroscopy (RAS) demonstrates that the DNA is oriented essentially vertically to the surface. RAS is able to detect the hybridisation between the attached strand and the homologous sequence. Copyright (C) EPLA, 2009 AD - [Smith, C. I.; Bowfield, A.; Cuquerella, M. C.; Mansley, C. P.; Farrell, T.; Harrison, P.; Martin, D. S.; Weightman, P.] Univ Liverpool, Dept Phys, Liverpool L69 7ZE, Merseyside, England. L69 7ZB, Merseyside, England. Madison, WI 53706 USA. AN - ISI:000263692500038 AU - Smith, C. I. AU - Bowfield, A. AU - Cuquerella, M. C. AU - Mansley, C. P. AU - Farrell, T. AU - Harrison, P. AU - Martin, D. S. AU - Fernig, D. G. AU - Edwards, C. AU - Butler, J. E. AU - Hamers, R. J. AU - Sun, B. AU - Wang, X. AU - Weightman, P. DA - Jan DO - 18006 KW - Crystal-growth microarrays adsorption Physics, Multidisciplinary LB - ISI 2009 03 13 IS - 1 N1 - English Article 0295-5075 PY - 2009 ST - Detection of DNA hybridisation on a functionalised diamond surface using reflection anisotropy spectroscopy T2 - Epl TI - Detection of DNA hybridisation on a functionalised diamond surface using reflection anisotropy spectroscopy VL - 85 ID - 3821 ER - TY - JOUR AB - The carbon-nitrogen bond of carboxamides is extremely stable under most conditions. The present study reveals that simple zirconium- and hafnium-amido complexes are highly efficient catalysts for equilibrium-controlled transamidation reactions between secondary amines and tertiary amides. In a number of cases, transamidation proceeds rapidly at room temperature. We find that these new catalysts are sufficiently active to promote the metathesis of tertiary amides, which arises from successive transamidation cycles. The catalytic activities we observe are unprecedented and represent a substantial step toward a long-range goal of conducting equilibrium-controlled reactions with carboxamides. AD - [Stephenson, Nickeisha A.; Zhu, Jiang; Gellman, Samuel H.; Stahl, Shannon S.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000268395000046 AU - Stephenson, N. A. AU - Zhu, J. AU - Gellman, S. H. AU - Stahl, S. S. DA - Jul KW - Dynamic combinatorial chemistry intramolecular transamidation secondary carboxamides beta-lactams c-n amines hydroamination aminolysis complexes hydrolysis Chemistry, Multidisciplinary LB - ISI 2009 08 13 IS - 29 N1 - English Article NSF Collaborative Research in Chemistry program [CHE-0404704] PY - 2009 SP - 10003-10008 ST - Catalytic Transamidation Reactions Compatible with Tertiary Amide Metathesis under Ambient Conditions T2 - Journal of the American Chemical Society TI - Catalytic Transamidation Reactions Compatible with Tertiary Amide Metathesis under Ambient Conditions VL - 131 ID - 3991 ER - TY - JOUR AB - We report that polarization-shaped mid-infrared (IR) pulses can be used to enhance the vibrational population of one mode over another in a coupled molecular system. A genetic algorithm and a new mid-IR polarization shaper were used to alter the relative vibrational excitation of the two carbonyl stretching modes in Mn(CO)(5)Br. One mode could be selectively enhanced over the other by 2-3 times. Control over the polarization leads to better optimization than phase-only control. Several possible mechanisms that indicate how polarization shaping leads to selective vibrational excitation are discussed using a formalism that separates polarization shaping effects on the signal strength from amplitude or phase shaping. The techniques introduced herein will have broad applications in quantum gating schemes, controlling ground state chemistry and enhancing the sensitivity of multidimensional IR and visible spectroscopies. AD - [Strasfeld, David B.; Middleton, Chris T.; Zanni, Martin T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000271324900017 AU - Strasfeld, D. B. AU - Middleton, C. T. AU - Zanni, M. T. DA - Oct DO - 105046 KW - 2-dimensional infrared-spectroscopy coherent control quantum control femtosecond pulses laser-pulses phase amplitude molecules dynamics liquid Physics, Multidisciplinary LB - ISI 2009 11 12 N1 - English Article Packard Foundation ; National Institutes of Health [DK79895] PY - 2009 ST - Mode selectivity with polarization shaping in the mid-IR T2 - New Journal of Physics TI - Mode selectivity with polarization shaping in the mid-IR VL - 11 ID - 4067 ER - TY - JOUR AD - [Strasfeld, David B.; Shim, Sang-Hee; Zanni, Martin T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000266520500001 AU - Strasfeld, D. B. AU - Shim, S. H. AU - Zanni, M. T. KW - 2-dimensional infrared-spectroscopy intramolecular hydrogen-transfer femtosecond laser-pulses adiabatic passage bond dynamics phase dissociation excitation molecules ubiquitin LB - ISI 2009 06 19 N1 - ADVANCES IN CHEMICAL PHYSICS English Review National Science Foundation [CHE-0350518]; Beckman Foundation ; David-Lucile Packard Foundation PY - 2009 SP - 1-28 ST - New Advances in Mid-Ir Pulse Shaping and Its Application to 2d Ir Spectroscopy and Ground-State Coherent Control T2 - Advances in Chemical Physics, Vol 141 TI - New Advances in Mid-Ir Pulse Shaping and Its Application to 2d Ir Spectroscopy and Ground-State Coherent Control VL - 141 ID - 3942 ER - TY - JOUR AB - The liquid dynamics of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, named ROY for its red, orange, and yellow crystal polymorphs, was characterized by dielectric spectroscopy and differential scanning calorimetry. Four of these polymorphs show fast "diffusionless" crystal growth at low temperatures while three others do not. ROY was found to be a typical fragile organic liquid. Its alpha relaxation process has time-temperature superposition symmetry across the viscous range (tau(alpha)=100 s-100 ns) with the width of the relaxation peak characterized by a constant beta(KWW) of 0.73. No secondary relaxation peak was observed, even with glasses made by fast quenching. For the polymorphs not showing fast crystal growth in the glassy state, the growth rate has a power-law relation with tau(alpha), u proportional to tau(-xi)(alpha), where xi approximate to 0.7. For the polymorphs showing fast crystal growth in the glassy state, the growth is so fast near and below the glass transition temperature T-g that thousands of molecular layers can be added to the crystalline phase during one structural relaxation time of the liquid. In the glassy state, this mode of growth slows slightly over time. This slowdown is not readily explained by the effect of physical aging on the thermodynamic driving force of crystallization, the glass vapor pressure, or the rate of structural relaxation. This study demonstrates that from the same liquid or glass, the growth of some polymorphs is accurately described as being limited by the rate of structural relaxation or bulk diffusion, whereas the growth of other polymorphs is too fast to be under such control. AD - [Sun, Ye; Ediger, M. D.; Yu, Lian] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Xi, Hanmi; Yu, Lian] Univ Wisconsin, Sch Pharm, Madison, WI 53705 USA. [Richert, Ranko] Arizona State Univ, Dept Chem & Biochem, Tempe, AZ 85287 USA. AN - ISI:000269287200025 AU - Sun, Y. AU - Xi, H. M. AU - Ediger, M. D. AU - Richert, R. AU - Yu, L. DA - Aug DO - 074506 KW - ageing crystal growth crystal symmetry crystallisation dielectric relaxation differential scanning calorimetry diffusion glass transition liquid crystals organic compounds polymorphism quenching (thermal) Nucleation-based crystallization supercooled o-terphenyl solidification behavior aromatic-hydrocarbons physical-properties d-sorbitol t-g relaxation indomethacin equilibrium Physics, Atomic, Molecular & Chemical LB - ISI 2009 09 10 IS - 7 N1 - English Article NSF [DMR-0804786] PY - 2009 ST - Diffusion-controlled and "diffusionless" crystal growth near the glass transition temperature: Relation between liquid dynamics and growth kinetics of seven ROY polymorphs T2 - Journal of Chemical Physics TI - Diffusion-controlled and "diffusionless" crystal growth near the glass transition temperature: Relation between liquid dynamics and growth kinetics of seven ROY polymorphs VL - 131 ID - 4013 ER - TY - JOUR AB - The swelling of polymers in random matrices is studied using computer simulations and percolation theory. The model system consists of freely jointed hard sphere chains in a matrix of hard spheres fixed in space. The average size of the polymer is a nonmonotonic function of the matrix volume fraction, phi(m). For low values of phi(m) the polymer size decreases as phi(m) is increased but beyond a certain value of phi(m) the polymer size increases as phi(m) is increased. The qualitative behavior is similar for three different types of matrices. In order to study the relationship between the polymer swelling and pore percolation, we use the Voronoi tessellation and a percolation theory to map the matrix onto an irregular lattice, with bonds being considered connected if a particle can pass directly between the two vertices they connect. The simulations confirm the scaling relation R-G similar to(p-p(c))N-delta(0)nu, where R-G is the radius of gyration, N is the polymer degree of polymerization, p is the number of connected bonds, and p(c) is the value of p at the percolation threshold, with universal exponents delta(0)(approximate to-0.126 +/- 0.005) and nu(approximate to 0.6 +/- 0.01). The values of the exponents are consistent with predictions of scaling theory. AD - [Sung, Bong June] Sogang Univ, Dept Chem, Seoul 121742, South Korea. [Chang, Rakwoo] Kwangwoon Univ, Dept Chem, Seoul 139701, South Korea. [Yethiraj, Arun] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Yethiraj, Arun] Univ Wisconsin, Inst Theoret Chem, Madison, WI 53706 USA. AN - ISI:000264775200092 AU - Sung, B. J. AU - Chang, R. W. AU - Yethiraj, A. DA - Mar DO - 124908 KW - bonds (chemical) liquid theory percolation polymer solutions polymerisation porosity random processes swelling Self-avoiding-walks integral-equation theory monte-carlo simulations randomly diluted lattices quenched random-media percolation clusters chain conformations statistics dynamics liquids Physics, Atomic, Molecular & Chemical LB - ISI 2009 04 17 IS - 12 N1 - English Article 0021-9606 PY - 2009 ST - Swelling of polymers in porous media T2 - Journal of Chemical Physics TI - Swelling of polymers in porous media VL - 130 ID - 3883 ER - TY - JOUR AB - The diffusion of proteins in the cell membrane is investigated using computer simulations of a two-dimensional model. The membrane is assumed to be divided into compartments, with adjacent compartments separated by a barrier of stationary obstacles. Each compartment contains traps represented by stationary attractive disks. Depending on their size, these traps are intended to model either smaller compartments or binding sites. The simulations are intended to model the double-compartment model, which has been used to interpret single molecule experiments in normal rat kidney cells, where five regimes of transport are observed. The simulations show, however, that five regimes are observed only when there is a large separation between the sizes of the traps and large compartments, casting doubt on the double compartment model for the membrane. The diffusive behavior is sensitive to the concentration and size of traps and the strength of the barrier between compartments suggesting that the diffusion of proteins can be effectively used to characterize the structure of the membrane. AD - [Sung, Bong June] Sogang Univ, Dept Chem, Seoul 121742, South Korea. [Yethiraj, Arun] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000268428700008 AU - Sung, B. J. AU - Yethiraj, A. DA - Jul KW - Single-molecule techniques plasma-membrane particle tracking hop diffusion receptor fluid Biophysics LB - ISI 2009 08 06 IS - 2 N1 - English Article Korean Government (Ministry of Education and Human Resources Development) [KRF-2008-331-C00141]; Sogang University [20071116] PY - 2009 SP - 472-479 ST - Computer Simulations of Protein Diffusion in Compartmentalized Cell Membranes T2 - Biophysical Journal TI - Computer Simulations of Protein Diffusion in Compartmentalized Cell Membranes VL - 97 ID - 3989 ER - TY - JOUR AB - Highly stable glasses of tris-naphthylbenzene transform into a liquid when annealed above the glass transition temperature T-g. In contrast to the predictions of standard models, the observed transformation is spatially inhomogeneous. Secondary ion mass spectrometry experiments on isotopically labeled multilayer films show that the liquid grows into the stable glass with sharp growth fronts initiated at the free surface and at the interface with the substrate. For the free surface, the growth velocity is constant in time and has the same temperature dependence as self-diffusion in the equilibrium supercooled liquid. These stable glasses are packed so efficiently that surfaces and interfaces are required to initiate the transformation to the liquid even well above T-g. AD - [Swallen, Stephen F.; Traynor, Katherine; McMahon, Robert J.; Ediger, M. D.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Mates, Thomas E.] Univ Calif Santa Barbara, Dept Mat, Santa Barbara AN - ISI:000263389500035 AU - Swallen, S. F. AU - Traynor, K. AU - McMahon, R. J. AU - Ediger, M. D. AU - Mates, T. E. KW - Physics, Multidisciplinary LB - ISI 2009 03 05 N1 - English Article HETEROGENEOUS DYNAMICS; TEMPERATURE; RELAXATION FEB 13 6 PY - 2009 ST - Stable Glass Transformation to Supercooled Liquid via Surface-Initiated Growth Front T2 - Physical Review Letters TI - Stable Glass Transformation to Supercooled Liquid via Surface-Initiated Growth Front ID - 3763 ER - TY - JOUR AB - Highly stable glasses of tris-naphthylbenzene transform into a liquid when annealed above the glass transition temperature T-g. In contrast to the predictions of standard models, the observed transformation is spatially inhomogeneous. Secondary ion mass spectrometry experiments on isotopically labeled multilayer films show that the liquid grows into the stable glass with sharp growth fronts initiated at the free surface and at the interface with the substrate. For the free surface, the growth velocity is constant in time and has the same temperature dependence as self-diffusion in the equilibrium supercooled liquid. These stable glasses are packed so efficiently that surfaces and interfaces are required to initiate the transformation to the liquid even well above T-g. AN - ISI:000263389500035 AU - Swallen, S. F. AU - Traynor, K. AU - McMahon, R. J. AU - Ediger, M. D. AU - Mates, T. E. DA - Feb DO - 065503 10.1103/PhysRevLett.102.065503 LB - ISI 2009 03 05 (Library clean-up) IS - 6 N1 - Swallen, Stephen F. Traynor, Katherine McMahon, Robert J. Ediger, M. D. Mates, Thomas E. PY - 2009 SN - 0031-9007 ST - Stable Glass Transformation to Supercooled Liquid via Surface-Initiated Growth Front T2 - Physical Review Letters TI - Stable Glass Transformation to Supercooled Liquid via Surface-Initiated Growth Front UR - ://000263389500035 VL - 102 ID - 3770 ER - TY - JOUR AB - Protein phosphorylation is central to the understanding of cellular signaling, and cellular signaling is suggested to play a major role in the regulation of human embryonic stem (ES) cell pluripotency. Here, we describe the use of conventional tandem mass spectrometry-based sequencing technology-collision-activated dissociation ( CAD)-and the more recently developed method electron transfer dissociation (ETD) to characterize the human ES cell phosphoproteome. In total, these experiments resulted in the identification of 11,995 unique phosphopeptides, corresponding to 10,844 nonredundant phosphorylation sites, at a 1% false discovery rate (FDR). Among these phosphorylation sites are 5 localized to 2 pluripotency critical transcription factors-OCT4 and SOX2. From these experiments, we conclude that ETD identifies a larger number of unique phosphopeptides than CAD ( 8,087 to 3,868), more frequently localizes the phosphorylation site to a specific residue (49.8% compared with 29.6%), and sequences whole classes of phosphopeptides previously unobserved. AN - ISI:000262831600009 AU - Swaney, D. L. AU - Wenger, C. D. AU - Thomson, J. A. AU - Coon, J. J. DA - Jan DO - 10.1073/pnas.0811964106 LB - ISI 2009 02 12 IS - 4 N1 - Swaney, Danielle L. Wenger, Craig D. Thomson, James A. Coon, Joshua J. PY - 2009 SN - 0027-8424 SP - 995-1000 ST - Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry T2 - Proceedings of the National Academy of Sciences of the United States of America TI - Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry UR - ://000262831600009 VL - 106 ID - 3791 ER - TY - JOUR AB - The traceless Staudinger ligation can be mediated by phosphinothiols under physiological conditions. Proximal positive charges are necessary to achieve that transformation, presumably because those charges discourage protonation of the key iminophosphorane intermediate. Here, a series of cationic phosphinothiols is used to probe Coulombic effects on the traceless Staudinger ligation in aqueous buffers. The reagent bis(m-N,N-dimethylaminomethylphenyl) phosphinomethanethiol (3) is found to be superior to others, both in its ability to mediate the traceless Staudinger ligation in water and in the efficiency of its synthesis. (C) 2008 Elsevier Ltd. All rights reserved. AN - ISI:000262980500014 AU - Tam, A. AU - Raines, R. T. DA - Feb DO - 10.1016/j.bmc.2008.02.047 LB - ISI 2009 02 20 IS - 3 N1 - Tam, Annie Raines, Ronald T. PY - 2009 SN - 0968-0896 SP - 1055-1063 ST - Coulombic effects on the traceless Staudinger ligation in water T2 - Bioorganic & Medicinal Chemistry TI - Coulombic effects on the traceless Staudinger ligation in water UR - ://000262980500014 VL - 17 ID - 3789 ER - TY - JOUR AB - The engineering of proteins can illuminate their biological function and improve their performance in a variety of applications. Within the past decade, methods have been developed that facilitate the ability of chemists to manipulate proteins in a controlled manner. Here, we present the traceless Staudinger ligation as a strategy for the convergent chemical synthesis of proteins. This reaction unites a phosphinothioester and an azide to form an amide bond with no residual atoms. An important feature of this reaction is its ability to ligate peptides at noncysteine residues, thereby overcoming a limitation of alternative strategies. Attributes of the traceless Staudinger ligation are discussed, and an overall comparison of known reagents for effecting the reaction is presented. General methods are elaborated for the synthesis of the most efficacious phosphinothiol for mediating the traceless Staudinger ligation, as well as for the preparation of phosphinothioester and azide fragments and the ligation of peptides immobilized on a solid support. Together, this information facilitates the use of this emerging method to engineer proteins. AD - [Tam, Annie; Raines, Ronald T.] Univ Wisconsin, Dept Chem & Biochem, Madison, WI 53706 USA. AN - ISI:000269267100002 AU - Tam, A. AU - Raines, R. T. KW - Phase peptide-synthesis unnatural amino-acids stereoselective-synthesis convenient synthesis chemical-synthesis glycosyl amides azide immobilization selenocysteine semisynthesis LB - ISI 2009 09 17 N1 - Methods in Enzymology English Review PY - 2009 SP - 25-44 ST - Protein Engineering with the Traceless Staudinger Ligation T2 - Methods in Enzymology: Non-Natural Amino Acids TI - Protein Engineering with the Traceless Staudinger Ligation VL - 462 ID - 4017 ER - TY - JOUR AB - A hierarchical simulation framework that integrates information from all-atom simulations into a finite element model at the continuum level is established to study the mechanical response of a mechanosensitive channel of large conductance (MscL) in bacteria Escherichia coli (E. coli) embedded in a vesicle formed by the dipalmitoylphosphatidycholine (DPPC) lipid bilayer. Sufficient structural details of the protein are built into the continuum model, with key parameters and material properties derived from molecular mechanics simulations. The multi-scale framework is used to analyze the gating of MscL when the lipid vesicle is subjective to nanoindentation and patch clamp experiments, and the detailed structural transitions of the protein are obtained explicitly as a function of external load; it is currently impossible to derive such information based solely on all-atom simulations. The gating pathways of E. coli-MscL qualitatively agree with results from previous patch clamp experiments. The gating mechanisms under complex indentation-induced deformation are also predicted. This versatile hierarchical multi-scale framework may be further extended to study the mechanical behaviors of cells and biomolecules, as well as to guide and stimulate biomechanics experiments. AN - ISI:000262650700005 AU - Tang, Y. AU - Chen, X. AU - Yoo, J. AU - Yethiraj, A. AU - Cui, Q. DA - Feb DO - 10.1007/s11340-007-9060-x LB - ISI 2009 02 05 IS - 1 N1 - Tang, Y. Chen, X. Yoo, J. Yethiraj, A. Cui, Q. PY - 2009 SN - 0014-4851 SP - 35-46 ST - Numerical Simulation of Nanoindentation and Patch Clamp Experiments on Mechanosensitive Channels of Large Conductance in Escherichia coli T2 - Experimental Mechanics TI - Numerical Simulation of Nanoindentation and Patch Clamp Experiments on Mechanosensitive Channels of Large Conductance in Escherichia coli UR - ://000262650700005 VL - 49 ID - 3796 ER - TY - JOUR AB - Rate constants for the intramolecular electron-transfer reaction in the 2,7-dinitronaphthalene (2(-)), 4,4'-dinitrotolane (3(-)), and 2,2'-dimethyl-4,4'-dinitrobiphenyl (4(-)) radical anions in several polar aprotic solvents were estimated by simulating their ESR spectra at different temperatures. At 298 K, the rate constants are in the 2.0-8.0 x 10(9) s(-1) range for 2(-) and 3(-) and in the 0.4-2.6 x 10(9) s(-1) range for 4(-). The rate constants of 3(-) and 4(-), when corrected for changes in the activation energy (taken as the changes in lambda, the transition energy of the mixed valence band), correlate with the inverse of the solvent relaxation time, showing that the reaction is controlled by solvent dynamics. Solvent effects are only found for 2(-) in benzonitrile (PhCN), the most viscous solvent studied. Calculations of the rate constants using the Krarners-based theory adapted to the adiabatic limit fit the Eyring plots of 2(-) in PhCN and of 3(-) and 4(-) both in MeCN and PhCN rather well. AD - [Telo, Joao P.] Inst Super Tecn, Ctr Quim Estrutural, P-1049001 Lisbon, Portugal. [Nelsen, Stephen F.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Zhao, Yi] Xiamen Univ, Dept Chem, Coll Chem & Chem Engn, Xiamen 361005, Peoples R China. [Zhao, Yi] Xiamen Univ, State Key Lab Phys Chem Solid Surfaces, Coll Chem & Chem Engn, Xiamen 361005, Peoples R China. AN - ISI:000267694800005 AU - Telo, J. P. AU - Nelsen, S. F. AU - Zhao, Y. DA - Jul KW - Optical-spectra spin resonance spectroscopy regime transitions chemistry kinetics cations bridges systems Chemistry, Physical Physics, Atomic, Molecular & Chemical LB - ISI 2009 07 31 IS - 27 N1 - English Article National Science Foundation [CHE-0647719]; Fundacao Para a Cidncia e Tecnologia ; National Science Foundation of China [20773115, 20833004] PY - 2009 SP - 7730-7736 ST - Electron Transfer within Charge-Localized Dinitroaromatic Radical Anions T2 - Journal of Physical Chemistry A TI - Electron Transfer within Charge-Localized Dinitroaromatic Radical Anions VL - 113 ID - 3969 ER - TY - JOUR AB - Triplet carbene methylpentadiynylidene, MeC5H (1), was investigated in cryogenic matrices by IR, UV/vis, and EPR spectroscopy. Broadband irradiation (lambda > 497 nm) of the isomeric diazo compounds, 1-diazo-hexa-2,4-diyne (2) or 2-diazo-hexa-3,5-diyne (3), generates triplet carbene 1. EPR spectra yield zero-field splitting parameters (vertical bar D/hc vertical bar = 0.62 cm(-1), vertical bar E/hc vertical bar < 0.0006 cm-1), which are typical for a triplet carbene with axial symmetry. The electronic spectrum of triplet 1 is characterized by a weak absorption in the near-UV and visible region (350-430 nm) with vibronic progressions corresponding to excitations of the acetylenic stretching and the terminal C C-H bending modes. Chemical trapping of triplet 1 in an O-2-doped matrix affords carbonyl oxides derived predominantly from attack at C-3. Upon irradiation at A > 399 nm, triplet 1 undergoes photochemical 1,2-hydrogen migration to form hex-1-ene-3,5-diyne (6). AD - [Thomas, Phillip S.; Bowling, Nathan P.; McMahon, Robert J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000267630000064 AU - Thomas, P. S. AU - Bowling, N. P. AU - McMahon, R. J. DA - Jun KW - Electronic-absorption-spectra diffuse interstellar bands neutral-neutral reactions carbon-bearing molecules deuterated analogs chain molecules neon matrices o-oxide carbenes isomers Chemistry, Multidisciplinary LB - ISI 2009 07 17 IS - 24 N1 - English Article National Science Foundation [NSF-0412707, NSF-9013030, NSF-0091916, NSF-0342998] PY - 2009 SP - 8649-8659 ST - Spectroscopy and Photochemistry of Triplet Methylpentadiynylidene (Me-C C-d-C C-H) T2 - Journal of the American Chemical Society TI - Spectroscopy and Photochemistry of Triplet Methylpentadiynylidene (Me-C C-d-C C-H) VL - 131 ID - 3959 ER - TY - JOUR AB - When skin is compromised, a cascade of signals initiates the rapid repair of the epidermis to prevent fluid loss and provide defense against invading microbes. During this response, keratinocytes produce host defense peptides (HDPs) that have antimicrobial activity against a diverse set of pathogens. Using nonviral vectors we have genetically modified the novel, nontumorigenic, pathogenfree human keratinocyte progenitor cell line (NIKS) to express the human cathelicidin HDP in a tissue-specific manner. NIKS skin tissue that expresses elevated levels of cathelicidin possesses key histological features of normal epidermis and displays enhanced antimicrobial activity against bacteria in vitro. Moreover, in an in vivo infected burn wound model, this tissue results in a two log reduction in a clinical isolate of multidrug-resistant Acinetobacter baumannii. Taken together, these results suggest that this genetically engineered human tissue could be applied to burns and ulcers to counteract bacterial contamination and prevent infection. AD - [Thomas-Virnig, Christina L.; Schlosser, Sandy J.; Allen-Hoffmann, B. Lynn] Univ Wisconsin, Dept Pathol & Lab Med, Madison, WI 53706 USA. E.; Van Winkle, Kelly F.] Stratatech Corp, Madison, WI USA. Dept Surg & Cell Biol Neurobiol & Anat, Maywood, IL 60153 USA. 53706 USA. 53706 USA. Madison, WI 53706 USA. Sch Med & Publ Hlth, Madison, WI 53706 USA. AN - ISI:000263788200026 AU - Thomas-Virnig, C. L. AU - Centanni, J. M. AU - Johnston, C. E. AU - He, L. K. AU - Schlosser, S. J. AU - Van Winkle, K. F. AU - Chen, R. B. AU - Gibson, A. L. AU - Szilagyi, A. AU - Li, L. J. AU - Shankar, R. AU - Allen-Hoffmann, B. L. DA - Mar KW - Antimicrobial peptide ll-37 gram-negative bacteria human cathelicidin pseudomonas-aeruginosa immune-responses engineered skin lamellar bodies gene-transfer burn injury sepsis Biotechnology & Applied Microbiology Genetics & Heredity Medicine, Research & Experimental LB - ISI 2009 03 13 IS - 3 N1 - English Article 1525-0016 PY - 2009 SP - 562-569 ST - Inhibition of Multidrug-resistant Acinetobacter baumannii by Nonviral Expression of hCAP-18 in a Bioengineered Human Skin Tissue T2 - Molecular Therapy TI - Inhibition of Multidrug-resistant Acinetobacter baumannii by Nonviral Expression of hCAP-18 in a Bioengineered Human Skin Tissue VL - 17 ID - 3819 ER - TY - JOUR AB - Three new stable germylenes, rac-1,3-di-tert-butyl-4,5-dimethyl-1,3-diaza-2-germacyclopentane2-ylide (1), 1,3-di-tert-butyl-4,4-dimethyl-1,3-diaza-2-germacyclopentane-2-ylide (2), and rac-1,3,4-tritert-butyl-1,3-diaza-2-germacyclopentane-2-ylide (3) have been synthesized by the reaction of their corresponding germyl dichlorides with elemental lithium. Full synthetic procedures and characterizations are described. (c) 2009 Elsevier B.V. All rights reserved. AD - [Tomasik, Adam C.; Hill, Nicholas J.; West, Robert] Univ Wisconsin, Dept Chem, Organosilicon Res Ctr, Madison, WI 53706 USA. AN - ISI:000266270400023 AU - Tomasik, A. C. AU - Hill, N. J. AU - West, R. DA - Jun KW - Germylene Germanium Organogermanium General-synthesis aluminum-hydride complexes chemistry amines reactivity secondary silylene carbene amides Chemistry, Inorganic & Nuclear Chemistry, Organic LB - ISI 2009 06 19 IS - 13 N1 - English Article National Science Foundation [CHE-0451536] PY - 2009 SP - 2122-2125 ST - Synthesis and characterization of three new thermally stable N-heterocyclic germylenes T2 - Journal of Organometallic Chemistry TI - Synthesis and characterization of three new thermally stable N-heterocyclic germylenes VL - 694 ID - 3937 ER - TY - JOUR AB - Three new stable silylenes, rac-1,3,4-tri-tert-butyl-1,3-diaza-2-silacyclopentane-2-ylide (5), 1,3-di-tert-butyl-4,4-dimethyl-1,3-diaza-2-silacyclopentane-2-ylide (6), and rac-1,3di-tert-butyl-4-methyl-1,3-diaza-2-silacyclopentane-2-ylide (7), have been synthesized by the reaction of their corresponding dibromides with KC8. Unlike the analogous silylene 2, which lacks any, backbone substitution and tetramerizes in concentrated solution or as a solid, silylenes 5, 6, and 7 show no tendency to oligomerize. The reactions of 5 with tert-butanol and chloroalkanes give only 1:1 O-H or C-Cl insertion products; with adamantyl azide 5 yields the spirosilatetrazoline 8, while with mesityl azide it gives the azadisilacyclopropane 9. AD - [Tomasik, Adam C.; Mitra, Amitabha; West, Robert] Univ Wisconsin, Dept Chem, Organosilicon Res Ctr, Madison, WI 53706 USA. AN - ISI:000262177200047 AU - Tomasik, A. C. AU - Mitra, A. AU - West, R. DA - Jan KW - Stable silylenes secondary amines Chemistry, Inorganic & Nuclear Chemistry, Organic LB - ISI 2009 01 22 IS - 1 N1 - English Article 0276-7333 PY - 2009 SP - 378-381 ST - Synthesis and Reactivity of Three New N-Heterocyclic Silylenes T2 - Organometallics TI - Synthesis and Reactivity of Three New N-Heterocyclic Silylenes VL - 28 ID - 3732 ER - TY - JOUR AB - Onconase((R)) (ONC) is a member of the ribonuclease A superfamily that is toxic to cancer cells in vitro and in vivo. ONC is now in Phase IIIb clinical trials for the treatment of malignant mesothelioma. Internalization of ONC to the cytosol of cancer cells is essential for its cytotoxic activity, despite the apparent absence of a cell-surface receptor protein. Endocytosis and cytotoxicity do, however, appear to correlate with the net positive charge of ribonucleases. To dissect the contribution made by the endogenous arginine and lysine residues of ONC to its cytotoxicity, 22 variants were created in which cationic residues were replaced with alanine. Variants with the same net charge (+2 to +5) as well as equivalent catalytic activity and conformational stability were found to exhibit large (> 10-fold) differences in toxicity for the cells of a human leukemia line. In addition, a more cationic ONC variant could be either much more or much less cytotoxic than a less cationic variant, again depending on the distribution of its cationic residues. The endocytosis of variants with widely divergent cytotoxic activity was quantified by flow cytometry using a small-molecule fluorogenic label, and was found to vary by twofold or less. This small difference in endocytosis did not account for the large difference in cytotoxicity, implicating the distribution of cationic residues as being critical for lipid-bilayer translocation subsequent to endocytosis. This finding has fundamental implications for understanding the interaction of ribonucleases and other proteins with mammalian cells. AD - [Raines, Ronald T.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. [Lavis, Luke D.; Raines, Ronald T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Turcotte, Rebecca F.] Univ Wisconsin, Med Scientist Training Program, Madison, WI 53706 USA. [Turcotte, Rebecca F.] Univ Wisconsin, Biophys Grad Program, Madison, WI 53706 USA. AN - ISI:000267282400013 AU - Turcotte, R. F. AU - Lavis, L. D. AU - Raines, R. T. DA - Jul KW - cancer Coulombic interaction cytotoxin enzyme ribonuclease Ribonuclease inhibitor protein human pancreatic ribonuclease eosinophil cationic protein rana-pipiens oocytes conformational stability antitumor-activity catalytic-activity heparan-sulfate amphibian ribonuclease quantitative-analysis Biochemistry & Molecular Biology LB - ISI 2009 07 10 IS - 14 N1 - English Article NIH [CA073808, 08349, RR13790]; Wisconsin Distinguished Rath Graduate Fellowship ; Genentech Foundation ; NSF [BIR-9512577] PY - 2009 SP - 4270-4281 ST - Onconase cytotoxicity relies on the distribution of its positive charge T2 - FEBS Journal TI - Onconase cytotoxicity relies on the distribution of its positive charge VL - 276 ID - 3952 ER - TY - JOUR AB - Surface chemical changes or passivation can be used to enhance the electrical performance of device Structures. The solution-based (Nh(4))(2)S-t, treatment of ZnO single crystals of (0001), (10 (1) over bar0), and (000 (1) over bar) orientations as well as ZnO nanorods was studies by using X-ray and Ultraviolet photoelectron spectroscopies (XPS and ups). The (10 (1) over bar0) and (000 (1) over bar)-onented single crystals and ZnO nanorods each showed evidence that the ZnO was consumed, forming a ZnS layer at the surface In contrast, the ZnO (0001) crystal (lid not substantially react with the sulfide Solution. However, the surface hydroxyl species were displaced by a Sulfide passivation layer of 0.21 ML. This process resulted in all apparent increase in upward band bending by similar to 0.1 -0.3 eV. P3HT-ZnO photovoltaic devices fabricated oil O-polar single crystals showed electrical properties which can be correlated with ZnS formation due to the Sulfide treatment. AD - [Uhlrich, John J.; Kuech, Thomas F.] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA. [Franking, Ryan; Hamers, Robert J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000272560400019 AU - Uhlrich, John J. AU - Franking, Ryan AU - Hamers, Robert J. AU - Kuech, Thomas F. DA - Dec KW - Ray photoelectron-spectroscopy ti/au ohmic contacts zinc-oxide surfaces solar-cells electrical-properties structural-properties core-shell chemistry polymer film Chemistry, Physical Nanoscience & Nanotechnology Materials Science, Multidisciplinary LB - ISI 2009 12 24 IS - 50 N1 - English Article Materials Research Science and Engineering Center at the University of Wisconsin ; National Science Foundation Graduate Research PY - 2009 SP - 21147-21154 ST - Sulfide Treatment of ZnO Single Crystals and Nanorods and the Effect on P3HT-ZnO Photovoltaic Device Properties T2 - Journal of Physical Chemistry C TI - Sulfide Treatment of ZnO Single Crystals and Nanorods and the Effect on P3HT-ZnO Photovoltaic Device Properties VL - 113 ID - 4111 ER - TY - JOUR AB - The C-1027 enediyne antitumor antibiotic from Streptomyces globisporus possesses an (S)-3-chloro-5-hydroxy-beta-tyrosine moiety, the chloro- and hydroxy-substituents of which are installed by a flavin-dependent halogenase SgcC3 and monooxygenase SgcC, respectively. Interestingly, a single flavin reductase, SgcE6, can provide reduced flavin to both enzymes. Bioinformatics analysis reveals that, similar to other flavin reductases involved in natural product biosynthesis, SgcE6 belongs to the HpaC-like subfamily of the Class I flavin reductases. The present study describes the steady-state kinetic characterization of SgcE6 as a strictly NADH- and FAD-specific enzyme. AD - [Shen, Ben] Univ Wisconsin, Sch Pharm, Div Pharmaceut Sci, Madison, WI 53705 USA. [Shen, Ben] Univ Wisconsin, Natl Cooperat Drug Discovery Grp, Madison, WI 53705 USA. [Shen, Ben] Univ Wisconsin, Dept Chem, Madison, WI 53705 USA. AN - ISI:000270958800011 AU - Van Lanen, S. G. AU - Lin, S. J. AU - Horsman, G. P. AU - Shen, B. DA - Nov KW - C-1027 enediyne flavin reductase halogenase monooxygenase SgcE6 4-hydroxyphenylacetate 3-monooxygenase nad(p)h-flavin oxidoreductase escherichia-coli 2-component identification responses enzyme breaks Microbiology LB - ISI 2009 10 29 IS - 2 N1 - English Article NIH [CA78747, CA113297, CA1059845]; NSERC PY - 2009 SP - 237-241 ST - Characterization of SgcE6, the flavin reductase component supporting FAD-dependent halogenation and hydroxylation in the biosynthesis of the enediyne antitumor antibiotic C-1027 T2 - FEMS Microbiology Letters TI - Characterization of SgcE6, the flavin reductase component supporting FAD-dependent halogenation and hydroxylation in the biosynthesis of the enediyne antitumor antibiotic C-1027 VL - 300 ID - 4061 ER - TY - JOUR AB - A single-vesicle, fluorescence-based, SNARE-driven fusion assay enables simultaneous measurement of lipid mixing and content release with 5 ms/frame, or even 1 ms/frame, time resolution. The v-SNARE vesicles, labeled with lipid and content markers of different color, dock and fuse with a planar t-SNARE bilayer supported on glass. A narrow (<5 ms duration), intense spike of calcein fluorescence due to content release and dequenching coincides with inner-leaflet lipid mixing within 10 ms. The spike provides more sensitive detection of productive hemifusion events than do lipid labels alone. Consequently, many fast events previously thought to be prompt, full fusion events are now reclassified as productive hemifusion. Both full fusion and hemifusion occur with a time constant of 5-10 ms. At 60% phosphatidylethanolamine lipid composition, productive and dead-end hemifusion account for 65% of all fusion events. However, quantitative analysis shows that calcein is released into the space above the bilayer (vesicle bursting), rather than the thin aqueous space between the bilayer and glass. Evidently, at the instant of inner-leaflet mixing, flattening of the vesicle increases the internal pressure beyond the bursting point. This may be related to in vivo observations suggesting that membrane lysis often competes with membrane fusion. AD - [Wang, Tingting; Weisshaar, James C.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Smith, Elizabeth A.; Weisshaar, James C.] Univ Wisconsin, Grad Biophys Program, Madison, WI 53706 USA. [Chapman, Edwin R.] Univ Wisconsin, Dept Physiol, Howard Hughes Med Inst, Madison, WI 53706 USA. AN - ISI:000266312900024 AU - Wang, T. T. AU - Smith, E. A. AU - Chapman, E. R. AU - Weisshaar, J. C. DA - May KW - Phospholipid-bilayer membranes permeability changes neuronal snares planar membrane in-vitro exocytosis proteins complex ca2+ synaptotagmin Biophysics LB - ISI 2009 06 12 IS - 10 N1 - English Article National Institute of Neurological Disorders and Stroke [5R01NS051518] PY - 2009 SP - 4122-4131 ST - Lipid Mixing and Content Release in Single-Vesicle, SNARE-Driven Fusion Assay with 1-5 ms Resolution T2 - Biophysical Journal TI - Lipid Mixing and Content Release in Single-Vesicle, SNARE-Driven Fusion Assay with 1-5 ms Resolution VL - 96 ID - 3926 ER - TY - JOUR AB - Haloalkane dehalogenase (HD) catalyzes the hydrolysis of haloalkanes via a covalent enzyme-substrate intermediate. Fusing a target protein to an HD variant that cannot hydrolyze the intermediate enables labeling of the target protein with a haloalkane in cellulo. The utility of extant probes is hampered, however, by background fluorescence as well as limited membrane permeability. Here, we report on the synthesis and use of a fluorogenic affinity label that, after unmasking by an intracellular esterase, labels an HD variant in cellulo. Labeling is rapid and specific, as expected from the reliance upon enzymic catalysts and the high membrane permeance of the probe both before and after unmasking. Most notably, even high concentrations of the fluorogenic affinity label cause minimal background fluorescence without a need to wash the cells. We envision that such fluorogenic affinity labels, which enlist catalysis by two cellular enzymes, will find utility in pulse-chase experiments, high-content screening, and numerous other protocols. AD - [Watkins, Rex W.; Raines, Ronald T.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. [Lavis, Luke D.; Kung, Vanessa M.; Raines, Ronald T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Los, Georgyi V.] Promega Corp, Madison, WI 53711 USA. AN - ISI:000269892900013 AU - Watkins, R. W. AU - Lavis, L. D. AU - Kung, V. M. AU - Los, G. V. AU - Raines, R. T. KW - Trimethyl lock stereopopulation control latent fluorophore rate enhancement living cells permeability technology mechanism Chemistry, Organic LB - ISI 2009 10 01 IS - 19 N1 - English Article NIH [CA073808]; NSF Graduate Research Fellowship ; Chemistry-Biology Interface Training [GM008505]; ACS Division of Organic Chemistry Fellowship ; the Genentech Foundation ; Biotechnology Training [GM008349]; Barry M. Goldwater Scholarship and a Hilldale Undergraduate/Faculty Research Fellowship ; NMRFAM [P41RR02301] PY - 2009 SP - 3969-3975 ST - Fluorogenic affinity label for the facile, rapid imaging of proteins in live cells T2 - Organic & Biomolecular Chemistry TI - Fluorogenic affinity label for the facile, rapid imaging of proteins in live cells VL - 7 ID - 4027 ER - TY - JOUR AB - Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e. g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on similar to 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses. AD - [Wei, Fusheng; Zhang, Jianwei; Collura, Kristi; Kudrna, David; Currie, Jennifer; Lin, Jinke; Kim, HyeRan; Angelova, Angelina; Scara, Gabriel; Wissotski, Marina; Golser, Wolfgang; Yu, Yeisoo; Wing, Rod A.] Univ Arizona, Arizona Genom Inst, Sch Plant Sci, Tucson, AZ 85721 USA. [Wei, Fusheng; Zhang, Jianwei; Collura, Kristi; Kudrna, David; Currie, Jennifer; Lin, Jinke; Kim, HyeRan; Angelova, Angelina; Scara, Gabriel; Wissotski, Marina; Golser, Wolfgang; Yu, Yeisoo; Wing, Rod A.] Univ Arizona, Dept Ecol & Evolutionary Biol, Inst Collaborat Res BIO5, Tucson, AZ USA. [Stein, Joshua C.; Liang, Chengzhi; Pasternak, Shiran; Narechania, Apurva; Zhang, Lifang; Kramer, Melissa; Spiegel, Lori; Nascimento, Lydia; Martienssen, Robert A.; McCombie, W. Richard; Ware, Doreen] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA. [Fulton, Robert S.; Courtney, Laura; Kruchowski, Scott; Graves, Tina A.; Rock, Susan M.; Adams, Stephanie; Fulton, Lucinda A.; Fronick, Catrina; Courtney, William; Clifton, Sandra W.; Wilson, Richard K.] Washington Univ, Sch Med, Dept Genet, St Louis, MO 63110 USA. [Fulton, Robert S.; Courtney, Laura; Kruchowski, Scott; Graves, Tina A.; Rock, Susan M.; Adams, Stephanie; Fulton, Lucinda A.; Fronick, Catrina; Courtney, William; Clifton, Sandra W.; Wilson, Richard K.] Washington Univ, Genome Ctr, St Louis, MO 63110 USA. [Baucom, Regina S.; Yang, Lixing; Bennetzen, Jeffrey L.] Univ Georgia, Dept Genet, Athens, GA 30602 USA. [De Paoli, Emanuele; Green, Pamela J.; Meyers, Blake C.] Univ Delaware, Dept Plant & Soil Sci, Newark, DE 19717 USA. [De Paoli, Emanuele; Green, Pamela J.; Meyers, Blake C.] Univ Delaware, Delaware Biotechnol Inst, Newark, DE 19717 USA. [Zhou, Shiguo; Schwartz, David C.] Univ Wisconsin Madison, Genet Lab, Dept Chem, Lab Mol & Computat Gen, Madison, WI USA. [Han, Yujun; Nagel, Dawn H.; Wessler, Susan R.] Univ Georgia, Dept Plant Biol, Athens, GA 30602 USA. [Yeh, Cheng-Ting; Ying, Kai; Schnable, Patrick S.] Iowa State Univ, Dept Agron, Ames, IA USA. [Yeh, Cheng-Ting; Ying, Kai; Schnable, Patrick S.] Iowa State Univ, Ctr Plant Gen, Ames, IA USA. [Kalyanaraman, Ananth] Washington State Univ, Sch Elect Engn & Comp Sci, Pullman, WA 99164 USA. [Chaparro, Cristian; Deragon, Jean-Marc] Univ Perpignan Via Domitia, CNRS, UMR 5096, Perpignan, France. [Miguel, Phillip San] Purdue Univ, Dept Hort & Landscape Architecture, W Lafayette, IN 47907 USA. [Jiang, Ning] Michigan State Univ, Dept Hort, E Lansing, MI 48824 USA. [Aluru, Srinivas] Iowa State Univ, Dept Elect & Comp Engn, Ames, IA USA. AN - ISI:000272419500023 AU - Wei, Fusheng AU - Stein, Joshua C. AU - Liang, Chengzhi AU - Zhang, Jianwei AU - Fulton, Robert S. AU - Baucom, Regina S. AU - De Paoli, Emanuele AU - Zhou, Shiguo AU - Yang, Lixing AU - Han, Yujun AU - Pasternak, Shiran AU - Narechania, Apurva AU - Zhang, Lifang AU - Yeh, Cheng-Ting AU - Ying, Kai AU - Nagel, Dawn H. AU - Collura, Kristi AU - Kudrna, David AU - Currie, Jennifer AU - Lin, Jinke AU - Kim, HyeRan AU - Angelova, Angelina AU - Scara, Gabriel AU - Wissotski, Marina AU - Golser, Wolfgang AU - Courtney, Laura AU - Kruchowski, Scott AU - Graves, Tina A. AU - Rock, Susan M. AU - Adams, Stephanie AU - Fulton, Lucinda A. AU - Fronick, Catrina AU - Courtney, William AU - Kramer, Melissa AU - Spiegel, Lori AU - Nascimento, Lydia AU - Kalyanaraman, Ananth AU - Chaparro, Cristian AU - Deragon, Jean-Marc AU - Miguel, Phillip San AU - Jiang, Ning AU - Wessler, Susan R. AU - Green, Pamela J. AU - Yu, Yeisoo AU - Schwartz, David C. AU - Meyers, Blake C. AU - Bennetzen, Jeffrey L. AU - Martienssen, Robert A. AU - McCombie, W. Richard AU - Aluru, Srinivas AU - Clifton, Sandra W. AU - Schnable, Patrick S. AU - Ware, Doreen AU - Wilson, Richard K. AU - Wing, Rod A. DA - Nov DO - e1000728 KW - Quantitative trait loci comparative sequence-analysis plant arabidopsis-thaliana transposable elements ltr retrotransposons yield components tropical maize gene-fragment cereal crops grain-yield Genetics & Heredity LB - ISI 2009 12 17 IS - 11 N1 - English Review NSF [DBI-0527192, DBI-0333074, DBI-0501818, DBI-0638525, DBI-0607123]; USDA_ARS CRIS [190721000-014-00D] PY - 2009 ST - Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome T2 - Plos Genetics TI - Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome VL - 5 ID - 4078 ER - TY - JOUR AB - Maize is a major cereal crop and an important model system for basic biological research. Knowledge gained from maize research can also be used to genetically improve its grass relatives such as sorghum, wheat, and rice. The primary objective of the Maize Genome Sequencing Consortium (MGSC) was to generate a reference genome sequence that was integrated with both the physical and genetic maps. Using a previously published integrated genetic and physical map, combined with in-coming maize genomic sequence, new sequence-based genetic markers, and an optical map, we dynamically picked a minimum tiling path (MTP) of 16,910 bacterial artificial chromosome (BAC) and fosmid clones that were used by the MGSC to sequence the maize genome. The final MTP resulted in a significantly improved physical map that reduced the number of contigs from 721 to 435, incorporated a total of 8,315 mapped markers, and ordered and oriented the majority of FPC contigs. The new integrated physical and genetic map covered 2,120 Mb (93%) of the 2,300-Mb genome, of which 405 contigs were anchored to the genetic map, totaling 2,103.4 Mb (99.2% of the 2,120 Mb physical map). More importantly, 336 contigs, comprising 94.0% of the physical map (similar to 1,993 Mb), were ordered and oriented. Finally we used all available physical, sequence, genetic, and optical data to generate a golden path (AGP) of chromosome-based pseudomolecules, herein referred to as the B73 Reference Genome Sequence version 1 (B73 RefGen_v1). AD - [Wei, Fusheng; Zhang, Jianwei; He, Ruifeng; Collura, Kristi; Kudrna, David; Wissotski, Marina; Golser, Wolfgang; Wing, Rod A.] Univ Arizona, Dept Plant Sci, Arizona Genom Inst, Inst Collaborat Res BIO5, Tucson, AZ 85721 USA. [Wei, Fusheng; Zhang, Jianwei; He, Ruifeng; Collura, Kristi; Kudrna, David; Wissotski, Marina; Golser, Wolfgang; Wing, Rod A.] Univ Arizona, Dept Ecol & Evolutionary Biol, Arizona Genom Inst, Inst Collaborat Res BIO5, Tucson, AZ 85721 USA. [Zhou, Shiguo; Schwartz, David C.] Univ Wisconsin, Genet Lab, Dept Chem, Lab Mol & Computat Genom, Madison, WI 53706 USA. [Schaeffer, Mary; Coe, Ed] USDA ARS, Plant Genet Res Unit, Columbia, MO USA. [Schaeffer, Mary; Coe, Ed] Univ Missouri, Div Plant Sci, Columbia, MO USA. [Faga, Ben P.; Ware, Doreen] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA. [Rock, Susan M.; Graves, Tina A.; Fulton, Robert S.; Clifton, Sandra W.; Wilson, Richard K.] Washington Univ, Sch Med, Genome Ctr, St Louis, MO USA. [Schnable, Patrick S.] Iowa State Univ, Ctr Plant Genom, Ames, IA USA. [Wilson, Richard K.] Washington Univ, Sch Med, Dept Genet, St Louis, MO 63110 USA. AN - ISI:000272419500011 AU - Wei, Fusheng AU - Zhang, Jianwei AU - Zhou, Shiguo AU - He, Ruifeng AU - Schaeffer, Mary AU - Collura, Kristi AU - Kudrna, David AU - Faga, Ben P. AU - Wissotski, Marina AU - Golser, Wolfgang AU - Rock, Susan M. AU - Graves, Tina A. AU - Fulton, Robert S. AU - Coe, Ed AU - Schnable, Patrick S. AU - Schwartz, David C. AU - Ware, Doreen AU - Clifton, Sandra W. AU - Wilson, Richard K. AU - Wing, Rod A. DA - Nov DO - e1000715 KW - Map sequence markers resources grasses Genetics & Heredity LB - ISI 2009 12 17 IS - 11 N1 - English Article NSF Plant Genome Program-The Maize Genome Sequencing Project [DBI-0527192]; Maize Optical Map Project [DBI-0501818] PY - 2009 ST - The Physical and Genetic Framework of the Maize B73 Genome T2 - Plos Genetics TI - The Physical and Genetic Framework of the Maize B73 Genome VL - 5 ID - 4077 ER - TY - JOUR AB - Currently, there is a lack of a sensitive and reliable premortem diagnostic test for prion diseases. Here we examine mass spectrometry (MS)-based methods to search for protein biomarkers of prion diseases from plasma samples. Dynamic range of detection is increased by glycoprotein enrichment and multidimensional separations. By utilizing isotopic labeling, quantitative information of a panel of biomarker candidates is obtained. AD - [Wei, Xin; Li, Lingjun] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. Sci, Madison, WI 53706 USA. 53706 USA. AN - ISI:000263662200006 AU - Wei, X. AU - Herbst, A. AU - Schmidt, J. AU - Aikent, J. AU - Li, L. J. DA - Feb KW - Mass-spectrometry apolipoprotein-e scrapie chromatography astrocytes proteomics proteins cells Chemistry, Analytical LB - ISI 2009 03 13 IS - 2 N1 - English Article 1527-5949 PY - 2009 SP - 154-+ ST - Facilitating Discovery of Prion Disease Biomarkers by Quantitative Glycoproteomics T2 - Lc Gc North America TI - Facilitating Discovery of Prion Disease Biomarkers by Quantitative Glycoproteomics VL - 27 ID - 3820 ER - TY - JOUR AB - The effects were studied of high water concentrations on the kinetics of alcohol dehydration, as encountered in aqueous-phase processing of biomass-derived oxygenated hydrocarbons. These studies were carried out for dehydration of an aqueous solution of 10 wt% 2-butanol at 513 K, and at a total pressure of 52 bar to maintain the water in the liquid state. Under these high pressures of water, silica-alumina, niobium phosphate and niobic acid are found to be stable and active for the dehydration of butanol. These three catalysts showed an increase in rate after contact with liquid water, caused by an increase in the concentration of Bronsted acid sites. Zeolite catalysts (Beta, USY, H-ZSM-5) and zirconia based catalysts (WOx/ZrO2, MoOx/ZrO2, and MgO/ZrO2) were ineffective due to deactivation or low catalytic activity. The flow rate of inert gas at constant aqueous flow rate had a significant effect on the rate of butene production, due to vaporization of butanol and water. At low flow rates of gas, increasing the gas flow rate causes the preferential vaporization of butanol, leading to a decrease in the butanol pressure in the reactor and a corresponding decrease in the rate of dehydration. Above a critical gas flow rate, the liquid feed becomes completely vaporized in the reactor, and increasing the gas flow rate further leads to a decrease in the pressure of water and a corresponding increase in the rate of dehydration. In the vapor-liquid equilibrium regime, kinetic models predict that most of the catalyst is covered with multiple layers of water, and dehydration takes place by reaction of hydrated-adsorbed butanol with a hydrated surface site. In the vapor-only regime, kinetic models suggest that the fraction of vacant active sites increases with increasing gas flow rate, and dehydration takes place by reaction of adsorbed butanol with a vacant surface site. (C) 2008 Elsevier Inc. All rights reserved. AD - [West, Ryan M.; Braden, Drew J.; Dumesic, James A.] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA. AN - ISI:000264123000016 AU - West, R. M. AU - Braden, D. J. AU - Dumesic, J. A. DA - Feb KW - 2-Butanol Dehydration Water Aqueous phase processing Silica-alumina Niobium phosphate Niobic acid Butene Adsorption biomass methanol zeolites alkanes surface sites fuels Chemistry, Physical Engineering, Chemical LB - ISI 2009 03 26 IS - 1 N1 - English Article 0021-9517 PY - 2009 SP - 134-143 ST - Dehydration of butanol to butene over solid acid catalysts in high water environments T2 - Journal of Catalysis TI - Dehydration of butanol to butene over solid acid catalysts in high water environments VL - 262 ID - 3891 ER - TY - JOUR AB - Aqueous solutions of sugars and polyols can be converted in a single catalytic process to produce a spontaneously separating organic phase consisting of hydrophobic mono-functional hydrocarbons. The process is shown to be stable for over 2 months time on stream at typical reaction conditions (e.g., 503 K and 18 bar total pressure). The composition and yield of this organic phase can be controlled by adjusting process variables, such as temperature, pressure and space velocity. This organic phase contains primarily mono-functional species such as ketones, alcohols, heterocycles, and organic acids. These oxygenated hydrocarbons can serve as an intermediate platform for the conversion of renewable biomass resources into chemicals and fuels. The organic phase can be separated into individual chemicals or can be upgraded to yield specific classes of chemicals. For example, heterocycles can be separated and used as solvents, additives or blending agents for transportation fuels, while aldol-condensation of the ketones and alcohols can produce long chains species for use as alkane fuels. Alternatively, this platform can be tuned to produce alcohols by reducing the ketone and acid groups. Dehydration of these alcohols produces olefins that have use in either the polymer industry, or as feeds for liquid fuels. (C) 2009 Elsevier B.V. All rights reserved. AD - [West, Ryan M.; Kunkes, Edward L.; Simonetti, Dante A.; Dumesic, James A.] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA. AN - ISI:000269765200009 AU - West, R. M. AU - Kunkes, E. L. AU - Simonetti, D. A. AU - Dumesic, J. A. DA - Sep KW - Biomass Carbohydrates Fuels Acid catalyst Base catalyst Supported metal catalyst Liquid-phase oligomerization aldol condensation al-mts 1-hexene zeolites acetone silica vapor acid Chemistry, Applied Chemistry, Physical Engineering, Chemical LB - ISI 2009 09 24 IS - 2 N1 - English Proceedings Paper PY - 2009 SP - 115-125 ST - Catalytic conversion of biomass-derived carbohydrates to fuels and chemicals by formation and upgrading of mono-functional hydrocarbon intermediates T2 - Catalysis Today TI - Catalytic conversion of biomass-derived carbohydrates to fuels and chemicals by formation and upgrading of mono-functional hydrocarbon intermediates VL - 147 ID - 4025 ER - TY - JOUR AD - [Wiecinski, Paige N.; Heiden, Tisha C. King; Heideman, Warren; Peterson, Richard E.; Pedersen, Joel A.] Univ Wisconsin, Mol & Environm Toxicol Ctr, Madison, WI USA. [Metz, Kevin M.; Pedersen, Joel A.] Univ Wisconsin, Environm Sci & Technol Program, Madison, WI USA. [Mangham, Andrew N.; Hamers, Robert J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Heideman, Warren; Peterson, Richard E.] Univ Wisconsin, Sch Pharm, Madison, WI 53706 USA. [Pedersen, Joel A.] Univ Wisconsin, Dept Soil Sci, Madison, WI 53706 USA. AN - ISI:000267229903562 AU - Wiecinski, P. N. AU - Heiden, T. C. K. AU - Metz, K. M. AU - Mangham, A. N. AU - Hamers, R. J. AU - Heideman, W. AU - Peterson, R. E. AU - Pedersen, J. A. DA - Jun KW - Geochemistry & Geophysics LB - ISI 2009 07 31 IS - 13 N1 - English Meeting Abstract Suppl. S PY - 2009 SP - A1437-A1437 ST - Developmental toxicity of oxidatively degraded quantum dots T2 - Geochimica et Cosmochimica Acta TI - Developmental toxicity of oxidatively degraded quantum dots VL - 73 ID - 3970 ER - TY - JOUR AB - The toxicity of engineered nanoparticles is expected to depend in part on their stability in biological systems. To assess the biodurability of engineered nanomaterials in the human digestive system, we adapted an in vitro assay previously used to evaluate the bioaccessibility of metals in contaminated soils. The compositions of the simulated gastric and intestinal fluids, temperature and residence times were designed to closely mimic conditions in the stomach and duodenum of the small intestine. We demonstrated the utility of the assay using CdSecore/ZnSshell quantum dots functionalized with polyethylene glycol (PEG) thiol of two different molecular masses (PEG(350) and PEG(5000)). Under gastric conditions, removal of the PEG ligand diminished the stability of PEG(350)-quantum dot suspensions, while PEG(5000)-quantum dots were severely degraded. Inclusion of the glycoprotein mucin, but not the digestive protein pepsin, in simulated gastric fluids provided both PEG(350)-and PEG(5000)-coated quantum dots partial protection from transformations induced by gastric conditions. AD - [Pedersen, Joel A.] Univ Wisconsin, Dept Soil Sci, Madison, WI 53706 USA. [Jacobson, Kurt H.; Pedersen, Joel A.] Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI 53706 USA. [Mangham, Andrew N.; Hamers, Robert J.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Metz, Kevin M.; Pedersen, Joel A.] Univ Wisconsin, Environm Chem & Technol Program, Madison, WI 53706 USA. [Wiecinski, Paige N.; Pedersen, Joel A.] Univ Wisconsin, Mol & Environm Toxicol Ctr, Madison, WI 53706 USA. AN - ISI:000274526400007 AU - Wiecinski, Paige N. AU - Metz, Kevin M. AU - Mangham, Andrew N. AU - Jacobson, Kurt H. AU - Hamers, Robert J. AU - Pedersen, Joel A. KW - gastrointestinal biodurability ingestion quantum dot exposure assessment degradation mucin Self-assembled monolayers quartz-crystal microbalance quantum dots semiconductor nanocrystals protein adsorption redox potentials vitreous fibers risk-assessment gastric mucin soil Nanoscience & Nanotechnology Toxicology LB - ISI 2010 02 25 IS - 3 N1 - English Article National Science Foundation [DMR-0425880]; NIH [NIH 5 T32 GM08349] PY - 2009 SP - 202-U66 ST - Gastrointestinal biodurability of engineered nanoparticles: Development of an in vitro assay T2 - Nanotoxicology TI - Gastrointestinal biodurability of engineered nanoparticles: Development of an in vitro assay VL - 3 ID - 4182 ER - TY - JOUR AB - Background: Infection of cattle with Mycobacterium avium subspecies paratuberculosis (M. ap) causes severe economic losses to the dairy industry in the USA and worldwide. In an effort to better examine diversity among M. ap strains, we used optical mapping to profile genomic variations between strains of M. ap K-10 (sequenced strain) and M. ap ATCC 19698 (type strain). Results: The assembled physical restriction map of M. ap ATCC 19698 showed a genome size of 4,839 kb compared to the sequenced K-10 genome of 4,830 kb. Interestingly, alignment of the optical map of the M. ap ATCC 19698 genome to the complete M. ap K-10 genome sequence revealed a 648-kb inversion around the origin of replication. However, Southern blotting, PCR amplification and sequencing analyses of the inverted region revealed that the genome of M. ap K-10 differs from the published sequence in the region starting from 4,197,080 bp to 11,150 bp, spanning the origin of replication. Additionally, two new copies of the coding sequences > 99.8% were identified, identical to the MAP0849c and MAP0850c genes located immediately downstream of the MAP3758c gene. Conclusion: The optical map of M. ap ATCC 19698 clearly indicated the miss-assembly of the sequenced genome of M. ap K-10. Moreover, it identified 2 new genes in M. ap K-10 genome. This analysis strongly advocates for the utility of physical mapping protocols to complement genome sequencing projects. AN - ISI:000263111500001 AU - Wu, C. W. AU - Schramm, T. M. AU - Zhou, S. G. AU - Schwartz, D. C. AU - Talaat, A. M. DA - Jan DO - 25 10.1186/1471-2164-10-25 LB - ISI 2009 02 20 N1 - Wu, Chia-wei Schramm, Timothy M. Zhou, Shiguo Schwartz, David C. Talaat, Adel M. PY - 2009 SN - 1471-2164 ST - Optical mapping of the Mycobacterium avium subspecies paratuberculosis genome T2 - Bmc Genomics TI - Optical mapping of the Mycobacterium avium subspecies paratuberculosis genome UR - ://000263111500001 VL - 10 ID - 3788 ER - TY - JOUR AB - We use nonlinear 2D IR spectroscopy to study TiO2 nanocrystalline thin films sensitized with a Re dye. We find that the free electron signal, which often obscures the vibrational features in the transient absorption spectrum, is not observed in the 2D IR spectra. Its absence allows the vibrational features of the dye to be much better resolved than with the typical IR absorption probe, We observe multiple absorption bands but no cross peaks in the 2D IR spectra, which indicates that the dyes have at least three conformations. Furthermore, by using a pulse sequence in which we initiate electron transfer in the middle of the infrared pulse train, we are able to assign the excited state features by correlating them to the ground state vibrational modes and determine that the three conformations have different time scales and cross sections for electron injection. 2D IR spectroscopy is proving to be very useful in disentangling overlapping structural distributions in biological and chemical physics processes. These experiments demonstrate that nonlinear infrared probes are also a powerful new tool. for studying charge transfer at interfaces. AD - [Xiong, Wei; Laaser, Jennifer E.; Paoprasert, Peerasak; Franking Zanni, MT, Univ Wisconsin, Dept Chem, 1101 Univ Ave, Madison, WI 53706 USA. zanni@chem.wisc.edu AN - ISI:000273615400015 AU - Xiong, W. AU - Laaser, J. E. AU - Paoprasert, P. AU - Franking, R. A. AU - Hamers, R. J. AU - Gopalan, P. AU - Zanni, M. T. DA - Dec DO - 10.1021/ja908479r KW - electron-transfer infrared-spectroscopy ultrafast nanoparticles complexes light time LA - English LB - ISI 2010 02 02 IS - 50 M3 - Article N1 - Xiong, Wei Laaser, Jennifer E. Paoprasert, Peerasak Franking, Ryan A. Hamers, Robert J. Gopalan, Padma Zanni, Martin T. 16 Amer chemical soc; 1155 16th st, nw, washington, dc 20036 usa 543xy PY - 2009 SN - 0002-7863 SP - 18040-+ ST - Transient 2D IR Spectroscopy of Charge Injection in Dye-Sensitized Nanocrystalline Thin Films T2 - Journal of the American Chemical Society TI - Transient 2D IR Spectroscopy of Charge Injection in Dye-Sensitized Nanocrystalline Thin Films VL - 131 ID - 4166 ER - TY - JOUR AB - Two-dimensional infrared spectroscopy is a powerful tool for studying molecular structure and kinetics. However, standard ways of implementing the technique are not amenable to samples with high optical densities. In this paper, we demonstrate that a shaper-based automated 2D IR spectrometer largely compensates for most of the distortions caused by high optical densities. By comparing a series of 2D IR spectra collected with varying concentrations and sample thicknesses, we find that high quality 2D IR spectra can be obtained at optical densities of >1.2 when these spectra are collected using a pulse shaping method recently developed in our lab. Furthermore, distortions due to high OD primarily appear along the pump axis and are largely absent along the probe axis. Using this knowledge, we have applied Our approach to study a high optical density sample of a truncated form of the human islet amyloid peptide that is involved in Type 2 diabetes. Our methodology promises to aid in the interpretation of 2D IR lineshapes for systems where the optical density cannot be controlled, such as in protein folding or chemical reactions where large changes in optical density occur during the kinetics. Published by Elsevier B.V. AD - [Xiong, Wei; Strasfeld, David B.; Shim, Sang-Hee; Zanni, Martin T.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000266623000019 AU - Xiong, W. AU - Strasfeld, D. B. AU - Shim, S. H. AU - Zanni, M. T. DA - May KW - Infrared spectroscopy 2D IR spectroscopy Optical density Pulse shaping 2-dimensional infrared-spectroscopy islet amyloid polypeptide photon-echo spectroscopy propagation domain fibrillogenesis identification generation vibrations mechanism Chemistry, Analytical Chemistry, Physical Spectroscopy LB - ISI 2009 06 19 IS - 1 N1 - English Article NSF [CHE0350518]; Parkard Foundation Sp. Iss. SI PY - 2009 SP - 136-142 ST - Automated 2D IR spectrometer mitigates the influence of high optical densities T2 - Vibrational Spectroscopy TI - Automated 2D IR spectrometer mitigates the influence of high optical densities VL - 50 ID - 3932 ER - TY - JOUR AB - Electron-rich aromatic C-H bonds undergo regioselective chlorination and bromination in the presence of CuX2, LiX (X = Cl, Br) and molecular oxygen. Preliminary mechanistic insights suggest that the bromination and chlorination reactions proceed by different pathways. AD - [Yang, Lujuan; Lu, Zhan; Stahl, Shannon S.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Yang, Lujuan] Xiamen Univ, Dept Chem, Coll Chem & Chem Engn, Xiamen 361005, Peoples R China. [Yang, Lujuan] Xiamen Univ, State Key Lab Phys Chem Solid Surfaces, Xiamen 361005, Peoples R China. AN - ISI:000270973600039 AU - Yang, L. J. AU - Lu, Z. AU - Stahl, S. S. KW - C-h aromatic-compounds mild conditions bond formation complexes oxybromination efficient bromide phenols ketones Chemistry, Multidisciplinary LB - ISI 2009 10 29 IS - 42 N1 - English Article Department of Energy [DE-FG02-05ER15690]; China Scholarship Council PY - 2009 SP - 6460-6462 ST - Regioselective copper-catalyzed chlorination and bromination of arenes with O-2 as the oxidant T2 - Chemical Communications TI - Regioselective copper-catalyzed chlorination and bromination of arenes with O-2 as the oxidant ID - 4062 ER - TY - JOUR AB - Combined quantum mechanical/molecular mechanical (QM/MM) calculations with density functional theory are employed to analyze two issues related to the hydrolysis activity of adenosine triphosphate (ATP) in myosin. First, we compare the geometrical properties and electronic structure of ATP in the open (post-rigor) and closed (pre-powerstroke) active sites of the myosin motor domain. Compared to both solution and the open active site cases, the scissile P-gamma-O-3 beta bond of ATP in the closed active site is shown to be substantially elongated. Natural bond orbital (NBO) analysis clearly shows that this structural feature is correlated with the stronger anomeric effects in the closed active site, which involve charge transfers from the lone pairs in the nonbridging oxygen in the gamma-phosphate to the antibonding orbital of the scissile bond. However, an energetic analysis finds that the ATP molecule is not significantly destabilized by the P-gamma-O-3 beta bond elongation. Therefore, despite the notable perturbations in the geometry and electronic structure of ATP as its environment changes from solution to the hydrolysis-competent active site, ground-state destabilization is unlikely to play a major role in enhancing the hydrolysis activity in myosin. Second, two-dimensional potential energy maps are used to better characterize the energetic landscape near the hydrolysis transition state. The results indicate that the transition-state region is energetically flat and a range of structures representative of different mechanisms according to the classical nomenclature (e.g., "associative", "dissociative", and "concerted") are very close in energy. Therefore, at least in the case of ATP hydrolysis in myosin, the energetic distinction between different reaction mechanisms following the conventional nomenclature is likely small. This study highlights the importance of (i) explicitly evaluating the relevant energetic properties for determining whether a factor is essential to catalysis and (ii) broader explorations of the energy landscape beyond saddle points (even oil free-energy surface) for characterizing the molecular mechanism of catalysis. AD - [Yang, Yang] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. Univ Wisconsin, Inst Theoret Chem, Madison, WI 53706 USA. AN - ISI:000271428100015 AU - Yang, Yang AU - Cui, Qiang DA - Nov KW - Phosphate monoester hydrolysis polarizable continuum model reaction-path calculations molecular-orbital methods tight-binding method gaussian-basis sets x-ray structures atp hydrolysis motor domain muscle-contraction Chemistry, Physical Physics, Atomic, Molecular & Chemical LB - ISI 2009 12 11 IS - 45 N1 - English Article National Institutes of Health [R01-GM071428] PY - 2009 SP - 12439-12446 ST - The Hydrolysis Activity of Adenosine Triphosphate in Myosin: A Theoretical Analysis of Anomeric Effects and the Nature of the Transition State T2 - Journal of Physical Chemistry A TI - The Hydrolysis Activity of Adenosine Triphosphate in Myosin: A Theoretical Analysis of Anomeric Effects and the Nature of the Transition State VL - 113 ID - 4072 ER - TY - JOUR AB - The molecular modeling of polyelectrolyte solutions is considered one of the grand challenges of condensed phase physical chemistry. There have been many advances in our understanding of these systems, and the insight obtained from liquid state approaches is reviewed in this article. Integral equation theories have been successful in describing the structural properties of polyelectrolytes in good solvents. The theory provides an accurate description (when compared to computer simulations and experiment) of the static structure, conformational properties, surface forces, and osmotic pressure of polyelectrolyte solutions. Challenges remain for the description of strongly coupled systems and poor solvents, and some possible future directions are discussed. AN - ISI:000263134500001 AU - Yethiraj, A. DA - Feb DO - 10.1021/jp8069964 LB - ISI 2009 02 20 IS - 6 N1 - Yethiraj, Arun PY - 2009 SN - 1520-6106 SP - 1539-1551 ST - Liquid State Theory of Polyelectrolyte Solutions T2 - Journal of Physical Chemistry B TI - Liquid State Theory of Polyelectrolyte Solutions UR - ://000263134500001 VL - 113 ID - 3779 ER - TY - JOUR AB - Although many membrane additives are known to modulate the activities of membrane proteins via perturbing the properties of lipid membrane, the underlying mechanism is often not precisely understood. In this study, we investigate the impact of asymmetrically incorporating single-tailed lysophosphatidylcholine (LPC) into a membrane bilayer using coarse-grained molecular dynamics simulations. Using a simple computational protocol designed to approximately mimic a micropipette setting, we show that asymmetric incorporation of LPC can lead to significant curvature in a bilayer. Detailed analysis of geometrical and mechanical properties (pressure profile) of the resulting mound structure indicates that the degree of pressure profile perturbation is determined not by the local curvature per se but by the packing of lipid headgroups (i.e., area-per-lipid). The findings help provide a concrete basis for understanding the activation mechanism of mechanosensitive channels by asymmetric incorporation of LPC into membrane patches in patch-clamp experiments. The calculated local pressure profiles are valuable to the construction of realistic membrane models for the analysis of mechanosensation in a continuum mechanics framework. AD - [Yoo, Jejoong; Cui, Qiang] Univ Wisconsin, Grad Program Biophys, Madison, WI 53706 USA. [Cui, Qiang] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Cui, Qiang] Univ Wisconsin, Inst Theoret Chem, Madison, WI 53706 USA. AN - ISI:000270892000017 AU - Yoo, J. AU - Cui, Q. DA - Oct KW - Prokaryotic mechanosensitive channels molecular-dynamics simulations lipid-bilayer elasticity protein function force-field gating mechanisms large-conductance surface-tension cholesterol mscl Biophysics LB - ISI 2009 10 29 IS - 8 N1 - English Article National Institutes of Health [R01-GM071428] PY - 2009 SP - 2267-2276 ST - Curvature Generation and Pressure Profile Modulation in Membrane by Lysolipids: Insights from Coarse-Grained Simulations T2 - Biophysical Journal TI - Curvature Generation and Pressure Profile Modulation in Membrane by Lysolipids: Insights from Coarse-Grained Simulations VL - 97 ID - 4063 ER - TY - JOUR AB - Living cells sense extracellular signals and direct their movements in response to stimuli in environment. Such autonomous movement allows these machines to sample chemical change over a distance, leading to chemotaxis. Synthetic catalytic rods have been reported to chemotax toward hydrogen peroxide fuel. Nevertheless individualized autonomous control of movement of a population of biomolecules under physiological conditions has not been demonstrated. Here we show the first experimental evidence that a molecular complex consisting of a DNA template and associating RNA polymerases (RNAPs) displays chemokinetic motion driven by transcription substrates, nucleoside triphosphates (NTPs). Furthermore this molecular complex exhibits a biased migration into a concentration gradient of NTPs, resembling chemotaxis. We describe this behavior as "Molecular Propulsion", in which RNAP transcriptional actions deform DNA template conformation engendering measurable enhancement of motility. Our results provide new opportunities for designing and directing nanomachines by imposing external triggers within an experimental system. AD - [Yu, Hua; Jo, Kyubong; Kounovsky, Kristy L.; Schwartz, David C.] Univ Wisconsin, Dept Chem, Lab Mol & Computat Genom, Madison, WI 53706 USA. [de Pablo, Juan J.] Univ Wisconsin, Dept Biol & Chem Engn, Madison AN - ISI:000265460200004 AU - Yu, H. AU - Jo, K. AU - Kounovsky, K. L. AU - de Pablo, J. J. AU - Schwartz, D. C. DA - Apr KW - Transcription motor Chemistry, Multidisciplinary LB - ISI 2009 05 14 IS - 16 N1 - English Article National Institutes of Health, Human Genome Research Institute, USA ; National Science Foundation PY - 2009 SP - 5722-+ ST - Molecular Propulsion: Chemical Sensing and Chemotaxis of DNA Driven by RNA Polymerase T2 - Journal of the American Chemical Society TI - Molecular Propulsion: Chemical Sensing and Chemotaxis of DNA Driven by RNA Polymerase VL - 131 ID - 3981 ER - TY - JOUR AB - Nosiheptide (NOS), belonging to thee series of thiopeptide antibiotics that exhibit potent activity against various bacterial pathogens, bears a unique indole side ring system and regiospecific hydroxyl groups on the characteristic macrocyclic core. Here, cloning, sequencing, and characterization of the nos gene cluster from Streptomyces actuosus ATCC 25421 as a model for this series of thiopeptides has unveiled new insights Into their biosynthesis. Bioinformatics-based sequence analysis and In vivo Investigation Into the gene functions show that NOS biosynthesis shares a common strategy with recently characterized b or c series thiopeptides for forming the characteristic macrocyclic core, which features a ribosomally synthesized precursor peptide with conserved posttranslational modifications. However, it apparently proceeds via a different route for tailoring the thiopeptide framework, allowing the final product to exhibit the distinct structural characteristics of e series thiopeptides, such as the indole side ring system. Chemical complementation supports the notion that the S-adenosylmethionine-dependent protein NosL may play a central role in converting tryptophan to the key 3-methylindole moiety by an unusual carbon side chain rearrangement, most likely via a radical-initiated mechanism. Characterization of the indole side ring-opened analogue of NOS from the nosN mutant strain Is consistent with the proposed methyltransferase activity of Its encoded protein, shedding light into the timing of the individual steps for Indole side ring biosynthesis. These results also suggest the feasibility of engineering novel thiopeptides for drug discovery by manipulating the NOS biosynthetic machinery. AD - [Yu, Yi; Duan, Lian; Zhang, Qi; Liao, Rijing; Ding, Ying; Pan, Haixue; Tang, Gongli; Liu, Wen] Chinese Acad Sci, Shanghai Inst Organ Chem, State Key Lab Bioorgan & Nat Prod Chem, Shanghai 200032, Peoples R China. [Yu, Yi; Liu, Wen] Shanghai Jiao Tong Univ, Lab Microbial Metab, Shanghai 200030, Peoples R China. [Yu, Yi; Liu, Wen] Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, Shanghai 200030, Peoples R China. [Wendt-Pienkowski, Evelyn; Shen, Ben] Univ Wisconsin, Div Pharmaceut Sci, Sch Pharm, Madison, WI 53705 USA. AN - ISI:000272562000006 AU - Yu, Yi AU - Duan, Lian AU - Zhang, Qi AU - Liao, Rijing AU - Ding, Ying AU - Pan, Haixue AU - Wendt-Pienkowski, Evelyn AU - Tang, Gongli AU - Shen, Ben AU - Liu, Wen DA - Oct KW - Thiazolyl peptide antibiotics nocathiacin-i analogs streptomyces-actuosus posttranslational modifications antibacterial activity escherichia-coli assembly-line gene-cluster nocardia sp thiostrepton Biochemistry & Molecular Biology LB - ISI 2009 12 24 IS - 10 N1 - English Article NIH of U.S [CA094426]; National Natural Science Foundation of China [30525001, 90713012, 20832009]; Ministry of Science and Technology of China [2006AA022185, 2009ZX09501-008]; Chinese Academy of Sciences [KJCX2-YW-H08]; Science and Technology Commission of Shanghai Municipality [09QH1402700] PY - 2009 SP - 855-864 ST - Nosiheptide Biosynthesis Featuring a Unique Indole Side Ring Formation on the Characteristic Thiopeptide Framework T2 - ACS Chemical Biology TI - Nosiheptide Biosynthesis Featuring a Unique Indole Side Ring Formation on the Characteristic Thiopeptide Framework VL - 4 ID - 4114 ER - TY - JOUR AB - Poly-beta-peptides are attractive for biomedical applications because the backbone is similar enough to that of proteins for biocompatibility, but the backbone is sufficiently unnatural that these polymers evade proteolytic degradation. Prior investigations of poly-p-peptides have been hindered by two principal limitations: (1) most known examples are insoluble, and (2) the range of accessible side chain functionality has been quite limited (mostly simple hydrocarbon units). The present study describes innovations in poly-peptide synthesis that enable the preparation of diversely functionalized examples and provide the basis for broad exploration of the properties and applications of these nylon-3 materials. We describe several beta-lactams with a protected amino group in their side chain that readily undergo ring-opening polymerization (ROP). These monomers are available in large quantities via N-chlorosulfonylisocyanate (CSI) cycloaddition reactions with functionalized alkenes; previously CSI reactions have been limited to alkenes with hydrocarbon substituents. Postpolymerization deprotection of the amino groups leads to water-soluble poly-beta-peptides. In addition, we introduce a simple co-initiation strategy that allows placement of a wide variety of functional groups at the N-termini of poly-beta-peptide chains. ROP involving the new beta-lactams and co-initiation strategy exhibits characteristics of a controlled polymerization and enables the preparation of amphiphilic block copolymers. We have recently shown that cationic copoly-beta-peptides made available by these innovations mimic the selective antibacterial activity of host-defense peptides; the results described here provide the foundation for further exploration of this valuable activity and for the pursuit of other biological applications such as DNA/siRNA delivery and tissue engineering. AD - [Zhang, Jihua; Kissounko, Denis A.; Lee, Sarah E.; Gellman, Samuel H.; Stahl, Shannon S.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000264791800056 AU - Zhang, J. H. AU - Kissounko, D. A. AU - Lee, S. E. AU - Gellman, S. H. AU - Stahl, S. S. DA - Feb KW - Living anionic-polymerization host-defense peptides antimicrobial peptides poly(beta-peptides) therapeutics polypeptides copolymer chemistry Chemistry, Multidisciplinary LB - ISI 2009 04 17 IS - 4 N1 - English Article 0002-7863 PY - 2009 SP - 1589-1597 ST - Access to Poly-beta-Peptides with Functionalized Side Chains and End Groups via Controlled Ring-Opening Polymerization of beta-Lactams T2 - Journal of the American Chemical Society TI - Access to Poly-beta-Peptides with Functionalized Side Chains and End Groups via Controlled Ring-Opening Polymerization of beta-Lactams VL - 131 ID - 3880 ER - TY - JOUR AD - [Zhang, Xinhao; Zummack, Waltraud; Schwarz, Helmut] Tech Univ Berlin, Inst Chem, D-10623 Berlin, Germany. [Schroeder, Detlef] Acad Sci Czech Republic, Inst Organ Chem & Biochem, CR-16610 Prague 6, Czech Republic. [Weinhold, Frank A.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000272109100004 AU - Zhang, Xinhao AU - Zummack, Waltraud AU - Schroeder, Detlef AU - Weinhold, Frank A. AU - Schwarz, Helmut KW - hydrogen migration isotope effects keto-enol tautomerism nonergodic behavior reaction mechanisms Acetone radical-cation h bond activation correlated molecular calculations coupled-cluster singles gaussian-basis sets gas-phase nonstatistical dynamics polyatomic-molecules electron-affinities energy Chemistry, Multidisciplinary LB - ISI 2009 12 11 IS - 44 N1 - English Article Fonds der Chemischen Industrie, the Deutsche Forschungsgemeinschaft ; Academy of Sciences of the Czech Republic [Z40550506]; Alexander von Humboldt-Stiftung PY - 2009 SP - 11815-11819 ST - Isotope-Sensitive Degenerate [1,3]-Hydrogen Migration versus Competitive Enol-Keto Tautomerization T2 - Chemistry-A European Journal TI - Isotope-Sensitive Degenerate [1,3]-Hydrogen Migration versus Competitive Enol-Keto Tautomerization VL - 15 ID - 4075 ER - TY - JOUR AB - Conventional and temperature-modulated differential scanning calorimetry (DSC) experiments have been carried out oil miscible blends of polyisoprene (PI) and poly(4-tert-butylstyrene) (P4tBS) over a broad composition range. This system is characterized by all extraordinarily large T-g difference (similar to 215 K) between the two homopolymers. Two distinct calorimetric glass transitions were observed in blends of intermediate compositions(25%-50% PI) by both conventional and temperature-modulated DSC. Good agreement was found between the component T-g values measured by the two methods. Fitting of the component T-g values to the Lodge-McLeish model gives a phi(self) of around 0.63 for PI in this blend and 0.03 for P4tBS. The extracted phi(self) for PI is comparable to reported values for PEO in blends with PMMA and is significantly larger than values reported for PI in other blends with smaller homopolymer T-g differences. This observation is consistent with the presence of a nonequilibrium or confinement effect in PI/P4tBS blends, which results in enhanced dynamics of the fast component below the T-g of the slow component. AD - [Zhao, Junshu; Ediger, M. D.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Sun, Ye; Yu, Lian] Univ Wisconsin, Sch Pharm, Madison, WI 53705 USA. AN - ISI:000269635900054 AU - Zhao, J. S. AU - Ediger, M. D. AU - Sun, Y. AU - Yu, L. DA - Sep KW - Poly(ethylene oxide) dynamics segmental dynamics polymer blends terminal dynamics component dynamics poly(methyl methacrylate) poly(vinyl acetate) neutron-scattering solvent mixtures polyisoprene Polymer Science LB - ISI 2009 10 23 IS - 17 N1 - English Article National Science Foundation [DMR-0355470, DMR-0907607] PY - 2009 SP - 6777-6783 ST - Two DSC Glass Transitions in Miscible Blends of Polyisoprene/Poly(4-tert-butylstyrene) T2 - Macromolecules TI - Two DSC Glass Transitions in Miscible Blends of Polyisoprene/Poly(4-tert-butylstyrene) VL - 42 ID - 4054 ER - TY - JOUR AB - About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence build. For this purpose, we constructed a genome-wide, high-resolution optical map of the maize inbred line B73 genome containing >91,000 restriction sites (averaging 1 site/similar to 23 kb) accrued from mapping genomic DNA molecules. Our optical map comprises 66 contigs, averaging 31.88 Mb in size and spanning 91.5% (2,103.93 Mb/similar to 2,300 Mb) of the maize genome. A new algorithm was created that considered both optical map and unfinished BAC sequence data for placing 60/66 (2,032.42 Mb) optical map contigs onto the maize iMap. The alignment of optical maps against numerous data sources yielded comprehensive results that proved revealing and productive. For example, gaps were uncovered and characterized within the iMap, the FPC (fingerprinted contigs) map, and the chromosome-wide pseudomolecules. Such alignments also suggested amended placements of FPC contigs on the maize genetic map and proactively guided the assembly of chromosome-wide pseudomolecules, especially within complex genomic regions. Lastly, we think that the full integration of B73 optical maps with the maize iMap would greatly facilitate maize sequence finishing efforts that would make it a valuable reference for comparative studies among cereals, or other maize inbred lines and cultivars. AD - [Zhou, Shiguo; Bechner, Mike; Potamousis, Konstantinos; Goldstein, Steve; Pape, Louise; Churas, Chris; Forrest, Dan K.; Schwartz, David C.] Univ Wisconsin, Dept Chem, Lab Mol & Computat Genom, Lab Genet,Biotechnol Ctr, Madison, WI 53706 USA. [Wei, Fusheng; Wing, Rod A.] Univ Arizona, Dept Plant Sci, Arizona Genom Inst, Tucson, AZ 85721 USA. [Nguyen, John; Mehan, Michael R.; Waterman, Michael S.] Univ So Calif, Dept Math, Los Angeles, CA 90089 USA. [Nguyen, John; Mehan, Michael R.; Waterman, Michael S.] Univ So Calif, Dept Biol, Los Angeles, CA 90089 USA. [Nguyen, John; Mehan, Michael R.; Waterman, Michael S.] Univ So Calif, Dept Comp Sci, Los Angeles, CA 90089 USA. [Pasternak, Shiran; Ware, Doreen] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA. [Wise, Roger] ARS, USDA, Ames, IA USA. [Wise, Roger] Iowa State Univ, Dept Plant Pathol, Ames, IA USA. [Ware, Doreen] ARS, USDA, Ithaca, NY USA. [Livny, Miron] Univ Wisconsin, Dept Comp Sci, Madison, WI 53706 USA. AN - ISI:000272419500007 AU - Zhou, Shiguo AU - Wei, Fusheng AU - Nguyen, John AU - Bechner, Mike AU - Potamousis, Konstantinos AU - Goldstein, Steve AU - Pape, Louise AU - Mehan, Michael R. AU - Churas, Chris AU - Pasternak, Shiran AU - Forrest, Dan K. AU - Wise, Roger AU - Ware, Doreen AU - Wing, Rod A. AU - Waterman, Michael S. AU - Livny, Miron AU - Schwartz, David C. DA - Nov DO - e1000711 KW - Artificial chromosome library genetic-map optical maps plasmodium-falciparum sequence-analysis restriction maps plant genomes dna retrotransposons hybridization Genetics & Heredity LB - ISI 2009 12 17 IS - 11 N1 - English Article NSF [DBI-0501818]; NHGRI [R01 HG000225] PY - 2009 ST - A Single Molecule Scaffold for the Maize Genome T2 - Plos Genetics TI - A Single Molecule Scaffold for the Maize Genome VL - 5 ID - 4076 ER - TY - JOUR AB - Our research on the triplet photochemistry of vinylcyclopropenes has dealt with a diverse series of systems, providing a series of experimental examples and mechanstic studies. It perhaps is not surprising that the reaction mechanisms have been controversial. The present study is theoretical and provides evidence for control by a critical T-1 diradical intermediate which has a high spin-orbit coupling with S-0 ground-state along the mechanistic pathway. The evidence now for the one pathway derives from independent generation and behavior of this diradical, prediction of the reaction regioselectivity in nine diverse examples, the S-0 and T-1 hypersurfaces in the reaction, arid an S-0-T-1 degeneracy with SOC for the critical diradical. This triplet diradical when independently generated gives the same regioselectivity observed in examples starting with the vinylcyclopropene triplet itself. The overall reaction provides a useful synthesis of cyclopentadienes. AN - ISI:000263004300036 AU - Zimmerman, H. E. DA - Feb DO - 10.1021/jo802313r LB - ISI 2009 02 20 IS - 3 N1 - Zimmerman, Howard E. PY - 2009 SN - 0022-3263 SP - 1247-1251 ST - Triplet Photochemistry of Vinyl Cyclopropenes: Mechanistic and Exploratory Organic Photochemistry T2 - Journal of Organic Chemistry TI - Triplet Photochemistry of Vinyl Cyclopropenes: Mechanistic and Exploratory Organic Photochemistry UR - ://000263004300036 VL - 74 ID - 3781 ER - TY - JOUR AB - The Type-A photochemistry of cyclohexadienones is well-studied and follows a well-established mechanistic pathway. One early example is the rearrangement of santonin to lumisantonin. Another example is the rearrangement of 4,4-diphenylcyclohexa-1,5-dienone. Remarkably, replacement of one carbon by nitrogen alters the reaction course to give a regioselective phenyl migration. AD - [Zimmerman, Howard E.; Shorunov, Sergey] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. AN - ISI:000268480300037 AU - Zimmerman, H. E. AU - Shorunov, S. DA - Aug KW - Chemistry, Organic LB - ISI 2009 08 13 IS - 15 N1 - English Article National Science Foundation PY - 2009 SP - 5411-5416 ST - Heterocyclic Photochemistry in Contrast with Carbon Behavior. Regioselective Photochemical Rearrangement of an Azacyclohexadienone: Mechanistic and Exploratory Organic Photochemistry T2 - Journal of Organic Chemistry TI - Heterocyclic Photochemistry in Contrast with Carbon Behavior. Regioselective Photochemical Rearrangement of an Azacyclohexadienone: Mechanistic and Exploratory Organic Photochemistry VL - 74 ID - 3993 ER -