Top Publications

  1. ncbi Gold nanoparticles: assembly, supramolecular chemistry, quantum-size-related properties, and applications toward biology, catalysis, and nanotechnology
    Marie Christine Daniel
    Molecular Nanosciences and Catalysis Group, LCOO, UMR CNRS No 5802, Universite Bordeaux I, 33405 Talence Cedex, France
    Chem Rev 104:293-346. 2004
  2. ncbi Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis
    Marcin Nowotny
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Cell 121:1005-16. 2005
  3. pmc A general two-metal-ion mechanism for catalytic RNA
    T A Steitz
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
    Proc Natl Acad Sci U S A 90:6498-502. 1993
  4. ncbi Industrial biocatalysis today and tomorrow
    A Schmid
    Institute of Biotechnology, , , Switzerland
    Nature 409:258-68. 2001
  5. ncbi Pd-Pt bimetallic nanodendrites with high activity for oxygen reduction
    Byungkwon Lim
    Department of Biomedical Engineering, Washington University, St Louis, MO 63130, USA
    Science 324:1302-5. 2009
  6. pmc Ligand effects in homogeneous Au catalysis
    David J Gorin
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Chem Rev 108:3351-78. 2008
  7. ncbi Single-atom catalysis of CO oxidation using Pt1/FeOx
    Botao Qiao
    State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
    Nat Chem 3:634-41. 2011
  8. ncbi Allosteric regulation and catalysis emerge via a common route
    Nina M Goodey
    Montclair State University, Department of Chemistry and Biochemistry, 1 Normal Avenue, Montclair, New Jersey 07043, USA
    Nat Chem Biol 4:474-82. 2008
  9. ncbi Mechanistic evidence for a front-side, SNi-type reaction in a retaining glycosyltransferase
    Seung Seo Lee
    Department of Chemistry, University of Oxford, Oxford, United Kingdom
    Nat Chem Biol 7:631-8. 2011
  10. ncbi Programming biomolecular self-assembly pathways
    Peng Yin
    Department of Bioengineering, California Institute of Technology, Pasadena, California 91125, USA
    Nature 451:318-22. 2008

Research Grants

Detail Information

Publications370 found, 100 shown here

  1. ncbi Gold nanoparticles: assembly, supramolecular chemistry, quantum-size-related properties, and applications toward biology, catalysis, and nanotechnology
    Marie Christine Daniel
    Molecular Nanosciences and Catalysis Group, LCOO, UMR CNRS No 5802, Universite Bordeaux I, 33405 Talence Cedex, France
    Chem Rev 104:293-346. 2004
  2. ncbi Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis
    Marcin Nowotny
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    Cell 121:1005-16. 2005
    ..RNase H complexed with an RNA/DNA hybrid and a mechanism for substrate recognition and two-metal-ion-dependent catalysis. RNase H specifically recognizes the A form RNA strand and the B form DNA strand...
  3. pmc A general two-metal-ion mechanism for catalytic RNA
    T A Steitz
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
    Proc Natl Acad Sci U S A 90:6498-502. 1993
    ..The mechanism postulates that chemical catalysis is facilitated by two divalent metal ions 3...
  4. ncbi Industrial biocatalysis today and tomorrow
    A Schmid
    Institute of Biotechnology, , , Switzerland
    Nature 409:258-68. 2001
    ..As the use of biocatalysis for industrial chemical synthesis becomes easier, several chemical companies have begun to increase significantly the number and sophistication of the biocatalytic processes used in their synthesis operations...
  5. ncbi Pd-Pt bimetallic nanodendrites with high activity for oxygen reduction
    Byungkwon Lim
    Department of Biomedical Engineering, Washington University, St Louis, MO 63130, USA
    Science 324:1302-5. 2009
    ..The Pd-Pt nanodendrites were two and a half times more active on the basis of equivalent Pt mass for the ORR than the state-of-the-art Pt/C catalyst and five times more active than the first-generation supportless Pt-black catalyst...
  6. pmc Ligand effects in homogeneous Au catalysis
    David J Gorin
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Chem Rev 108:3351-78. 2008
  7. ncbi Single-atom catalysis of CO oxidation using Pt1/FeOx
    Botao Qiao
    State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
    Nat Chem 3:634-41. 2011
  8. ncbi Allosteric regulation and catalysis emerge via a common route
    Nina M Goodey
    Montclair State University, Department of Chemistry and Biochemistry, 1 Normal Avenue, Montclair, New Jersey 07043, USA
    Nat Chem Biol 4:474-82. 2008
    ..In this review, conformational mobility as the common route between allosteric regulation and catalysis is discussed...
  9. ncbi Mechanistic evidence for a front-side, SNi-type reaction in a retaining glycosyltransferase
    Seung Seo Lee
    Department of Chemistry, University of Oxford, Oxford, United Kingdom
    Nat Chem Biol 7:631-8. 2011
    ..Together, these comprehensive, quantitative data substantiate this unusual enzymatic reaction mechanism. Its discovery should prompt useful reassessment of many biocatalysts and their substrates and inhibitors...
  10. ncbi Programming biomolecular self-assembly pathways
    Peng Yin
    Department of Bioengineering, California Institute of Technology, Pasadena, California 91125, USA
    Nature 451:318-22. 2008
  11. ncbi Crystal structure of a self-spliced group II intron
    Navtej Toor
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, Bass Building, New Haven, CT 06511, USA
    Science 320:77-82. 2008
    ..coordinate two divalent metal ions in a configuration that is consistent with a two-metal ion mechanism for catalysis. Structural and functional analogies support the hypothesis that group II introns and the spliceosome share a ..
  12. pmc Generating disulfides enzymatically: reaction products and electron acceptors of the endoplasmic reticulum thiol oxidase Ero1p
    Einav Gross
    Department of Structural Biology, The Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 103:299-304. 2006
    ..In particular, Ero1p can catalyze reduction of exogenous FAD in solution. Free FAD is not required for the catalysis of dithiol oxidation by Ero1p, but it is sufficient to drive disulfide bond formation under anaerobic conditions...
  13. ncbi SU5416 is a potent and selective inhibitor of the vascular endothelial growth factor receptor (Flk-1/KDR) that inhibits tyrosine kinase catalysis, tumor vascularization, and growth of multiple tumor types
    T A Fong
    SUGEN, Inc, South San Francisco, California 94080, USA
    Cancer Res 59:99-106. 1999
    ..These findings support that pharmacological inhibition of the enzymatic activity of the vascular endothelial growth factor receptor represents a novel strategy for limiting the growth of a wide variety of tumor types...
  14. pmc Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction
    Justin B Siegel
    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
    Science 329:309-13. 2010
    ..Designed stereoselective catalysts for carbon-carbon bond-forming reactions should be broadly useful in synthetic chemistry...
  15. ncbi The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants
    K Scheffzek
    Max Planck Institut fur molekulare Physiologie, Abteilung Strukturelle Biologie, Rheinlanddamm 201, 44139 Dortmund, Germany
    Science 277:333-8. 1997
    ..thus allowing glutamine-61 of Ras, mutation of which activates the oncogenic potential, to participate in catalysis. The structural arrangement in the active site is consistent with a mostly associative mechanism of phosphoryl ..
  16. ncbi Improving enzymes by using them in organic solvents
    A M Klibanov
    Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA
    Nature 409:241-6. 2001
    ..Enzyme-catalysed reactions in organic solvents, and even in supercritical fluids and the gas phase, have found numerous potential applications, some of which are already commercialized...
  17. pmc The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation
    Yuri A Nedialkov
    Department of Biochemistry and Molecular Biology, Michigan State University, E Lansing, MI 48824 1319, USA
    Biochim Biophys Acta 1829:187-98. 2013
    The bridge α-helix in the β' subunit of RNA polymerase (RNAP) borders the active site and may have roles in catalysis and translocation...
  18. ncbi Gold and platinum catalysis--a convenient tool for generating molecular complexity
    Alois Fürstner
    Max Planck Institut fur Kohlenforschung, D 45470 Mulheim Ruhr, Germany
    Chem Soc Rev 38:3208-21. 2009
    This critical review intends to familiarize the reader with the essence of pi-acid catalysis, in particular with reactions or reaction cascades effected by gold and platinum complexes...
  19. ncbi Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA
    S D Bruner
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Nature 403:859-66. 2000
    ..One known mutation, R154H, converts hOGG1 to a promutator by relaxing the specificity of the enzyme for the base opposite oxoG...
  20. ncbi Catalysis of guanine nucleotide exchange on Ran by the mitotic regulator RCC1
    F R Bischoff
    Deutsches Krebsforschungszentrum, Heidelberg, Germany
    Nature 354:80-2. 1991
    ..Here we show that RCC1 specifically catalyses the exchange of guanine nucleotides on the Ran protein but not on the protein c-Ha-ras p21 (p21ras)...
  21. pmc The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
    Craig T Porter
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 32:D129-33. 2004
    ..The CSA will be updated on a monthly basis to include homologous sites found in new PDBs, and new hand-annotated enzymes as and when their annotation is completed...
  22. ncbi Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions
    Matthew W Powner
    School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
    Nature 459:239-42. 2009
    ..For prebiotic reaction sequences, our results highlight the importance of working with mixed chemical systems in which reactants for a particular reaction step can also control other steps...
  23. ncbi Enhanced hydrogen evolution catalysis from chemically exfoliated metallic MoS2 nanosheets
    Mark A Lukowski
    Department of Chemistry, University of Wisconsin Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
    J Am Chem Soc 135:10274-7. 2013
    ..Here we report dramatically enhanced HER catalysis (an electrocatalytic current density of 10 mA/cm(2) at a low overpotential of -187 mV vs RHE and a Tafel slope ..
  24. ncbi Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity
    H Pelletier
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093 0506, USA
    Biochemistry 35:12742-61. 1996
    ..turn), and GXK corresponds to a part of the HhH motif that is proposed to be critical for DNA binding and catalysis for both enzymes...
  25. ncbi Alanine racemase from Tolypocladium inflatum: a key PLP-dependent enzyme in cyclosporin biosynthesis and a model of catalytic promiscuity
    Martino L di Salvo
    Dipartimento di Scienze Biochimiche A Rossi Fanelli, Sapienza Universita di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
    Arch Biochem Biophys 529:55-65. 2013
    ..A three-dimensional model of T. inflatum alanine racemase was constructed on the basis of threonine aldolase crystal structure. The model helped rationalise the experimental data and explain the catalytic properties of the enzymes...
  26. ncbi Immobilization of MP-11 into a mesoporous metal-organic framework, MP-11@mesoMOF: a new platform for enzymatic catalysis
    Vasiliki Lykourinou
    Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, USA
    J Am Chem Soc 133:10382-5. 2011
    ..for the first time been successfully immobilized into a mesoporous metal-organic framework (MOF) consisting of nanoscopic cages and it demonstrates superior enzymatic catalysis performances compared to its mesoporous silica counterpart.
  27. ncbi Dioxygen activation at mononuclear nonheme iron active sites: enzymes, models, and intermediates
    Miquel Costas
    Departament de Quimica, Universitat de Girona, 17071, Girona, Spain
    Chem Rev 104:939-86. 2004
  28. ncbi Dynamic personalities of proteins
    Katherine Henzler-Wildman
    Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
    Nature 450:964-72. 2007
    ..This requires addition of a fourth dimension, time, to structural biology so that the positions in space and time of all atoms in a protein can be described in detail...
  29. pmc Iridium N-heterocyclic carbene complexes as efficient catalysts for magnetization transfer from para-hydrogen
    Michael J Cowley
    Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
    J Am Chem Soc 133:6134-7. 2011
    ..Deuterium labeling yields an additional 60% improvement in signal, an observation that offers insight into strategies for optimizing this approach...
  30. pmc An artificial di-iron oxo-protein with phenol oxidase activity
    Marina Faiella
    Department of Chemistry, University Federico II of Napoli, Complesso Universitario Monte S Angelo, Italy
    Nat Chem Biol 5:882-4. 2009
    ..Sufficient stability was, however, obtained by optimizing the sequence of a loop distant from the active site...
  31. pmc Multiple translational products from a five-nucleotide ribozyme
    Rebecca M Turk
    Department of Molecular, Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309 0347, USA
    Proc Natl Acad Sci U S A 107:4585-9. 2010
    ..Small size and minimal requirements for regiospecific translational activity strongly support the hypothesis that minuscule RNA enzymes participated in early forms of translation...
  32. ncbi Design and evolution of new catalytic activity with an existing protein scaffold
    Hee Sung Park
    Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373 1, Kusung dong, Yusung Gu, Daejon 305 701, Korea
    Science 311:535-8. 2006
    ..8 x 10(2) (mole/liter)(-1) second(-1), thus increasing resistance to Escherichia coli growth on cefotaxime by a factor of about 100...
  33. ncbi The antiquity of RNA-based evolution
    Gerald F Joyce
    Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Nature 418:214-21. 2002
    ..This earlier era is referred to as the 'RNA world', during which the genetic information resided in the sequence of RNA molecules and the phenotype derived from the catalytic properties of RNA...
  34. pmc Hidden alternative structures of proline isomerase essential for catalysis
    James S Fraser
    Department of Molecular and Cell Biology QB3, University of California, Berkeley, California 94720 3220, USA
    Nature 462:669-73. 2009
    A long-standing challenge is to understand at the atomic level how protein dynamics contribute to enzyme catalysis. X-ray crystallography can provide snapshots of conformational substates sampled during enzymatic reactions, while NMR ..
  35. ncbi Structural basis for tumor pyruvate kinase M2 allosteric regulation and catalysis
    Jill D Dombrauckas
    Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60607, USA
    Biochemistry 44:9417-29. 2005
  36. ncbi Diverse effects of pathogenic mutations of Parkin that catalyze multiple monoubiquitylation in vitro
    Noriyuki Matsuda
    Laboratory of Frontier Science, Tokyo Metropolitan Institute of Medical Science, Bunkyo ku, Tokyo 113 8613
    J Biol Chem 281:3204-9. 2006
  37. ncbi Physiological and biochemical aspects of hydroxylations and demethylations catalyzed by human 2-oxoglutarate oxygenases
    Christoph Loenarz
    Chemistry Research Laboratory and the Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
    Trends Biochem Sci 36:7-18. 2011
    ..The combination of new molecular biological and analytical techniques is likely to reveal further roles for oxygenase-mediated modifications to biomacromolecules...
  38. ncbi Accurate sequence-based prediction of catalytic residues
    Tuo Zhang
    College of Mathematical Science and LPMC, Nankai University, Tianjin, PRC
    Bioinformatics 24:2329-38. 2008
    ..We propose a sequence-based catalytic residue predictor that provides predictions with quality comparable to modern structure-based methods and that exceeds quality of state-of-the-art sequence-based methods...
  39. ncbi Product-assisted catalysis in base-excision DNA repair
    J Christopher Fromme
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Nat Struct Biol 10:204-11. 2003
    ..reveal that the enzyme sequesters the excised lesion base and exploits it as a cofactor to participate in catalysis. To our knowledge, the present example represents the first documented case of product-assisted catalysis in an ..
  40. pmc HIV-2 and SIVmac accessory virulence factor Vpx down-regulates SAMHD1 enzyme catalysis prior to proteasome-dependent degradation
    Maria Delucia
    Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
    J Biol Chem 288:19116-26. 2013
  41. pmc O-GlcNAc transferase invokes nucleotide sugar pyrophosphate participation in catalysis
    Marianne Schimpl
    College of Life Sciences, University of Dundee, Dundee, UK
    Nat Chem Biol 8:969-74. 2012
    ..This mechanism seems to be a unique evolutionary solution to the spatial constraints imposed by a bulky protein acceptor substrate and explains the unexpected specificity of a recently reported metabolic OGT inhibitor...
  42. ncbi Gold catalysis in total synthesis--an update
    Matthias Rudolph
    Organisch Chemisches Institut, Universitat Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
    Chem Soc Rev 41:2448-62. 2012
    In this critical review, the strongly increasing amount of new applications of gold catalysis in total synthesis is summarised and, for the new developed methods, the mode of activation of the substrate by the gold catalyst is discussed (..
  43. pmc Large-scale domain dynamics and adenosylcobalamin reorientation orchestrate radical catalysis in ornithine 4,5-aminomutase
    Kirsten R Wolthers
    Faculty of Life Sciences, University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, United Kingdom
    J Biol Chem 285:13942-50. 2010
    ..different catalytic states that together demonstrate unusual stability of the AdoCbl Co-C bond and that radical catalysis is coupled to large-scale domain motion. The 2...
  44. ncbi Taking Ockham's razor to enzyme dynamics and catalysis
    David R Glowacki
    Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
    Nat Chem 4:169-76. 2012
    The role of protein dynamics in enzyme catalysis is a matter of intense current debate...
  45. pmc Characterization of purified human Bact spliceosomal complexes reveals compositional and morphological changes during spliceosome activation and first step catalysis
    Sergey Bessonov
    Department of Cellular Biochemistry, MPI of Biophysical Chemistry, D 37077 Gottingen, Germany
    RNA 16:2384-403. 2010
    ..The overall architecture of the human and S. cerevisiae B(act) complex is similar, suggesting that many of the higher order interactions among spliceosomal components, as well as their dynamics, are also largely conserved...
  46. ncbi Crystallographic evidence that the dinuclear copper center of tyrosinase is flexible during catalysis
    Yasuyuki Matoba
    Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
    J Biol Chem 281:8981-90. 2006
    ..Our crystallographic study shows evidence that the tyrosinase active center formed by dinuclear coppers is flexible during catalysis.
  47. ncbi Highly enantioselective relay catalysis in the three-component reaction for direct construction of structurally complex heterocycles
    Chao Wang
    Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
    Org Lett 12:2266-9. 2010
  48. ncbi Structural insights into phosphoinositide 3-kinase catalysis and signalling
    E H Walker
    MRC Laboratory of Molecular Biology, MRC Centre, Cambridge, UK
    Nature 402:313-20. 1999
  49. pmc Structural plasticity and catalysis regulation of a thermosensor histidine kinase
    Daniela Albanesi
    Institut Pasteur, Unité de Biochimie Structurale and Plateforme de Cristallogenèse et Diffraction de Rayons X, URA 2185 Centre National de la Recherche Scientifique, Paris 75015, France
    Proc Natl Acad Sci U S A 106:16185-90. 2009
  50. ncbi The interplay of catalysis and toxicity by amyloid intermediates on lipid bilayers: insights from type II diabetes
    James A Hebda
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    Annu Rev Biophys 38:125-52. 2009
    ..Remarkably, the precursors of these fibers are intrinsically disordered, and yet catalysis of beta-sheet formation appears to be mediated by the stabilization of alpha-helical states...
  51. pmc Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility
    Pablo E Tomatis
    Instituto de Biologia Molecular y Celular de Rosario IBR, Consejo Nacional de Investigaciones Cientificas y Tecnicas de Argentina, Biophysics Section, Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, Suipacha
    Proc Natl Acad Sci U S A 105:20605-10. 2008
    ..Directed evolution aided by a thorough characterization of the selected proteins can be successfully used to predict future evolutionary events and design inhibitors with an evolutionary perspective...
  52. pmc RNA folding and catalysis mediated by iron (II)
    Shreyas S Athavale
    School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
    PLoS ONE 7:e38024. 2012
    ..and experiment to evaluate Fe²⁺ in the absence of free oxygen as a replacement for Mg²⁺ in RNA folding and catalysis. We describe both quantum mechanical calculations and experiments that suggest that the roles of Mg²⁺ in RNA ..
  53. ncbi Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate
    D J Vocadlo
    Protein Engineering Network of Centres of Excellence and the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
    Nature 412:835-8. 2001
    ..We formulate a general catalytic mechanism for all retaining beta-glycosidases that includes substrate distortion, formation of a covalent intermediate, and the electrophilic migration of C1 along the reaction coordinate...
  54. ncbi Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding
    C W Muller
    Institut fur Organische Chemie und Biochemie, 79104 Freiburg im Breisgau, Germany
    Structure 4:147-56. 1996
    ..Because these changes have been studied by comparison of structures from different species, which share approximately one-third of their residues, only rough descriptions have been possible to date...
  55. ncbi In situ formation of an oxygen-evolving catalyst in neutral water containing phosphate and Co2+
    Matthew W Kanan
    Department of Chemistry, 6 335, Massachusetts Institute of Technology, Cambridge, MA 02139 4307, USA
    Science 321:1072-5. 2008
    ..This catalyst not only forms in situ from earth-abundant materials but also operates in neutral water under ambient conditions...
  56. doi Alternative synthetic methods through new developments in catalysis by gold
    Antonio Arcadi
    Department of Chemistry, Chemical Engineering and Materials, University of L Aquila, Via Vetoio, 67010 Coppito AQ, Italy
    Chem Rev 108:3266-325. 2008
  57. ncbi Engineering entropy-driven reactions and networks catalyzed by DNA
    David Yu Zhang
    Computation and Neural Systems, California Institute of Technology, MC 136 93, 1200 East California Boulevard, Pasadena, CA91125, USA
    Science 318:1121-5. 2007
    ..We have constructed and characterized several circuits that amplify nucleic acid signals, including a feedforward cascade with quadratic kinetics and a positive feedback circuit with exponential growth kinetics...
  58. pmc Weak coordination as a powerful means for developing broadly useful C-H functionalization reactions
    Keary M Engle
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Acc Chem Res 45:788-802. 2012
  59. pmc Biochemical activities of highly purified, catalytically active human APOBEC3G: correlation with antiviral effect
    Yasumasa Iwatani
    Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, Bethesda, MD 20892 2780, USA
    J Virol 80:5992-6002. 2006
    ..In contrast, deamination is associated exclusively with the second zinc finger. Moreover, zinc finger two is more important than finger one for the antiviral effect, demonstrating a correlation between deaminase and antiviral activities...
  60. ncbi Invariant Asp-1122 and Asp-1124 are essential residues for polymerization catalysis of family D DNA polymerase from Pyrococcus horikoshii
    Y Shen
    National Institute of Bioscience and Human Technology, Tsukuba, Ibaraki 305, Japan
    J Biol Chem 276:27376-83. 2001
    ..Furthermore we determined the molecular mass of the recombinant enzyme by gel filtration and proposed a heterotetrameric structure for this enzyme...
  61. ncbi A convenient catalyst for aqueous and protein Suzuki-Miyaura cross-coupling
    Justin M Chalker
    Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
    J Am Chem Soc 131:16346-7. 2009
    ..The convenience and activity of this catalyst prompts use in both general synthesis and bioconjugation...
  62. ncbi Enzymes for chemical synthesis
    K M Koeller
    Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
    Nature 409:232-40. 2001
    ..Enzyme-catalysed chemical transformations are now widely recognized as practical alternatives to traditional (non-biological) organic synthesis, and as convenient solutions to certain intractable synthetic problems...
  63. pmc Catalysis of cis/trans isomerization in native HIV-1 capsid by human cyclophilin A
    Daryl A Bosco
    Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
    Proc Natl Acad Sci U S A 99:5247-52. 2002
    ..In addition, conformational changes in CA(N) distal to the CypA binding loop are observed on CypA binding and catalysis. The results provide experimental evidence for efficient CypA catalysis on a natively folded and biologically ..
  64. pmc DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA
    T Hollis
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
    EMBO J 19:758-66. 2000
    ..The structure of the AlkA-DNA complex offers the first glimpse of a helix-hairpin-helix (HhH) glycosylase complexed to DNA. Modeling studies suggest that other HhH glycosylases can bind to DNA in a similar manner...
  65. pmc Catalysis of electron transfer during activation of O2 by the flavoprotein glucose oxidase
    Justine P Roth
    Department of Chemistry and, University of California, Berkeley, 94720, USA
    Proc Natl Acad Sci U S A 100:62-7. 2003
    ..0 kcal.mol(-1) (0.26 eV). Within the context of Marcus theory, catalysis of electron transfer is attributed to a 19-kcal.mol(-1) (0...
  66. ncbi Critical residues for structure and catalysis in short-chain dehydrogenases/reductases
    Charlotta Filling
    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 171 77 Stockholm, Sweden
    J Biol Chem 277:25677-84. 2002
    ..emphasize the critical role of residues Thr-12, Asp-60, Asn-86, Asn-87, and Ala-88 in coenzyme binding and catalysis. The data also demonstrate essential interactions of Asn-111 with active site residues...
  67. ncbi Catalysis in the nitrilase superfamily
    Charles Brenner
    Structural Biology and Bioinformatics Program, Kimmel Cancer Center, Philadelphia, PA 19107, USA
    Curr Opin Struct Biol 12:775-82. 2002
    ..Recent experimental results confirm the essentiality of the catalytic triad residues and specify the biochemical functions of additional branches and sub-branches of the nitrilase superfamily...
  68. pmc Characterization of NocL involved in thiopeptide nocathiacin I biosynthesis: a [4Fe-4S] cluster and the catalysis of a radical S-adenosylmethionine enzyme
    Qi Zhang
    State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
    J Biol Chem 286:21287-94. 2011
    ..Furthermore, a free radical was observed by EPR during the catalysis, which is in good agreement with the hypothesis of a glycyl radical intermediate...
  69. pmc Snapshots of enzymatic Baeyer-Villiger catalysis: oxygen activation and intermediate stabilization
    Roberto Orru
    Department of Genetics and Microbiology, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy
    J Biol Chem 286:29284-91. 2011
    ..analogs, we have captured several snapshots along the catalytic cycle which highlight key features in enzyme catalysis. After acting as electron donor, the enzyme-bound NADP(H) forms an H-bond with the flavin cofactor...
  70. ncbi The protein kinase family: conserved features and deduced phylogeny of the catalytic domains
    S K Hanks
    Molecular Biology Laboratory, Salk Institute for Biological Studies, San Diego, CA 92138
    Science 241:42-52. 1988
    ..Phylogenetic mapping of the conserved protein kinase catalytic domains can serve as a useful first step in the functional characterization of these newly identified family members...
  71. pmc Key role of cysteine residues in catalysis and subcellular localization of sulfur oxygenase-reductase of Acidianus tengchongensis
    Zhi Wei Chen
    Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, People s Republic of China
    Appl Environ Microbiol 71:621-8. 2005
    ..We tentatively propose that these enzymes are located in close proximity on the membrane to catalyze sulfur oxidation in A. tengchongensis...
  72. pmc Role of the RNA polymerase trigger loop in catalysis and pausing
    Jinwei Zhang
    Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, USA
    Nat Struct Mol Biol 17:99-104. 2010
    ..However, the roles of the TL/TH in transcript cleavage, catalysis, substrate selectivity and pausing remain ill defined...
  73. pmc Crystal structure of the catalytic portion of human HMG-CoA reductase: insights into regulation of activity and catalysis
    E S Istvan
    Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, TX 75235 9050, USA
    EMBO J 19:819-30. 2000
    ..The active site architecture of human HMGR is different from that of bacterial HMGR; this may explain why binding of HMGR inhibitors to bacterial HMGRs has not been reported...
  74. pmc PR65, the HEAT-repeat scaffold of phosphatase PP2A, is an elastic connector that links force and catalysis
    Alison Grinthal
    Departments of Molecular and Cellular Biology, and Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 107:2467-72. 2010
    ..PR65-dominated fluctuations of PP2A have the effect of opening and closing the enzyme's substrate binding/catalysis interface, as well as altering the positions of certain catalytic residues...
  75. pmc Triple-helix structure in telomerase RNA contributes to catalysis
    Feng Qiao
    Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Campus Box 215, University of Colorado, Boulder, Colorado 80309 0215, USA
    Nat Struct Mol Biol 15:634-40. 2008
    ..Instead, 2'-OH groups protruding from the triple helix participate in both yeast and human telomerase catalysis; they may orient the primer-template relative to the active site in a manner analogous to group I ribozymes...
  76. ncbi Structural basis for Ca(2+)-induced activation of human PAD4
    Kyouhei Arita
    Graduate School of Integrated Science, Yokohama City University, 1 7 29 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Nat Struct Mol Biol 11:777-83. 2004
    ..Our findings identify a novel mechanism for enzyme activation by Ca(2+) ions, and are important for understanding the mechanism of protein citrullination and for developing PAD-inhibiting drugs for the treatment of rheumatoid arthritis...
  77. ncbi Kemp elimination catalysts by computational enzyme design
    Daniela Röthlisberger
    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
    Nature 453:190-5. 2008
    ..biocatalysts is a challenge for protein engineering and is a critical test of our understanding of enzyme catalysis. Here we describe the computational design of eight enzymes that use two different catalytic motifs to catalyse ..
  78. pmc Flexibility, diversity, and cooperativity: pillars of enzyme catalysis
    Gordon G Hammes
    Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
    Biochemistry 50:10422-30. 2011
    This brief review discusses our current understanding of the molecular basis of enzyme catalysis. A historical development is presented, beginning with steady state kinetics and progressing through modern fast reaction methods, nuclear ..
  79. pmc Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release
    Marcin Nowotny
    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    EMBO J 25:1924-33. 2006
    In two-metal catalysis, metal ion A has been proposed to activate the nucleophile and metal ion B to stabilize the transition state. We recently reported crystal structures of RNase H-RNA/DNA substrate complexes obtained at 1.5-2...
  80. ncbi Electrostatic basis for enzyme catalysis
    Arieh Warshel
    Department of Chemistry, University of Southern California, SGM Building 418, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
    Chem Rev 106:3210-35. 2006
  81. ncbi Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair
    Magnus Wolf-Watz
    Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, USA
    Nat Struct Mol Biol 11:945-9. 2004
    A fundamental question is how enzymes can accelerate chemical reactions. Catalysis is not only defined by actual chemical steps, but also by enzyme structure and dynamics...
  82. pmc Network of coupled promoting motions in enzyme catalysis
    Pratul K Agarwal
    Department of Chemistry, 152 Davey Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 99:2794-9. 2002
    ..This type of network has broad implications for an expanded role of the protein fold in catalysis as well as ancillaries such as the engineering of altered protein function and the action of drugs distal to the ..
  83. ncbi Molecular recognition and catalysis in translation termination complexes
    Bruno P Klaholz
    IGBMC Institute of Genetics and of Molecular and Cellular Biology, Department of Structural Biology and Genomics, Illkirch, France
    Trends Biochem Sci 36:282-92. 2011
    ..Moreover, ongoing research also promises to reveal the structure-function relations of class-II RFs...
  84. pmc A single mutation in the 729 residue modulates human DNA topoisomerase IB DNA binding and drug resistance
    Carmen Losasso
    Department of Biology, University of Padova, Via U Bassi 58 B, Padua 35131, Italy
    Nucleic Acids Res 36:5635-44. 2008
    ..To understand the contribution of this residue in drug resistance, we have studied the effect on hTop1p catalysis and CPT sensitivity of four different substitutions in the Thr729 position (Thr729Ala, Thr729Glu, Thr729Lys and ..
  85. ncbi Similar enzyme activation and catalysis in hemocyanins and tyrosinases
    Heinz Decker
    Institut für Molekulare Biophysik, Johannes Gutenberg Universitat, 55099 Mainz, Germany
    Gene 398:183-91. 2007
    ..In spite of these differences a common mechanism of activation and catalysis seems to have been preserved throughout evolution...
  86. ncbi Crystal structures of fructose 1,6-bisphosphatase: mechanism of catalysis and allosteric inhibition revealed in product complexes
    J Y Choe
    Department of Biochemistry, Iowa State University, Ames 50011, USA
    Biochemistry 39:8565-74. 2000
    ..Development of negative charge on the 1-oxygen of F6P is stabilized by its coordination to the Mg(2+) at site 1...
  87. ncbi Polytriazoles as copper(I)-stabilizing ligands in catalysis
    Timothy R Chan
    Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, USA
    Org Lett 6:2853-5. 2004
    ..The C3-symmetric derivative, TBTA, was shown to be a powerful stabilizing ligand for copper(I), protecting it from oxidation and disproportionation, while enhancing its catalytic activity...
  88. ncbi Mechanism of cysteine desulfurase Slr0387 from Synechocystis sp. PCC 6803: kinetic analysis of cleavage of the persulfide intermediate by chemical reductants
    Elham Behshad
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Biochemistry 43:12220-6. 2004
    ..the persulfide intermediate, and it has been suggested that persulfide cleavage is the rate-limiting step for catalysis. In this study, the kinetics and mechanisms of cleavage of the persulfide intermediate in Slr0387 (CD-0387), a ..
  89. ncbi Click chemistry with DNA
    Afaf H El-Sagheer
    School of Chemistry, University of Southampton, Highfield, Southampton, UK SO17 1BJ
    Chem Soc Rev 39:1388-405. 2010
    ..In this critical review we describe some of the pioneering work that has been carried out in this area (78 references)...
  90. ncbi Palladium-catalyzed oxidative diarylating carbocyclization of enynes
    Min Jiang
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE 106 91 Stockholm, Sweden
    Org Lett 14:3538-41. 2012
    ..Control experiments suggest that the reaction starts with an arylpalladation of the alkyne, followed by carbocyclization, transmetalation, and reductive elimination to afford the diarylated product...
  91. ncbi Evolution of the protein repertoire
    Cyrus Chothia
    Structural Studies Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 300:1701-3. 2003
    ..Proteins of known structure can be matched to about 50% of genome sequences, and these data provide a quantitative description and can suggest hypotheses about the origins of these processes...
  92. ncbi Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases
    Nushin Aghajari
    Institut de Biologie et Chimie des Proteines, UMR 5086, Laboratoire de Bio Cristallographie, CNRS et Université Claude Bernard Lyon I, Lyon, France
    Proteins 50:636-47. 2003
    ..Finally, the active site is more accessible due to deletions occurring in surrounding loop regions...
  93. ncbi Free-energy landscape of enzyme catalysis
    Stephen J Benkovic
    Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Biochemistry 47:3317-21. 2008
    ..Experimental and theoretical evidence is presented to support this concept...
  94. pmc Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme
    Timothy J Wilson
    Cancer Research United Kingdom Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
    Proc Natl Acad Sci U S A 107:11751-6. 2010
    ..satellite (VS) ribozyme accelerates the cleavage of a specific phosphodiester bond using general acid-base catalysis. The key functionalities are the nucleobases of adenine 756 in helix VI of the ribozyme, and guanine 638 in the ..
  95. ncbi Investigations of the esterase, phosphatase, and sulfatase activities of the cytosolic mammalian carbonic anhydrase isoforms I, II, and XIII with 4-nitrophenyl esters as substrates
    Alessio Innocenti
    Universita degli Studi di Firenze, Laboratorio di Chimica Bioinorganica, Rm 188, Via della Lastruccia 3, I 50019 Sesto Fiorentino, Firenze, Italy
    Bioorg Med Chem Lett 18:2267-71. 2008
    ..CA XIII was the most effective esterase and phosphatase. CA XIII might catalyze other physiological reactions than CO(2) hydration, based on its relevant phosphatase activity...
  96. pmc Interrupted catalysis: the EF4 (LepA) effect on back-translocation
    Hanqing Liu
    Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
    J Mol Biol 396:1043-52. 2010
    ..EF4 may be thought of as performing an interrupted catalysis of back-translocation, stopping at the formation of I(3) rather than catalyzing the complete process of back-..
  97. ncbi Mechanistic analysis of the immunomodulatory effects of a catalytic antioxidant on antigen-presenting cells: implication for their use in targeting oxidation-reduction reactions in innate immunity
    Hubert M Tse
    Diabetes Institute, Division of Immunogenetics, Department of Pediatrics, Children s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15213 3205, USA
    Free Radic Biol Med 36:233-47. 2004
  98. ncbi Palladium-catalyzed oxidative carbocyclization/arylation of enallenes
    Tuo Jiang
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE 10691, Stockholm, Sweden
    Org Lett 13:5838-41. 2011
    ..The reaction shows wide tolerance toward highly functionalized arylboronic acids and results in a cis addition of two carbon moieties to an olefin in good to excellent yields...
  99. ncbi Bioconjugation with strained alkenes and alkynes
    Marjoke F Debets
    Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, The Netherlands
    Acc Chem Res 44:805-15. 2011
    ..In the search for bioorthogonal reactions, cycloadditions of cyclic alkenes and alkynes have now established themselves as powerful tools in reagent-free bioconjugations...
  100. ncbi Analysis of proanthocyanidin cleavage products following acid-catalysis in the presence of excess phloroglucinol
    J A Kennedy
    Department of Horticulture, Viticulture and Oenology, University of Adelaide, Waite Campus, PMB 1, Glen Osmond, South Australia 5064, Australia
    J Agric Food Chem 49:1740-6. 2001
    The analysis of proanthocyanidin cleavage products after acid-catalysis in the presence of excess phloroglucinol was investigated. In the developed analytical method, a solution of 0...
  101. pmc A natural ribozyme with 3',5' RNA ligase activity
    Quentin Vicens
    Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, UCB 215, Boulder, Colorado 80309 0215, USA
    Nat Chem Biol 5:97-9. 2009
    ..In the process, this ribozyme forms a unique circular RNA that incorporates the exogenous guanosine cofactor added during self-splicing. This finding may have relevance to a prebiotic RNA world and to modern biology...

Research Grants66

    Pi Wan Cheng; Fiscal Year: 2010
    ..Determine the active site of C2GnT-M by X-ray crystallography and then confirm the amino acids involved in catalysis by site-directed mutagenesis followed by measurement of enzyme activities using core 1, core 3, and blood group ..
  2. A Thioredoxin Mimetic for Radiocontrast Nephropathy
    GARRY JOHN SOUTHAN; Fiscal Year: 2012
    ..Based on its ultrapotent catalysis of redox stress, and the critical relevance of redox stress to the pathophysiology of CIN, we now propose to ..
  3. The Role of MYST Histone Acetyltransferase in Genome Stability
    M Mitchell Smith; Fiscal Year: 2013
    ..We recently made the surprising discovery that catalysis is not the essential function of Esa1, as previously believed...
  4. PARP Inhibitor and Redox Catalyst for Ventilatory Trauma
    Prakash Jagtap; Fiscal Year: 2013
    ..bifunctional small molecule, R-503, that: 1) prevents the generation of peroxynitrite via broad-spectrum redox catalysis, and 2) competitively inhibits the nuclear DNA repair enzyme poly(ADP-ribose) polymerase 1 ("PARP- 1")...
  5. Glutathione in mitochondrial dysfunction and disease progression in ALS-models
    Marcelo R Vargas; Fiscal Year: 2011
    ..Several hypotheses, including oxidative stress induced by SOD1 aberrant catalysis, and mitochondrial dysfunction have been proposed to explain the toxic effect of mutant SOD1...
  6. Biosynthesis of Microbial Isoprenoids
    David E Cane; Fiscal Year: 2013
    ..The mechanistic focus will be on discovering new cyclases and on unraveling the protein structural basis for catalysis and product specificity using a combination of site-directed mutagenesis and protein crystallography...
  7. Tyrosinase Model Complexes using Imidazole Ligands
    JOHN BRANNON GARY; Fiscal Year: 2013
    ..Many proteins in nature contain copper in their active sites, and these sites are typically involved in redox catalysis performing a wide array biological functions such as electron carrier proteins (azurin, plastocyanin), oxygenase ..
  8. Regulations of DNA Alkylation/Deamination Damage Repair
    Rabindra Roy; Fiscal Year: 2013
    ..whereas AP-endonuclease, the next enzyme in the same BER pathway binds several MPG substrate lesions without catalysis and inhibit MPG activity, and notably, not present in MPG pre-repair complex in the human cells...
    David P Bartel; Fiscal Year: 2013
  10. Challenges in beta-Lactamase Mediated Resistance
    Robert A Bonomo; Fiscal Year: 2013
    ..aeruginosa, PDC-3. Our central hypothesis is that a better understanding of the molecular details of catalysis and inhibition of [unreadable]-lactamase enzymes can lead to the design of more effective inhibitors...
  11. 2011 Nucleic Acids Gordon Research Conference
    Christopher D Lima; Fiscal Year: 2011
    ..RNA;RNA Stability and Export;Ribosome Biogenesis, Function and Regulation;Nucleic Acid Structure and Catalysis. The significance of this application is that this Gordon Research Conference will provide a forum for bringing ..
  12. Activation of PI Specific Phospholipase C Enzymes
    MARY FEDARKO ROBERTS; Fiscal Year: 2013
    ..components of the membrane surface and how binding at nonsubstrate interfacial sites is translated to enhanced catalysis. L...
  13. Transport ATPases: From Molecules to Maladies
    Rajini Rao; Fiscal Year: 2010
    ..Sessions will include Rotary Catalysis, Structure and Mechanism of ATPases, Membrane Dynamics and Vesicle Fusion, Orphan ATPases, Transport ATPases and ..
  14. Role of Polyamine Oxidase in Apoptosis Studies with RNA Interference
    GLENN KUEHN; Fiscal Year: 2009
    ..We have gained strong evidence that PAO catalysis is indeed the major source of H2O2 in a plant model system undergoing the hypersensitive response (HR)...
  15. RNA Modification Enzymes: Methyltransferase/psi-synthase
    Robert M Stroud; Fiscal Year: 2012
    ..The aim of this application is to determine the basis for selectivity and catalysis in two of the most abundant families of RNA modifying enzymes: 5-methyl uracil (m5U) methyltransferases (MTases) ..
    Sergey A Krupenko; Fiscal Year: 2013
    ..abundant folate enzymes, 10-formyltetrahydrofolate dehydrogenase (FDH, ALDH1L1), and how the inhibition of its catalysis is involved in pathogenesis...
  17. Mechanisms of Neurotransmitter Biosynthesis
    Paul F Fitzpatrick; Fiscal Year: 2011
    ..of rapid reaction methods and spectroscopy, with the goal of characterizing individual iron species in catalysis. The role of protein dynamics in catalysis by tyrosine and phenylalanine hydroxylase will be studied by ..
  18. Identification, Discovery, and Public Archiving of RNA Structural Motifs
    Shaojie Zhang; Fiscal Year: 2013
    ..provided by applicant): The non-coding RNAs play many functional roles in biological processes, such as catalysis, gene expression regulation and RNA splicing...
    Paul R Ortiz de Montellano; Fiscal Year: 2013 the catalytic mechanisms of HO-1 and HO-2, and clarify the overall mechanism of the latter steps of HO catalysis. 4...
  20. Nox4 and Vascular Homeostasis
    John F Keaney; Fiscal Year: 2013
    ..of Nox4 levels in the endothelium will help us determine the implications for NO7 bioactivity and eNOS catalysis. We will then probe the involvement of known Nox4 targets such as Akt, PTP1B, and SOD1...
  21. Investigation of the structure and function of urea amidolyase
    MARTIN RAOUL ST. MAURICE; Fiscal Year: 2012
    ..and will combine crystallography with protein engineering and steady-state kinetics to clarify the mechanism of catalysis and intermediate channeling in UAL...
  22. Studies of YlxM of Streptococcus mutans, a newly identified component of the Sign
    MATTHEW LAWRENCE WILLIAMS; Fiscal Year: 2013 the translocon channel;and a small cytoplasmic RNA (scRNA) that is involved in the stability of Ffh-FtsY and catalysis of GTPase activity...
  23. Glutathione in mitochondrial dysfunction and disease progression in ALS-models
    Marcelo R Vargas; Fiscal Year: 2013
    ..Several hypotheses, including oxidative stress induced by SOD1 aberrant catalysis, and mitochondrial dysfunction have been proposed to explain the toxic effect of mutant SOD1...
  24. Studies toward the development of monoamine oxidase B specific inhibitors
    ERIKA MARIE MILCZEK; Fiscal Year: 2010
    ..b>Catalysis is accomplished through amine oxidation to the corresponding aldehyde...
  25. Regulation and Catalysis of Human Insulin Degrading Enzyme
    Wei Jen Tang; Fiscal Year: 2013
    ..are to understand (1) the molecular basis for the open-closed conformational switch and dynamics of IDE during catalysis and (2) the molecular mechanism for the regulation of IDE...
  26. Enzymology of RNA Processing
    Carol A Fierke; Fiscal Year: 2013
    ..These enzymes provide an ideal system for defining catalytic features that distinguish RNA- and protein-based catalysis. Furthermore, the distinct subunit compositions highlight the potential of bacterial RNase P as a novel ..
  27. Structural and Biochemical Basis of the Vitamin K cycle
    Weikai Li; Fiscal Year: 2013
    ..We will also use purified VKOR proteins to study the biochemistry of VKOR catalysis and warfarin inhibition. The studies will provide the basis for rational drug design...
  28. Structure and dynamics of the Tetrahymena telomerase ribonucleoprotein
    Michael D Stone; Fiscal Year: 2013 within telomerase RNA and protein subunits coordinate the processes of telomerase RNP assembly and catalysis. To address the substantial challenges associated with structural analysis of telomerase we will study the ..
    Mark R Denison; Fiscal Year: 2013
    ..concluded that functional nsp5 dimeric, and have identified structure/function determinants of dimerization and catalysis, but none of these have been tested in a replicating virus...
  30. Pharmacogenomics of Human P450 Oxidoreductase
    Walter L Miller; Fiscal Year: 2012
    ..and gonadal steroid hormone synthesis, require electron donation from P450 oxidoreductase (POR) to mediate catalysis. POR is a 680 amino-acid, 78 kDa protein that contains two flavins, a flavin adenine dinucleotide moiety (FAD), ..
  31. Functional Analysis of ACAT
    Ta Yuan Chang; Fiscal Year: 2013
    ..Thus, the aims of this project are 1) to identify key amino acid residues involved in substrate binding, catalysis, and/or allosteric control of ACAT1;and 2) to delineate the effects of inactivating macrophage Acat1 during the ..
  32. 2012 Iron Sulfur Enzymes Gordon Research Conference
    Markus W Ribbe; Fiscal Year: 2012
    ..iron-sulfur cofactors perform a variety of biological functions, ranging across electron transfer, acid- base catalysis, and sensing where they are agents for cell regulation through transcription (DNA) or translation (RNA)...
  33. Simultaneous Time-Resolved X-ray Spectroscopy and Crystallography: A Mechanistic
    Rosalie Tran; Fiscal Year: 2013
    ..with functional roles in O2 metabolism since the identification of Mn as an essential metal in biological redox catalysis. These include a mitochondrial Mn-superoxide dismutase (SOD2) that detoxifies superoxide radicals into O2 and ..
  34. Biochemistry of recombination in gametogenesis
    Wayne P Wahls; Fiscal Year: 2010
    ..Amino acid substitutions affecting specifically DNA binding or catalysis can be distinguished in vitro...
  35. NMR Studies of Structures and Dynamics of Proteins
    Arthur G Palmer; Fiscal Year: 2013
    ..such as heat capacity and thermal stability;for mechanistic interpretations of kinetic processes, such as enzyme catalysis and ligand recognition;and for design of novel proteins and protein ligands, including pharmaceutical agents...
    Stephen G Sligar; Fiscal Year: 2012
    ..innovative biochemical and biophysical means to understand the global mechanisms of heme protein reductase catalysis, thus precisely defining the structure and dynamics of key intermediates in the control of electron and proton ..
  37. Developing fluorescent probes for the endogenous gaseous transmitters NO and H2S
    MICHAEL PLUTH; Fiscal Year: 2013
    ..of Kenneth Raymond and Robert Bergman where he studied host-guest chemistry, molecular recognition, and catalysis in water-soluble supramolecular complexes...
  38. Novel targets and drugs for the control of platyhelminth infections
    MARCOS GUSTAVO SALINAS; Fiscal Year: 2012
    ..In addition, we will further investigate catalysis and regulation of platyhelminth TGRs...
  39. Mechanisms of selective excision and oxidative repair of alkylated DNA
    Manel Camps; Fiscal Year: 2013
    ..The precise determinants for the specificity and catalysis of these enzymes toward 3mA and eA remain unclear...
  40. EPR and Mossbauer Characterization of Mn and Fe Proteins, Models, Intermediates
    Michael P Hendrich; Fiscal Year: 2013
    ..and to aid our understanding of the structural and chemical aspect of metalloenzymes that are important in catalysis. Our goal in this proposal is to provide insight into how these enzymes perform their function by studying the ..
  41. mRNA Capping Enzymes
    STEWART H SHUMAN; Fiscal Year: 2013
    ..pombe Fcp1, an essential CTD phosphatase that preferentially hydrolyzes Ser2- PO4, are yielding deep insights to catalysis of CTD dephosphorylation in vitro...
  42. Structural and Functional Studies of the Sac Family Phosphoinositide Phosphatases
    Yuxin Mao; Fiscal Year: 2013
    ..substrate specificity of Sac phosphatases;(2) Probe the membrane interaction and the mechanism for interfacial catalysis of Sac1;(3) Elucidate the mechanism for the regulation of enzymatic activity of Sac1...
  43. Coordinating Translesion DNA Synthesis Opposite Damaged DNA
    Robert L Eoff; Fiscal Year: 2010
    ..These so-called replicative polymerases are often less able to bypass damaged DNA because each step in catalysis has stringent molecular checkpoints that must be met before DNA synthesis occurs...
  44. Structure and Function of HAD Phosphatase Partners Dullard and Lipin
    Debra Dunaway-Mariano; Fiscal Year: 2013
    ..Aim 2: Delineate the structural determinants of substrate recognition and catalysis in dullard-mediated lipin1 dephosphorylation...
  45. Analysis of metallo-beta-lactamase sequence constraints at high resolution
    Timothy Palzkill; Fiscal Year: 2013
    ..comparisons are made for each of the active site positions, a high resolution picture of the determinants of catalysis and substrate specificity for an MBL will emerge...
  46. Reductive Dehalogenation in Mammals by Iodotyrosine Deiodinase
    Steven E Rokita; Fiscal Year: 2012
    ..The novel properties of this enzyme will extend the known repertoire of flavin-dependent catalysis and pathways available in biology to process halogenated compounds...
  47. Radical Intermediates of Nitric Oxide Synthase &Myocardial Ischemia Reperfusion
    Ah Lim Tsai; Fiscal Year: 2013
    ..recent studies disclosed very different radical intermediate profile and regulation mechanism in eNOS and nNOS catalysis. The central hypothesis of this proposal is that understanding the interplay of the various regulatory molecules ..
  48. Structural Analysis of Mechanism and Regulation of Glutamine Amidotransferases
    AMBER MARIE SMITH; Fiscal Year: 2013
    ..The progression of catalysis from the glutaminase domain to the synthase domain is highly regulated by substrate binding and the mechanism by ..
  49. Genetic requirements of Helicobacter pylori infection
    NINA REDA SALAMA; Fiscal Year: 2013 of DNA damage encountered during infection 2.) generation of adaptive genetic variation and 3). catalysis of genetic switching events affecting the expression of genes promoting (or limiting) colonization...
  50. Biochemical Studies of Oxalate Decarboxylase
    NIGEL GORDON RICHARDS; Fiscal Year: 2013 of site-specific mutants of the enzyme will be measured to delineate their functional roles in catalysis and/or active site dynamics...
  51. Fungal Polyketide Synthases and Environmental Toxin Biosynthesis
    CRAIG ARTHUR TOWNSEND; Fiscal Year: 2013
    ..These enzymes exhibit the unusual property of iterative catalysis where a small basis set of catalytic domains is reused multiple times but a fixed number of times to a specific, ..
  52. Activation and Inhibition of Aldehyde Dehydrogenase 2
    Thomas D Hurley; Fiscal Year: 2013
    ..With this as the basis for a new set of studies, our overriding hypothesis is that the unique aspects of catalysis in ALDH2, the high prevalence of the ALDH2*2 allele and their roles in alcohol metabolism and cardiovascular ..
  53. Selenodeidinase Processing by the Proteasome System
    Antonio C Bianco; Fiscal Year: 2012
    ..D2 is constantly ubiquitinated under basal conditions but this is accelerated by T4 catalysis. The identity of the critical steps in these processes is unknown...
  54. Regulation of Endothelial Cell Branching Morphogenesis via MCAK-targted Control
    KENNETH ALBERT MYERS; Fiscal Year: 2013
    ..During mitosis, MCAK-mediated catalysis of MT catastrophe is phospho-regulated, yet the regulation of cytoplasmic MCAK at growing MT ends, and its roles ..
  55. Extra-translational roles of aminoacyl tRNA synthetases in connection to disease
    Xiang Lei Yang; Fiscal Year: 2013
    ..It is chemically the same reaction as the first step of catalysis by GlyRS in aminoacylation...
  56. Coupled Transfers of Electrons and Protons
    James M Mayer; Fiscal Year: 2013
    ..The phenol studies, for instance, will shed light on the formation of tyrosyl radicals in enzymatic catalysis or under oxidative stress...
  57. 950 MHz NMR Spectrometer with Cryogenic Probe
    DAVID JOSEPH WEBER; Fiscal Year: 2010
    ..Molecular recognition: structural and dynamic basis for RNA-macromolecular interactions in gene regulation and catalysis;5. Dr. Bruce Johnson (UMBC) Continued development and maintenance of NMRview;6. Dr...
  58. Molecular mechanism of omega-3 response
    JAMES T BRENNA; Fiscal Year: 2013
    ..AT are modulated by dietary PUFA and by hormones via splicing factors (SF) in a manner consistent with enhanced catalysis (e.g. FADS1AT1) or inhibition (e.g. FADS3 AT) of desaturation...
  59. The molecular bases of inherited urea cycle disorders and ureagenesis regulation
    Mendel Tuchman; Fiscal Year: 2010
    ..chromatography, analytical ultracentrifugation, protein cross-linking and mass spectrometry, and the effects on catalysis will be studied by enzyme kinetics experiments...
  60. Chaperone-Enabled studies of epigenetic regulation enzymes
    Anthony A Kossiakoff; Fiscal Year: 2013 applicant): The overarching goal of this project is to elucidate the molecular mechanism governing the catalysis and regulation of histone modification enzymes...
  61. Functional Dynamics of Mammalian and Viral DNA Repair Polymerases
    W M BUJALOWSKI; Fiscal Year: 2013
    ..polymerases is that the DNA repair enzyme must recognize a specific structure of the damaged DNA prior to the catalysis, in the context of overwhelmingly dsDNA conformation...
  62. Catalytic Antibodies To Staphylococcus Aureus: Identification and Characterizatio
    Eric L Brown; Fiscal Year: 2010
    ..aureus carriage state, characterize the proteolytic specificity and rates, and determine the effects of catalysis on virulence protein function. PUBLIC HEALTH RELEVANCE: S...
  63. Structural Basis for Bridged Bimetallic Enzyme Catalysis
    Dagmar Ringe; Fiscal Year: 2009
    ..Yet little is understood about how the two metal ions work together in catalysis, or how the protein environment modulates the intrinsic chemical reactivity of the dimetal center...
  64. Regulation of Substrate Binding and Catalysis in tRNase Z
    LOUIS F LEVINGER; Fiscal Year: 2010
    ..a His cluster (HxHxDH) which is the signature sequence of the -lactamase superfamily, are required for tRNase Z catalysis, but not for substrate pre-tRNA binding...
  65. The Role of MgATP in Nitrogenase Catalysis
    John Peters; Fiscal Year: 2007
    ..term goal of the proposal is to gain structural and mechanistic insights into the role of MgATP in nitrogenase catalysis. Nitrogenase is a complex metal-containing enzyme that catalyzes the conversion of nitrogen gas to ammonia...
    RODNEY BEDNAR; Fiscal Year: 1990
    ..conducted to determine the mechanism of action of chalcone isomerase and the factors which are responsible for catalysis. The isomerization of chalcones to flavanones is an intramolecular reaction and a membrane of the class of ..