hydrogen bonding


Summary: A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.

Top Publications

  1. pmc MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, NC, USA
    Nucleic Acids Res 35:W375-83. 2007
  2. ncbi Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
    Raphael Guerois
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    J Mol Biol 320:369-87. 2002
  3. ncbi Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    W Kabsch
    Biopolymers 22:2577-637. 1983
  4. ncbi Automatic atom type and bond type perception in molecular mechanical calculations
    Junmei Wang
    College of Chemistry, Peking University, Beijing 100871, China
    J Mol Graph Model 25:247-60. 2006
  5. pmc MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, NC 27710 3711, USA
    Nucleic Acids Res 32:W615-9. 2004
  6. ncbi Crystal structure of rhodopsin: A G protein-coupled receptor
    K Palczewski
    Department of Ophthalmology, University of Washington, Seattle, WA 98195, USA
    Science 289:739-45. 2000
  7. pmc The structural basis for agonist and partial agonist action on a β(1)-adrenergic receptor
    Tony Warne
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Nature 469:241-4. 2011
  8. ncbi Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes
    Holger Gohlke
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Biol 330:891-913. 2003
  9. pmc Improved prediction of protein side-chain conformations with SCWRL4
    Georgii G Krivov
    Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, USA
    Proteins 77:778-95. 2009
  10. pmc The structural basis of agonist-induced activation in constitutively active rhodopsin
    Jörg Standfuss
    Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
    Nature 471:656-60. 2011

Detail Information

Publications403 found, 100 shown here

  1. pmc MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, NC, USA
    Nucleic Acids Res 35:W375-83. 2007
    ..This service is available free to all users at http://molprobity.biochem.duke.edu...
  2. ncbi Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
    Raphael Guerois
    EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    J Mol Biol 320:369-87. 2002
    ..FOLDEF is available via a web-interface at http://fold-x.embl-heidelberg.de..
  3. ncbi Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    W Kabsch
    Biopolymers 22:2577-637. 1983
  4. ncbi Automatic atom type and bond type perception in molecular mechanical calculations
    Junmei Wang
    College of Chemistry, Peking University, Beijing 100871, China
    J Mol Graph Model 25:247-60. 2006
    ..for most organic molecules. The algorithms behind the manipulations may be useful for other molecular mechanical packages as well as applications that need to designate atom types and bond types...
  5. pmc MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, NC 27710 3711, USA
    Nucleic Acids Res 32:W615-9. 2004
    ..This service is available free to all users at http://kinemage.biochem.duke.edu...
  6. ncbi Crystal structure of rhodopsin: A G protein-coupled receptor
    K Palczewski
    Department of Ophthalmology, University of Washington, Seattle, WA 98195, USA
    Science 289:739-45. 2000
    ..Identification of a set of residues that mediate interactions between the transmembrane helices and the cytoplasmic surface, where G-protein activation occurs, also suggests a possible structural change upon photoactivation...
  7. pmc The structural basis for agonist and partial agonist action on a β(1)-adrenergic receptor
    Tony Warne
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Nature 469:241-4. 2011
  8. ncbi Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes
    Holger Gohlke
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Mol Biol 330:891-913. 2003
    ..This explains the finding of a conformational change in this region upon complex formation with Ras, and it may trigger a larger structural change in Raf, which is considered to be necessary for activation of the effector by Ras...
  9. pmc Improved prediction of protein side-chain conformations with SCWRL4
    Georgii G Krivov
    Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, USA
    Proteins 77:778-95. 2009
    ..averaging over samples of conformations about the positions in the rotamer library; (3) a fast anisotropic hydrogen bonding function; (4) a short-range, soft van der Waals atom-atom interaction potential; (5) fast collision detection ..
  10. pmc The structural basis of agonist-induced activation in constitutively active rhodopsin
    Jörg Standfuss
    Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
    Nature 471:656-60. 2011
    ..We thus show how an agonist ligand can activate its GPCR...
  11. pmc The role of DNA shape in protein-DNA recognition
    Remo Rohs
    Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 Saint Nicholas Avenue, New York, New York 10032, USA
    Nature 461:1248-53. 2009
  12. ncbi Structural plasticity and the evolution of antibody affinity and specificity
    Jun Yin
    Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA
    J Mol Biol 330:651-6. 2003
  13. pmc RNA tertiary interactions in the large ribosomal subunit: the A-minor motif
    P Nissen
    Department of Molecular Biophysics and Biochemistry, Yale University and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA
    Proc Natl Acad Sci U S A 98:4899-903. 2001
    ..It may prove to be the universally most important long-range interaction in large RNA structures...
  14. ncbi Intramolecular hydrogen bonding in medicinal chemistry
    Bernd Kuhn
    Discovery Chemistry, F Hoffmann La Roche AG, CH 4070 Basel, Switzerland
    J Med Chem 53:2601-11. 2010
    ..A number of general guidelines for medicinal chemists emerge from this study...
  15. ncbi Further development and validation of empirical scoring functions for structure-based binding affinity prediction
    Renxiao Wang
    Medical Chemistry and Comprehensive Cancer Center, University of Michigan, Ann Arbor 48109 0934, USA
    J Comput Aided Mol Des 16:11-26. 2002
    ..These scoring functions include terms accounting for van der Waals interaction, hydrogen bonding, deformation penalty, and hydrophobic effect...
  16. pmc Autofluorescent proteins with excitation in the optical window for intravital imaging in mammals
    Michael Z Lin
    Department of Pharmacology, University of California, San Diego, La Jolla, 92093, USA
    Chem Biol 16:1169-79. 2009
    ..The crystal structure of Neptune reveals a novel mechanism for red-shifting involving the acquisition of a new hydrogen bond with the acylimine region of the chromophore...
  17. pmc RNA tertiary interactions in a riboswitch stabilize the structure of a kink turn
    Kersten T Schroeder
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, UK
    Structure 19:1233-40. 2011
    ..This study shows that the folded structure of the k-turn can be stabilized by tertiary interactions within a larger RNA structure...
  18. ncbi The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure
    Tetsuji Okada
    Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, 2 41 6 Aomi, Koto ku, Tokyo 135 0064, Japan
    J Mol Biol 342:571-83. 2004
    ..Other differences between the experimental and theoretical structures in the chromophore binding site are discussed with respect to the unique spectral properties and excited state reactivity of the chromophore...
  19. pmc 3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization
    Debswapna Bhattacharya
    Department of Computer Science, University of Missouri, Columbia, Missouri 65211, USA
    Proteins 81:119-31. 2013
    ..The first step is based on optimization of hydrogen bonding (HB) network and the second step applies atomic-level energy minimization on the optimized model using a ..
  20. ncbi Self-propagating, molecular-level polymorphism in Alzheimer's beta-amyloid fibrils
    Aneta T Petkova
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health NIH, Bethesda, MD 20892 0520, USA
    Science 307:262-5. 2005
    ..These results have implications for the mechanism of amyloid formation, the phenomenon of strains in prion diseases, the role of amyloid fibrils in amyloid diseases, and the development of amyloid-based nano-materials...
  21. pmc Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level
    N M Luscombe
    Biomolecular Structures and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London WC1E 6BT, UK
    Nucleic Acids Res 29:2860-74. 2001
    ..An interactive Web-based atlas of side chain-base contacts provides access to the collected data, including analyses and visualisation of the three-dimensional geometry of the interactions...
  22. pmc VADAR: a web server for quantitative evaluation of protein structure quality
    Leigh Willard
    Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2N8, Canada
    Nucleic Acids Res 31:3316-9. 2003
    ..excluded volume, accessible surface area, backbone and side chain dihedral angles, secondary structure, hydrogen bonding partners, hydrogen bond energies, steric quality, solvation free energy as well as local and overall fold ..
  23. ncbi Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures
    N Morozova
    Department of Biochemistry and Cell Biology, Rice University 6100 Main Street, Houston, TX 77005, USA
    Bioinformatics 22:2746-52. 2006
    ..The diversity of RNA structures suggests that RNA recognition is substantially different than that of DNA...
  24. ncbi A semiempirical free energy force field with charge-based desolvation
    Ruth Huey
    Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92102, USA
    J Comput Chem 28:1145-52. 2007
    ..The force field shows improvement in redocking simulations over the previous AutoDock3 force field...
  25. ncbi The structure of the potassium channel: molecular basis of K+ conduction and selectivity
    D A Doyle
    Laboratory of Molecular Neurobiology and Biophysics and the Howard Hughes Medical Institute, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Science 280:69-77. 1998
    ..The architecture of the pore establishes the physical principles underlying selective K+ conduction...
  26. ncbi A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    Yong Duan
    Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
    J Comput Chem 24:1999-2012. 2003
    ..charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed...
  27. pmc Minimal conformational plasticity enables TCR cross-reactivity to different MHC class II heterodimers
    Christopher J Holland
    Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
    Sci Rep 2:629. 2012
    ..Thermodynamic analysis revealed that limited plasticity and extreme favorable entropy underpinned the ability of the HA1.7 T-cell clone to cross-react with HA(306-318) presented by multiple MHC-II alleles...
  28. pmc Carbon-oxygen hydrogen bonding in biological structure and function
    Scott Horowitz
    Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
    J Biol Chem 287:41576-82. 2012
    Carbon-oxygen (CH···O) hydrogen bonding represents an unusual category of molecular interactions first documented in biological structures over 4 decades ago...
  29. pmc A major role for side-chain polyglutamine hydrogen bonding in irreversible ataxin-3 aggregation
    Antonino Natalello
    Department of Biotechnologies and Biosciences, University of Milano Bicocca, Milan, Italy
    PLoS ONE 6:e18789. 2011
    ..By H/D exchange experiments we show for the first time that they can be ascribed to glutamine side-chain hydrogen bonding, which is therefore the hallmark of irreversibly SDS-insoluble aggregated protein...
  30. ncbi Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    Jeffrey J Gray
    Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, J 567 Health Sciences, Box 357350, Seattle, WA 98195, USA
    J Mol Biol 331:281-99. 2003
    ..function dominated by van der Waals interactions, an implicit solvation model, and an orientation-dependent hydrogen bonding potential. Top-ranking decoys are clustered to select the final predictions...
  31. ncbi The structure of the first coordination shell in liquid water
    Ph Wernet
    Stanford Synchrotron Radiation Laboratory, Post Office Box 20450, Stanford, CA 94309, USA
    Science 304:995-9. 2004
    ..Serious discrepancies with structures based on current molecular dynamics simulations are observed...
  32. ncbi Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations
    Y Cho
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021
    Science 265:346-55. 1994
    ..The structure supports the hypothesis that DNA binding is critical for the biological activity of p53, and provides a framework for understanding how mutations inactivate it...
  33. pmc Insight into the mechanism of the influenza A proton channel from a structure in a lipid bilayer
    Mukesh Sharma
    Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
    Science 330:509-12. 2010
    ..This mechanism explains the main observations on M2 proton conductance...
  34. pmc 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
    Xiang Jun Lu
    Department of Chemistry and Chemical Biology, Wright Rieman Laboratories, Rutgers The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854 8087, USA
    Nucleic Acids Res 31:5108-21. 2003
    ..Regular helical models based on X-ray diffraction measurements of various repeating sequences can also be generated within the program...
  35. ncbi Self-assembly of peptide-amphiphile nanofibers: the roles of hydrogen bonding and amphiphilic packing
    Sergey E Paramonov
    Department of Chemistry, Rice University, 6100 Main Street, MS60, Houston, Texas 77005, USA
    J Am Chem Soc 128:7291-8. 2006
    The role of hydrogen bonding and amphiphilic packing in the self-assembly of peptide-amphiphiles (PAs) was investigated using a series of 26 PA derivatives, including 19 N-methylated variants and 7 alanine mutants...
  36. ncbi Protein flexibility predictions using graph theory
    D J Jacobs
    Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, USA
    Proteins 44:150-65. 2001
    ..This approach is demonstrated by comparison with experimental measures of flexibility for three proteins in which hinge and loop motion are essential for biological function: HIV protease, adenylate kinase, and dihydrofolate reductase...
  37. pmc Dissecting protein-RNA recognition sites
    Ranjit Prasad Bahadur
    School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D 28759 Bremen, Germany
    Nucleic Acids Res 36:2705-16. 2008
    ..The 2'OH is a major player in protein-RNA recognition, and shape complementarity an important determinant, whereas electrostatics and direct base-protein interactions play a lesser part than in protein-DNA recognition...
  38. ncbi Electrostatic aspects of protein-protein interactions
    F B Sheinerman
    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
    Curr Opin Struct Biol 10:153-9. 2000
    ..The past year also witnessed significant progress in our understanding of the effect of electrostatics on protein association kinetics, specifically in the characterization of a partially desolvated encounter complex...
  39. ncbi Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase
    - Madhusudan
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 0654, USA
    Nat Struct Biol 9:273-7. 2002
    ..This arrangement suggests that aluminum fluoride mimics the transition state and provides the first direct structural evidence for the in-line mechanism of phosphoryl transfer in a protein kinase...
  40. ncbi C-H...pi-interactions in proteins
    M Brandl
    Department of Structural Biology and Crystallography, Institute of Molecular Biology, Jena, Germany
    J Mol Biol 307:357-77. 2001
    ..It is likely that the C-H...pi-interactions contribute significantly to the overall stability of a protein...
  41. ncbi Structures of the bacterial ribosome at 3.5 A resolution
    Barbara S Schuwirth
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Science 310:827-34. 2005
  42. pmc Insights from modeling the 3D structure of New Delhi metallo-β-lactamse and its binding interactions with antibiotic drugs
    Jing Fang Wang
    Key Laboratory of Systems Biomedicine Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
    PLoS ONE 6:e18414. 2011
    ..It is anticipated that the findings reported here may provide useful insights for developing new antibiotic drugs to overcome the resistance problem...
  43. ncbi Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS
    Kuo Chen Chou
    Gordon Life Science Institute, 7088 Arbor Valley, Kalamazoo, MI 49009, USA
    Biochem Biophys Res Commun 308:148-51. 2003
    ..Meanwhile, the idea of how to develop inhibitors of the SARS enzyme based on the knowledge of its own peptide substrates (the so-called "distorted key" approach) was also briefly elucidated...
  44. ncbi Structure-based analysis of protein-RNA interactions using the program ENTANGLE
    J Allers
    Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA
    J Mol Biol 311:75-86. 2001
    ..a JAVA-based program that uses available structural models in their PDB format and searches for appropriate hydrogen bonding, stacking, electrostatic, hydrophobic and van der Waals interactions...
  45. pmc Photoisomerization of a rotaxane hydrogen bonding template: light-induced acceleration of a large amplitude rotational motion
    Francesco G Gatti
    School of Chemistry, University of Edinburgh, The King s Buildings, West Mains Road, United Kingdom
    Proc Natl Acad Sci U S A 100:10-4. 2003
    ..Here we demonstrate that the rate of rotation of the interlocked components of fumaramide-derived [2]rotaxanes can be accelerated, by >6 orders of magnitude, by isomerizing them to the corresponding maleamide [2]rotaxanes by using light...
  46. ncbi A hydrogen bond surrogate approach for stabilization of short peptide sequences in alpha-helical conformation
    Anupam Patgiri
    Department of Chemistry, New York University, New York, New York 10003, USA
    Acc Chem Res 41:1289-300. 2008
    ..Notably, our preliminary studies illustrate that HBS helices can target their expected protein receptors with high affinity...
  47. pmc Structural basis for the regulation of protein kinase A by activation loop phosphorylation
    Jon M Steichen
    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA
    J Biol Chem 287:14672-80. 2012
    ..main chain conformations for the magnesium positioning loop and catalytic loop causing a complete loss of hydrogen bonding between these two active site structural elements...
  48. ncbi Substrate specificity and affinity of a protein modulated by bound water molecules
    F A Quiocho
    Howard Hughes Medical Institute, Houston, Texas, 77030
    Nature 340:404-7. 1989
    ..These observations illustrate how ordered water molecules can contribute directly to the properties of proteins by influencing their interaction with ligands...
  49. pmc The plasticity of a structural motif in RNA: structural polymorphism of a kink turn as a function of its environment
    Peter Daldrop
    Cancer Research UK Nucleic Acid Structure Research Group, MSI WTB complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
    RNA 19:357-64. 2013
    ..The adenine bases of consecutive G•A pairs are directed toward the minor groove of the opposing helix, hydrogen bonding in a typical A-minor interaction...
  50. pmc Modeling of human prokineticin receptors: interactions with novel small-molecule binders and potential off-target drugs
    Anat Levit
    Institute of Biochemistry, Food Science and Nutrition, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
    PLoS ONE 6:e27990. 2011
    ..Blocking PKRs may serve as a therapeutic tool for various diseases, including acute pain, inflammation and cancer...
  51. ncbi More hydrogen bonds for the (structural) biologist
    M S Weiss
    Institute of Molecular Biotechnology, Beutenbergstr 11, D 07745 Jena, Germany
    Trends Biochem Sci 26:521-3. 2001
    ..Now, a general concept of hydrogen bonding in proteins is emerging...
  52. pmc Structural aspects of binding of α-linked digalactosides to human galectin-1
    Michelle C Miller
    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Health Sciences Center, 6 155 Jackson Hall, 321 Church Street, Minneapolis, MN 55455, USA
    Glycobiology 21:1627-41. 2011
    ..typical CH-π interaction is significantly diminished, yet binding appears to be partially compensated for by hydrogen bonding. Overall, these findings reveal that the type of α-linkage in digalactosides has an impact on maintaining CH-..
  53. pmc Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes
    Jiro Kondo
    Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7 1 Kioi cho, Chiyoda ku, 102 8554 Tokyo, Japan
    Nucleic Acids Res 39:8628-37. 2011
    ..The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues...
  54. ncbi Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain
    P H Kussie
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Science 274:948-53. 1996
    ..The structure also suggests that the amphipathic alpha helix may be a common structural motif in the binding of a diverse family of transactivation factors to the TATA-binding protein-associated factors...
  55. pmc Variations in protein-flavin hydrogen bonding in a light, oxygen, voltage domain produce non-Arrhenius kinetics of adduct decay
    Brian D Zoltowski
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390 8816, USA
    Biochemistry 50:8771-9. 2011
    ..Kinetic and spectroscopic analyses reveal that hydrogen bonding interactions between the FMN N1, O2, and ribityl hydroxyls and the surrounding protein regulate photocycle ..
  56. ncbi How T cell receptors interact with peptide-MHCs: a multiple steered molecular dynamics study
    Michel A Cuendet
    Swiss Institute of Bioinformatics, Genopode, 1015 Lausanne, Switzerland
    Proteins 79:3007-24. 2011
    ..Importantly, we illustrate how two TCRs with similar reactivity and structures can have essentially different binding strategies...
  57. ncbi Computational alanine scanning of the 1:1 human growth hormone-receptor complex
    Shuanghong Huo
    Department of Pharmaceutical Chemistry, University of California, San Francisco 94143 0446, USA
    J Comput Chem 23:15-27. 2002
    ..Our approach can be extended to rapid screening of a variety of possible modifications to binding sites...
  58. ncbi Correlations in liquid water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP models
    David J Huggins
    Cambridge Molecular Therapeutics Programme, Hutchison MRC Research Centre, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, United Kingdom
    J Chem Phys 136:064518. 2012
    ..However, they are expected to be very important when considering water molecules around solutes and are thus a key consideration in modelling solvent entropy...
  59. pmc Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: a molecular dynamics study
    Danilo Roccatano
    Dipartimento di Chimica, Ingegneria Chimica e Materiali Università Degli Studi, Via Vetoio, 67010 L Aquila, Italy
    Proc Natl Acad Sci U S A 99:12179-84. 2002
    ..Because TFE interacts only weakly with nonpolar residues, hydrophobic interactions within the peptides are not disrupted. As a consequence, TFE promotes stability rather than inducing denaturation...
  60. ncbi Application of inhomogeneous fluid solvation theory to model the distribution and thermodynamics of water molecules around biomolecules
    David J Huggins
    University of Cambridge, Hutchison MRC Research Centre, Hills Road, Cambridge, CB2 0XZ, UK
    Phys Chem Chem Phys 14:15106-17. 2012
    ..In addition, the predicted thermodynamic properties of hydration sites with the potential for direct hydrogen bonding interactions are found to disagree significantly for two different water models...
  61. ncbi Statistical analysis of atomic contacts at RNA-protein interfaces
    M Treger
    , , , 4 Rue Kirshleger, F-67000 Strasbourg, France
    J Mol Recognit 14:199-214. 2001
  62. ncbi Structure of D-allose binding protein from Escherichia coli bound to D-allose at 1.8 A resolution
    B N Chaudhuri
    Department of Molecular Biology, Uppsala University, Uppsala, SE 751 24, Sweden
    J Mol Biol 286:1519-31. 1999
    ..Details of the ligand-binding cleft reveal the features that determine substrate specificity. Extensive hydrogen bonding as well as hydrophobic interactions are found to be important...
  63. ncbi Strong N-H...pi hydrogen bonding in amide-benzene interactions
    Philipp Ottiger
    Departement für Chemie and Biochemie, Universitat Bern, Freiestrasse 3, CH 3012 Bern, Switzerland
    J Phys Chem B 113:2937-43. 2009
    ..Symmetry-adapted perturbation theory calculations show that the N--H...pi interaction is by far the dominant stabilization factor...
  64. ncbi Atomic interactions and profile of small molecules disrupting protein-protein interfaces: the TIMBAL database
    Alicia P Higueruelo
    Department of Biochemistry, University of Cambridge, UK
    Chem Biol Drug Des 74:457-67. 2009
    ..from the PDB) reveals that TIMBAL molecules tend to form mainly hydrophobic interactions with only a few hydrogen bonding contacts...
  65. ncbi Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics
    Giovanni Bussi
    Computational Science, Department of Chemistry and Applied Biosciences, Eidgenossische Technische Hochschule Zurich, c o USI Campus, Via Buffi 13, CH 6900 Lugano, Switzerland
    J Am Chem Soc 128:13435-41. 2006
    ..We use our results to calculate the difference in entropy and enthalpy between the folded and the unfolded state and to characterize the most populated configurations in the relevant free-energy basins...
  66. ncbi The role of local hydration and hydrogen-bonding dynamics in ion and solute release from ion-coupled secondary transporters
    Chunfeng Zhao
    Institute for Biocomplexity and Informatics and Department of Biological Sciences, University of Calgary, 2500 University Drive, BI558, Calgary, Alberta, Canada T2N 1N4
    Biochemistry 50:1848-56. 2011
  67. ncbi Molecular recognition of fatty acids by peroxisome proliferator-activated receptors
    H E Xu
    Glaxo Wellcome Research and Development, Research Triangle Park, North Carolina 27709, USA
    Mol Cell 3:397-403. 1999
    ..These structures provide molecular insight into the propensity for PPARs to interact with a variety of synthetic and natural compounds, including FAs that vary in both chain length and degree of saturation...
  68. ncbi Functional evaluation of Asp76, 84, 102 and 150 in human arsenic(III) methyltransferase (hAS3MT) interacting with S-adenosylmethionine
    Xiangli Li
    State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
    FEBS Lett 587:2232-40. 2013
    ..Asp76 and 84 were located in the SAM-binding pocket, and Asp102 significantly affected SAM-binding via forming hydrogen bonds with SAM...
  69. pmc Proton transfer via a transient linear water-molecule chain in a membrane protein
    Erik Freier
    Department of Biophysics, Ruhr University Bochum, Universitatsstrasse 150, 44780 Bochum, Germany
    Proc Natl Acad Sci U S A 108:11435-9. 2011
    ..Our discovery provides insight into proton-transfer mechanisms through hydrophobic core regions of ubiquitous membrane spanning proteins such as G-protein coupled receptors or cytochrome C oxidases...
  70. pmc Structure of the cross-beta spine of amyloid-like fibrils
    Rebecca Nelson
    Howard Hughes Medical Institute, UCLA DOE Institute for Genomics and Proteomics, Box 951570, UCLA, Los Angeles, California 90095 1570, USA
    Nature 435:773-8. 2005
    ..The structure illuminates the stability of amyloid fibrils, their self-seeding characteristic and their tendency to form polymorphic structures...
  71. ncbi Refined crystal structures of native human angiogenin and two active site variants: implications for the unique functional properties of an enzyme involved in neovascularisation during tumour growth
    D D Leonidas
    Department of Biology and Biochemistry, University of Bath, Claverton Down, BA2 7AY, UK
    J Mol Biol 285:1209-33. 1999
    ..The H13A structure shows some changes beyond the ribonucleolytic site, but sites involved in cell-binding and nuclear translocation are essentially unaffected by the amino acid replacement...
  72. ncbi Crystal structures of high affinity human T-cell receptors bound to peptide major histocompatibility complex reveal native diagonal binding geometry
    Malkit Sami
    Avidex Limited subsidiary of Medigene Ag, 57C Milton Park, Abingdon, Oxon OX14 4RX, UK
    Protein Eng Des Sel 20:397-403. 2007
    ..Most notably, there is a marked increase in the SC for the central methionine and tryptophan peptide motif over the native TCR...
  73. ncbi DNA binding and nucleotide flipping by the human DNA repair protein AGT
    Douglas S Daniels
    Skaggs Institute for Chemical Biology, The Scripps Research Institute, MB 4, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Nat Struct Mol Biol 11:714-20. 2004
    ..Structural and biochemical results further support an unpredicted role for Tyr114 in nucleotide flipping through phosphate rotation and an efficient kinetic mechanism for locating alkylated bases...
  74. ncbi Tuning the mechanical properties of graphene oxide paper and its associated polymer nanocomposites by controlling cooperative intersheet hydrogen bonding
    Owen C Compton
    Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
    ACS Nano 6:2008-19. 2012
    ..For graphene oxide paper at an optimal concentration of ~5 wt % water, the degree of cooperative hydrogen bonding within the network comprising adjacent nanosheets and water molecules was found to optimally enhance the ..
  75. ncbi Steered molecular dynamics investigations of protein function
    B Isralewitz
    Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
    J Mol Graph Model 19:13-25. 2001
  76. pmc Mechanisms of loss of functions of human angiogenin variants implicated in amyotrophic lateral sclerosis
    Aditya K Padhi
    School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
    PLoS ONE 7:e32479. 2012
  77. pmc Identification of potent EGFR inhibitors from TCM Database@Taiwan
    Shun Chieh Yang
    Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung, Taiwan
    PLoS Comput Biol 7:e1002189. 2011
    ..Based on the results of this study, 2-O-caffeoyl tartaric acid, Emitine, Rosmaricine, and 2-O-feruloyl tartaric acid are suggested to be potential EGFR inhibitors...
  78. ncbi Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations
    Jing Fang Wang
    Key Laboratory of Systems Biomedicine Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
    J Mol Model 18:2717-25. 2012
  79. pmc Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation
    Stuart A Sievers
    Department of Biological Chemistry, Howard Hughes Medical Institute, UCLA, Box 951970, Los Angeles, California 90095 1570, USA
    Nature 475:96-100. 2011
    ..Because the inhibiting peptides have been designed on structures of dual-β-sheet 'steric zippers', the successful inhibition of amyloid fibril formation strengthens the hypothesis that amyloid spines contain steric zippers...
  80. pmc Structure of a serine protease poised to resynthesize a peptide bond
    Elena Zakharova
    Department of Biology, University of Utah, Salt Lake City, UT 84112 0840, USA
    Proc Natl Acad Sci U S A 106:11034-9. 2009
    ..The results also provide insights into the mechanism by which inhibitors like BPTI normally resist hydrolysis when bound to their target proteases...
  81. ncbi Ionization properties of phosphatidylinositol polyphosphates in mixed model membranes
    Edgar E Kooijman
    Department of Biological Sciences, Kent State University, Kent, Ohio 44242, USA
    Biochemistry 48:9360-71. 2009
  82. ncbi Screening from the world's largest TCM database against H1N1 virus
    Tung Ti Chang
    Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan
    J Biomol Struct Dyn 28:773-86. 2011
    ..Molecular dynamics simulations show that these derivatives form strong hydrogen bonding with Glu83 but interact transiently with Asp103...
  83. pmc Correlated motion and the effect of distal mutations in dihydrofolate reductase
    Thomas H Rod
    Department of Molecular Biology, The Scripps Research Institute, TPC6, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 100:6980-5. 2003
    ..On the basis of our new findings, we discuss the role of coupled motions between distant regions in the enzyme, which previously was reported by Radkiewicz and Brooks...
  84. pmc NCI: A server to identify non-canonical interactions in protein structures
    M Madan Babu
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nucleic Acids Res 31:3345-8. 2003
    ..In addition, the user can view the RasMol image highlighting the interactions in the protein structure and download the RasMol script. The NCI server is available at: http://www.mrc-lmb.cam.ac.uk/genomes/nci/...
  85. ncbi Crystal structure of glucose dehydrogenase from Bacillus megaterium IWG3 at 1.7 A resolution
    K Yamamoto
    Department of Chemistry, Nara Medical University, Shijo, Kashihara, Nara 634 8521, Japan
    J Biochem 129:303-12. 2001
    ..Hydrogen bonds between Q-axis related subunits are also less common than in the other SDRs. The GlcDH tetramer dissociates into inactive monomers at pH 9.0, which can be attributed mainly to the weakness of the Q-axis interface...
  86. pmc Chemical-scale studies on the role of a conserved aspartate in preorganizing the agonist binding site of the nicotinic acetylcholine receptor
    Amanda L Cashin
    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
    Biochemistry 46:630-9. 2007
  87. ncbi Cooperative hydrogen bonding effects are key determinants of backbone amide proton chemical shifts in proteins
    Laura L Parker
    Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA
    J Am Chem Soc 128:9863-72. 2006
    ..We present a simple model that accurately relates the protein structure to delta(H)...
  88. ncbi Structural and functional constraints in the evolution of protein families
    Catherine L Worth
    Biochemistry Department, University of Cambridge, UK
    Nat Rev Mol Cell Biol 10:709-20. 2009
    ..These constraints arise from the need to conserve a specific architecture and to retain interactions that mediate functions in protein families and superfamilies...
  89. ncbi Structure of a DNA glycosylase searching for lesions
    Anirban Banerjee
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Science 311:1153-7. 2006
    ..MutM therefore actively interrogates the intact DNA helix while searching for damage...
  90. ncbi The structure of an intermediate in class II MHC maturation: CLIP bound to HLA-DR3
    P Ghosh
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Nature 378:457-62. 1995
    ..The structure is the substrate for the loading of antigenic peptides by an exchange process catalysed by DM...
  91. ncbi Cation-pi/H-bond stair motifs at protein-DNA interfaces
    Marianne Rooman
    Ingénierie Biomoléculaire CP 165 64, Universite Libre de Bruxelles, 50 Avenue Roosevelt, B 1050 Bruxelles, Belgium
    J Mol Biol 319:67-76. 2002
  92. ncbi Adaptive recognition by nucleic acid aptamers
    T Hermann
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Science 287:820-5. 2000
    ..specificity to the aptamer-ligand association, including the precise stacking of flat moieties, specific hydrogen bonding, and molecular shape complementarity...
  93. ncbi Replacement of catalytic histidine-195 of chloramphenicol acetyltransferase: evidence for a general base role for glutamate
    A Lewendon
    Department of Biochemistry, University of Leicester, U K
    Biochemistry 33:1944-50. 1994
    ..plays an essential part in the proposed general base mechanism of chloramphenicol acetyltransferase (CAT), hydrogen bonding to and a abstracting a proton from the primary hydroxyl group of chloramphenicol...
  94. ncbi SNPs, protein structure, and disease
    Z Wang
    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA
    Hum Mutat 17:263-70. 2001
    ..In sharp contrast, over 70% of the population set are found to be neutral. The remaining 30% are potentially involved in polygenic disease...
  95. ncbi Pi-organogels of self-assembled p-phenylenevinylenes: soft materials with distinct size, shape, and functions
    Ayyappanpillai Ajayaghosh
    Photosciences and Photonics Group, Chemical Sciences and Technology Division, National Institute for Interdisciplinary Science and Technology NIST, CSIR, Trivandrum 695 019, India
    Acc Chem Res 40:644-56. 2007
  96. ncbi Effect of hydrogen bonding interactions on the release mechanism of felodipine from nanodispersions with polyvinylpyrrolidone
    Evangelos Karavas
    Department of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki, Greece
    Eur J Pharm Biopharm 63:103-14. 2006
    ..Microscopic observation of the dissolution behaviour showed that FEL remains in fine dispersion in aqueous solution, verifying the release mechanism...
  97. ncbi Site-specific incorporation of a photo-crosslinking component into RNA by T7 transcription mediated by unnatural base pairs
    Michiko Kimoto
    Protein Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Chem Biol 11:47-55. 2004
  98. pmc Crystal structure of a translation termination complex formed with release factor RF2
    Andrei Korostelev
    Center for Molecular Biology of RNA and Departments of Molecular, Cell and Developmental Biology and Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
    Proc Natl Acad Sci U S A 105:19684-9. 2008
    ..We show that when the H-bonding capability of the main-chain N-H of the conserved glutamine is eliminated by substitution with proline, peptidyl-tRNA esterase activity is abolished, consistent with its proposed role in catalysis...
  99. ncbi Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy
    Florian Garczarek
    Lehrstuhl fur Biophysik, Ruhr Universitat Bochum, D 44780 Bochum, Germany
    Nature 439:109-12. 2006
    ..Our findings support the emerging paradigm that intraprotein water molecules are as essential for biological functions as amino acids...
  100. ncbi Molecular dynamics study of the beta amyloid peptide of Alzheimer's disease and its divalent copper complexes
    Duilio F Raffa
    Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
    J Phys Chem B 111:3789-99. 2007
    ..The results of the Cu(II)/Abeta1-42 systems are compared to the Cu(II)-free Abeta1-42 simulation...
  101. ncbi The X-ray crystal structure of the Trichoderma reesei family 12 endoglucanase 3, Cel12A, at 1.9 A resolution
    M Sandgren
    Department of Cell and Molecular Biology, Uppsala University, Sweden
    J Mol Biol 308:295-310. 2001
    ..The structure of the fungal family 12 enzyme presented here allows a complete structural characterization of the glycoside hydrolase-C clan...

Research Grants66

  1. Neonatal Phototherapy / Bilirubin Excretion
    DAVID LIGHTNER; Fiscal Year: 2007
    ..2) Clarify the carboxylic acid pKa of bilirubin, its dependence on hydrogen bonding and aggregation, its influence on polarity and its role in bilirubin transport and metabolism...
    PALMER WILLIAM TAYLOR; Fiscal Year: 2013
    ..also will examine the inductive role of the oxyanion hole, the nucleophile rendering catalytic triad and the hydrogen bonding network between the proximal serine hydroxyls at the base of the gorge...
  3. Electron Transfer in Iron and Copper Proteins
    Jay R Winkler; Fiscal Year: 2013
    ..Efforts will focus on oxidative generation of Compounds I and II in cytochromes P450 (Aim 3) and a bacterial enzyme that exhibits NOS-like reactivity (Aim 4). ..
  4. Biosynthetic Protein Models of Heme-copper Oxidases and Nitric Oxide Reductases
    Yi Lu; Fiscal Year: 2013
    ..is covalently linked to a CuB-His ligand, and non-covalent interactions, such as water and the associated hydrogen bonding network;2) elucidate structural features responsible for NOR function, specifically the FeB site and nearby ..
    Sharon Hammes Schiffer; Fiscal Year: 2010
    ..The calculations will probe the roles of electrostatics, hydrogen bonding, hydrogen tunneling, and protein motion in enzyme reactions...
  6. Computational Design of Small Molecule Drugs Inhibiting the Zinc Finger Transcrip
    David Sherris; Fiscal Year: 2010
    ..the VEZF1/DNA complex, 2) cavities with at least some hydrophobic regions, and 3) polar atoms available for hydrogen bonding with ligand atoms...
  7. RNA Modification Enzymes: Methyltransferase/psi-synthase
    Robert M Stroud; Fiscal Year: 2012
    ..altering the stability, higher-order structure, and activity of RNA through changes in base stacking and hydrogen bonding. These generally conserved modifications are located at key functional regions and are required for optimal ..
  8. Targeting of alpha7 nAChR for therapeutic effects
    Roger L Papke; Fiscal Year: 2013
    ..We will investigate the potential importance of hydrogen bonding and hydrophobic interactions on the binding, gating, and desensitizing properties of the specific receptor/..
  9. Identification, Discovery, and Public Archiving of RNA Structural Motifs
    Shaojie Zhang; Fiscal Year: 2013
    ..a new computational search tool which will, in addition to 3D geometry, take into account base pairing (hydrogen bonding forces) and base stack- ing (magnetic and electrostatic forces) information...
  10. Control of AMPA receptor function by phosphorylation
    Stephen F Traynelis; Fiscal Year: 2013
    ..regulation of AMPA receptor function? We will identify intracellular GluR1 residues as phospho-Ser831 hydrogen bonding partners...
  11. Structure-Function Studies of the Proton-Gated Urea Channel from H. Pylori
    Hartmut Luecke; Fiscal Year: 2013
    ..Mutagenesis studies have shown that the proton gating of HpUreI is regulated by hydrogen bonding between histidines and carboxylic acid residues in these three periplasmic regions...
  12. Ribonucleotide Reductase: Structure and Function
    JoAnne Stubbe; Fiscal Year: 2013
    ..coli RNR, and are sensitive to changes in protein conformation, hydrogen bonding networks, and redox potentials...
  13. The Molecular Basis of Alcohol's Actions
    DAVID NIGEL JONES; Fiscal Year: 2010
    ..and biochemical studies of this protein led to the discovery that concerted interactions from multiple hydrogen bonding resides were required to form an ethanol binding site...
  14. Computational Modeling of Post-translational Modifications in Proteins
    CHAYA K RAPP; Fiscal Year: 2011
    ..b>Hydrogen bonding will further be studied using molecular dynamics simulation of tripeptides Arg-Gly-xTyr and Lys-Gly-xTyr, ..
  15. Expanding the Genetic Alphabet by Design and Selection
    Floyd E Romesberg; Fiscal Year: 2013
    ..Completion of the proposed work will also position us at the doorstep of creating the first semi-synthetic organism, able to store, retrieve, and evolve, with more information than natural organisms. ..
    John M Tomich; Fiscal Year: 2013
    ..Specific amino acid replacements will be introduced to modulate pore lining residues with regard to hydrogen bonding capabilities or electrostatic properties. Other replacements will alterpore length and rigidity...
    Feng Gai; Fiscal Year: 2013
    ..2D IR exposes spatial arrangements across the membrane, hydrophobic effects, polarity, hydrogen bonding and other weak interactions between buried residues that enlighten the mechanisms and structural basis of ..
    Sharon Hammes-Schiffer; Fiscal Year: 2013
    ..These calculations will probe the roles of hydrogen bonding, electrostatics, active site reorganization, and conformational sampling in both protein and RNA enzyme ..
  19. Understanding protein radicals
    Cecilia Tommos; Fiscal Year: 2012
    ..To increase our knowledge in this research area, we have developed a library of well- structured model proteins specifically made to study the chemical properties of protein radicals. ..
  20. Light Scattering & Flourescence Study of Sugar Solutions as Cryoprotective Agents
    DAVID LEE SIDEBOTTOM; Fiscal Year: 2010
    ..that stability of the biomolecule is a result of how water near the protein is preferentially replaced by hydrogen bonding to the sugar...
  21. Exploring tyrosine redox chemistry in model proteins
    MELISSA MARTINEZ-RIVERA; Fiscal Year: 2013
    ..For this reason, we have developed a series of model protein scaffolds with the characteristics necesary to investigate the relation between the thermodynamics of amino-acid redox chemistry and the surrounding protein environment. ..
    Martin Egli; Fiscal Year: 2012
    ..Aim (4) we will address the recent hypothesis that certain DNA polymerases appear to rely more on shape than hydrogen bonding for accurate and efficient replication...
  23. Structural bioinformatics software for epitope selection and antibody engineering
    STEVEN JOSEPH DARNELL; Fiscal Year: 2012
    ..sequence and the biophysics that mediate protein-protein interactions, including solvent accessibility, hydrogen bonding, residue flexibility, binding nuclei, and geometric contours of the molecular surface...
    Audra L Stinchcomb; Fiscal Year: 2010
  25. Chemistry and energy transduction in kinesin motor proteins
    Sunyoung Kim; Fiscal Year: 2013
    ..Building upon these findings, our principal goal is to define novel roles for proton transfer and hydrogen bonding for ATP hydrolysis and chemo-mechanical coupling in the human Kinesin-5 protein, essential for mitosis and a ..
  26. Understanding Beta-Sheet Structure in Aqueous Solution
    Jeffery W Kelly; Fiscal Year: 2013
    ..properties of the aromatic ring, the amphiphilicity of the N-linked carbohydrate, and the hydrophobicity and hydrogen bonding potential of the Thr residue to understand the stabilizing aspects of this tripartite interaction in distinct ..
    Chang An Yu; Fiscal Year: 2009
    ..studies, including the Q-binding at the Qo site pocket, the proton transfer path, structure water, hydrogen bonding, and the interaction domain between cytochromes c\ and c...
  28. Chemical Structure Effects on Bone Response to Mechanical Load
    MICHAEL DAVID MORRIS; Fiscal Year: 2013
    ..In Aim 2 we will investigate the role of water in stabilizing both the mineral and matrix components via hydrogen bonding and enthalpic stabilization. Changes in collagen secondary structure will be measured through 13C resonances...
  29. Artificial Metalloproteins: Confining Metal Complexes within Protein Hosts. (Orig
    Andrew S Borovik; Fiscal Year: 2013
    ..This collaborative supplement application builds on the existing research efforts in Hydrogen Bonding Cavity Motifs about Metal Ions (2 Ro1 GM050781-21) by offering a new approach that combines both synthetic ..
  30. Structure of reaction intermediates in the bc1 complex
    Sergei A Dikanov; Fiscal Year: 2010
    ..mechanism, we need detailed information about the local reaction environment, including protein structure, hydrogen bonding, and distances, to provide the parameters that control rates, and partitioning of electrons to different ..
  31. Mixed Hydrogen-Bonding Flavin Catalysis for Asymmetric Transformations
    NOAH ZACHARY BURNS; Fiscal Year: 2011
    ..Since this proposal seeks to create new methods for the selective synthesis of small molecules with no hazardous byproducts it is of particular relevance to public health. ..
  32. Pre-steady State Kinetic Analysis of cis-3-Chloroacrylic Acid Dehalogenase
    ..The aims of this proposal will assess the influence of protein motion, loop identity, and distal hydrogen bonding networks involving active site residues on each step of the catalytic cycle...
  33. Synthesis and Evaluation of Antibacterial Anionic Dendritic Amphiphiles
    ERIC LAWRENCE DANE; Fiscal Year: 2013
    ..We propose to introduce a hydrogen bonding core, based on a diaryl urea capable of complementary hydrogen bonding, into the amphiphiles to address this ..
  34. Excision of Environmental Carcinogen-DNA Lesions by Human NER enzymes
    Nicholas E Geacintov; Fiscal Year: 2012
    ..distortions caused by the lesions and the subsequent strand separation suggest that base-base stacking and hydrogen bonding interactions are first weakened and then broken during these initial phenomena...
  35. Evolution of p450's Machinery for C-H Amination
    TODD KURT HYSTER; Fiscal Year: 2013
    ..to simple esters using directed evolution;(2) Aminate alkyl acids using directed evolution in concert with a hydrogen bonding additive...
  36. Evaluating Aspects of O2-Activation by Bacterial Multicomponent Monooxygenases
    RACHEL BEHAN WOLLACOTT; Fiscal Year: 2010
  37. Using Second Coordination Sphere Interactions of Rhenium(I) Complexes to Promote
    LOI HUNG DO; Fiscal Year: 2012
    ..ligand provides an opportunity to explore the influence of second coordination sphere interactions, such as hydrogen bonding, Lewis acid activation, and electrostatic attraction, on the reactivity of metal carbonyl species toward ..
  38. Spectroscopic markers for blue-fluorescing tryptophan in proteins
    LAURA JEANNE JUSZCZAK; Fiscal Year: 2012
    ..fluorescence emission bands, and many have already been associated with specific tryptophan features such as hydrogen bonding at the indole amine...
    Jacqueline K Barton; Fiscal Year: 2013
    ..of mismatches targeted to include the more stable guanine mismatches by functionalizing the Rh complexes for hydrogen bonding into guanine-containing mismatches. We will also prepare a new Rh scaffold for bifunctional conjugates...
  40. The dopamine transporter and ions, substrates, blockers
    MAARTEN E REITH; Fiscal Year: 2010
    ..We will study the role of hydrogen bonding between carboxyl groups in cocaine (or hydroxyls in DA) and hydroxyls of tyrosine or serine in DAT, or cation-..
  41. Active Site Modifications in De Novo Designed Metalloenzymes
    VIRGINIA MAY CANGELOSI; Fiscal Year: 2013
    ..Finally, hydrogen bonding residues will be incorporated near the active site which should activate the hydroxide ligand on Zn(II) as ..
  42. Structure and Activation Mechanism of the Visual Pigment Rhodopsin
    STEVEN OWEN SMITH; Fiscal Year: 2013
    ..In addition, our studies address how specific mutations lead to retinal diseases through constitutive activation, receptor misfolding or stabilization of non-functional receptor conformations. ..
  43. Understanding the thermodynamics and structure of RNA secondary structure motifs
    BRENT ZNOSKO; Fiscal Year: 2013
    ..solved RNA structures, the use of NMR to identify structural properties of underrepresented RNA motifs, and hydrogen bonding and base stacking calculations...
    Philip E Dawson; Fiscal Year: 2010
    ..These studies indicate that backbone modification provides direct information on the formation of backbone hydrogen bonding in the native state and folding transition state ensemble that is not observed using traditional side chain ..
  45. Refinement of Macromolecular Assembly Structure using Electron Microscopy
    Michael S Chapman; Fiscal Year: 2010
    ..This work will include development of restraints for continuum electrostatics and hydrogen bonding, and a comparison of atomistic restraints with heuristics that might enhance convergence at low resolution...
    Kendall N Houk; Fiscal Year: 2013
    ..These are critical elements in the synthesis of effective pharmaceutical agents. ..
  47. Development of Chemical Receptors for Proteins
    Sanku Mallik; Fiscal Year: 2005
    ..stable, chemical receptors for proteins by creating a three-dimensional pattern of metal-ions, ion-pairs and hydrogen bonding sites on liposomes, complimentary to the pattern exhibited by the MMP-13...
  48. Computational Design of Protein-Protein Interactions
    BRIAN A KUHLMAN; Fiscal Year: 2013
    ..b>Hydrogen bonding between the edge strands of the two proteins will establish the relative positioning of the proteins and ..
    JEROME SOLOMON; Fiscal Year: 1999
    ..This research will provide a clearer understanding of the molecular mechanisms of initiation of carcinogenesis by an environmentally significant class of carcinogens for which the mechanism of somatic mutagenesis in unknown. ..
  50. Gene Delivery of P53 in a Tumor-bearing Mouse Model
    ARCHIBALD MIXSON; Fiscal Year: 2007
    ..Whether hydrogen bonding or hydrophobic properties of histidine stabilize the HK:liposome:DNA complexes in the presence of serum will ..
  51. Mechanisms of ribosomal reactions: peptide bond formation, peptide release and mR
    Scott A Strobel; Fiscal Year: 2013
    ..Novel analogs to define the orientation of the water and the contribution made by charge stabilization and hydrogen bonding to the peptide released TS. mRNA Cleavage by RelE (Aim 3)...
  52. Development of Catalysts for Asymmetric Synthesis
    VIRESH RAWAL; Fiscal Year: 2009
    ..Whereas the previous proposal described both metal-based catalysts and hydrogen bonding based catalysts, the current proposal focuses entirely on the latter class of compounds...
    Patrick Stayton; Fiscal Year: 2001
    ..Because streptavidin utilizes common aromatic, hydrogen bonding, and flexible loop interaction motifs to generate uncommonly high- affinity, the principles elucidated here ..
    Patrick Stayton; Fiscal Year: 2002
    ..Because streptavidin utilizes common aromatic, hydrogen bonding, and flexible loop interaction motifs to generate uncommonly high- affinity, the principles elucidated here ..
  55. Protein Stabilization in Ionic Liquids
    Gloria Elliott; Fiscal Year: 2009
    ..This will have a direct and immediate impact on national health and welfare issues. ..
    DIWAKAR DESHMUKH; Fiscal Year: 1993
    ..the barbiturates are the nearest in structure to inositol; both contain a six-membered ring with several hydrogen bonding sites (O, OH, or NH groups)...
    PAUL BLATZ; Fiscal Year: 1990
    ..In this work, the hydrogen bonding (H-bond) and proton transferring reactions of CH3(CH=CH)5C=NC4H9 (compound I) and NRBA are to be studied both ..
    DAVID MORRIS GRANT; Fiscal Year: 2010
    ..Theoretical computations tie experimental data to structure and allow the influence of hydrogen bonding, conformation and stereo-chemistry to be systematically evaluated through analysis of hypothetical model ..
    RONALD BORCHARDT; Fiscal Year: 2007
    ..prodrugs of a model opioid peptide (DADLE) that exhibit physicochemical properties (hydrophobicity, low hydrogen bonding potential, no charge) favorable for high transcellular permeation...
    TAD KOCH; Fiscal Year: 2001
    ..Vancomycin and eremomycin appear to function as head-to- tail type dimers, associated through hydrogen bonding of their peptide backbones...
    Wayne Anderson; Fiscal Year: 1993
    ..Potential drug candidates which evolve from the proposed studies will be evaluated for water solubility, chemical stability and other properties that must be assessed in new drug development studies. ..
    STANLEY GILL; Fiscal Year: 1992
    ..first step requires accurate thermodynamic characterization of the specific interactions in proteins such as hydrogen bonding, van der Waals contacts, ion pairing and hydrophobic effects...
  63. Structure and stability of Holliday junctions
    PUI HO; Fiscal Year: 2005
    ..The contribution of the direct and solvent mediated hydrogen bonding interactions within the ACC-core on the formation of Holliday junctions will be studied using a ..
  64. Evolution of tRNA Synthetases for Incorporation of Novel Backbone Structures
    CHARLES MELANCON; Fiscal Year: 2009
    ..utility of altering backbone structure in studying the contributions of backbone conformational rigidity and hydrogen bonding to protein stability, catalysis, and regulation...
    Teruna Siahaan; Fiscal Year: 2000
    ..physicochemical properties of the prodrugs and the parent compounds will be evaluated, including solubility, hydrogen bonding potential, average hydrodynamic volumes, partition coefficients, lipophilicity and conformation...
    Duane Miller; Fiscal Year: 1992
    ..agonist and antagonist amines in the protonated form can bind to the receptor in an additional manner: by hydrogen bonding. This hydrogen bonding would reinforce the ionic bond resulting in a stronger bond between the receptor and ..