- 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...
- Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
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..
- Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
Biopolymers 22:2577-637. 1983
- Automatic atom type and bond type perception in molecular mechanical calculations
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...
- 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...
- Crystal structure of rhodopsin: A G protein-coupled receptor
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...
- The structural basis for agonist and partial agonist action on a β(1)-adrenergic receptor
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
Nature 469:241-4. 2011
- Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes
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...
- 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 ..
- The structural basis of agonist-induced activation in constitutively active rhodopsin
Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
Nature 471:656-60. 2011
..We thus show how an agonist ligand can activate its GPCR...
- The role of DNA shape in protein-DNA recognition
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
- Structural plasticity and the evolution of antibody affinity and specificity
Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA
J Mol Biol 330:651-6. 2003
- RNA tertiary interactions in the large ribosomal subunit: the A-minor motif
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...
- Intramolecular hydrogen bonding in medicinal chemistry
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...
- Further development and validation of empirical scoring functions for structure-based binding affinity prediction
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...
- 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...
- 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...
- The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure
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...
- 3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization
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 ..
- 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...
- 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...
- VADAR: a web server for quantitative evaluation of protein structure quality
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 ..
- Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures
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...
- A semiempirical free energy force field with charge-based desolvation
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...
- 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...
- A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
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...
- 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...
- Carbon-oxygen hydrogen bonding in biological structure and function
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...
- A major role for side-chain polyglutamine hydrogen bonding in irreversible ataxin-3 aggregation
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...
- 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...
- The structure of the first coordination shell in liquid water
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...
- Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations
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...
- Insight into the mechanism of the influenza A proton channel from a structure in a lipid bilayer
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...
- 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...
- 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...
- 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...
- 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...
- 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...
- Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase
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...
- C-H...pi-interactions in proteins
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...
- 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
- 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...
- 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...
- Structure-based analysis of protein-RNA interactions using the program ENTANGLE
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...
- 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 rotaxanes can be accelerated, by >6 orders of magnitude, by isomerizing them to the corresponding maleamide rotaxanes by using light...
- A hydrogen bond surrogate approach for stabilization of short peptide sequences in alpha-helical conformation
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...
- 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...
- 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...
- The plasticity of a structural motif in RNA: structural polymorphism of a kink turn as a function of its environment
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...
- Modeling of human prokineticin receptors: interactions with novel small-molecule binders and potential off-target drugs
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...
- 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...
- 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-..
- Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes
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...
- 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...
- 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 ..
- 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...
- Computational alanine scanning of the 1:1 human growth hormone-receptor complex
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...
- 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...
- Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: a molecular dynamics study
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...
- 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...
- Statistical analysis of atomic contacts at RNA-protein interfaces
, , , 4 Rue Kirshleger, F-67000 Strasbourg, France
J Mol Recognit 14:199-214. 2001
- 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...
- Strong N-H...pi hydrogen bonding in amide-benzene interactions
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...
- 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...
- Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics
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...
- The role of local hydration and hydrogen-bonding dynamics in ion and solute release from ion-coupled secondary transporters
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
- 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...
- Functional evaluation of Asp76, 84, 102 and 150 in human arsenic(III) methyltransferase (hAS3MT) interacting with S-adenosylmethionine
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...
- Proton transfer via a transient linear water-molecule chain in a membrane protein
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...
- Structure of the cross-beta spine of amyloid-like fibrils
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...
- 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...
- Crystal structures of high affinity human T-cell receptors bound to peptide major histocompatibility complex reveal native diagonal binding geometry
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...
- 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...
- 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 ..
- Steered molecular dynamics investigations of protein function
Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
J Mol Graph Model 19:13-25. 2001
- 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
- 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...
- 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
- 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...
- Structure of a serine protease poised to resynthesize a peptide bond
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...
- 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
- 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...
- 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...
- 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/...
- Crystal structure of glucose dehydrogenase from Bacillus megaterium IWG3 at 1.7 A resolution
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...
- 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
- 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)...
- 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...
- Structure of a DNA glycosylase searching for lesions
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...
- The structure of an intermediate in class II MHC maturation: CLIP bound to HLA-DR3
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...
- Cation-pi/H-bond stair motifs at protein-DNA interfaces
Ingénierie Biomoléculaire CP 165 64, Universite Libre de Bruxelles, 50 Avenue Roosevelt, B 1050 Bruxelles, Belgium
J Mol Biol 319:67-76. 2002
- Adaptive recognition by nucleic acid aptamers
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...
- Replacement of catalytic histidine-195 of chloramphenicol acetyltransferase: evidence for a general base role for glutamate
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...
- SNPs, protein structure, and disease
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...
- Pi-organogels of self-assembled p-phenylenevinylenes: soft materials with distinct size, shape, and functions
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
- Effect of hydrogen bonding interactions on the release mechanism of felodipine from nanodispersions with polyvinylpyrrolidone
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...
- Site-specific incorporation of a photo-crosslinking component into RNA by T7 transcription mediated by unnatural base pairs
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
- Crystal structure of a translation termination complex formed with release factor RF2
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...
- Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy
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...
- 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...
- The X-ray crystal structure of the Trichoderma reesei family 12 endoglucanase 3, Cel12A, at 1.9 A resolution
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...