How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding.

[1]  D. Koshland,et al.  CORRELATION OF STRUCTURE AND FUNCTION IN ENZYME ACTION. , 1963, Science.

[2]  G. N. Ramachandran,et al.  Stereochemistry of polypeptide chain configurations. , 1963, Journal of molecular biology.

[3]  G. N. Ramachandran,et al.  Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units. , 1965, Biophysical journal.

[4]  C. Venkatachalam Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units , 1968, Biopolymers.

[5]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[6]  G. Weber Ligand binding and internal equilibria in proteins. , 1972, Biochemistry.

[7]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[8]  Robert Huber,et al.  Conformational flexibility in protein molecules , 1979, Nature.

[9]  J. Janin,et al.  Structural domains in proteins and their role in the dynamics of protein function. , 1983, Progress in biophysics and molecular biology.

[10]  W. Bennett,et al.  Structural and functional aspects of domain motions in proteins. , 1984, CRC critical reviews in biochemistry.

[11]  N Srinivasan,et al.  Conformation of glycyl residues in globular proteins. , 2009, International journal of peptide and protein research.

[12]  M Karplus,et al.  Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop. , 1990, Science.

[13]  J. Thornton,et al.  Beta-turns and their distortions: a proposed new nomenclature. , 1990, Protein engineering.

[14]  E. Milner-White,et al.  Situations of gamma-turns in proteins. Their relation to alpha-helices, beta-sheets and ligand binding sites. , 1990, Journal of molecular biology.

[15]  J Moult,et al.  Analysis of the steric strain in the polypeptide backbone of protein molecules , 1991, Proteins.

[16]  C. Sander,et al.  Database of homology‐derived protein structures and the structural meaning of sequence alignment , 1991, Proteins.

[17]  M Gerstein,et al.  Analysis of protein loop closure. Two types of hinges produce one motion in lactate dehydrogenase. , 1991, Journal of molecular biology.

[18]  L. Delbaere,et al.  Active-centre torsion-angle strain revealed in 1.6 Å-resolution structure of histidine-containing phosphocarrier protein , 1993, Nature.

[19]  E. Kempner,et al.  Movable lobes and flexible loops in proteins Structural deformations that control biochemical activity , 1993, FEBS letters.

[20]  K. H. Kalk,et al.  Crystal structures of hevamine, a plant defence protein with chitinase and lysozyme activity, and its complex with an inhibitor. , 1994, Structure.

[21]  A. Lesk,et al.  Structural mechanisms for domain movements in proteins. , 1994, Biochemistry.

[22]  D. Davies,et al.  Comparison of two crystal structures of TGF-beta2: the accuracy of refined protein structures. , 1994, Acta crystallographica. Section D, Biological crystallography.

[23]  M Karplus,et al.  Analysis of two-residue turns in proteins. , 1994, Journal of molecular biology.

[24]  I. Wilson,et al.  Antigen-induced conformational changes in antibodies: a problem for structural prediction and design. , 1994, Trends in biotechnology.

[25]  J. Kwasigroch,et al.  A global taxonomy of loops in globular proteins. , 1996, Journal of molecular biology.

[26]  K. Gunasekaran,et al.  Disallowed Ramachandran conformations of amino acid residues in protein structures. , 1996, Journal of molecular biology.

[27]  D E Koshland,et al.  Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences. , 1997, Science.

[28]  P E Bourne,et al.  Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. , 1998, Protein engineering.

[29]  J M Yon,et al.  Conformational dynamics and enzyme activity. , 1998, Biochimie.

[30]  S E Ealick,et al.  Calf spleen purine nucleoside phosphorylase complexed with substrates and substrate analogues. , 1998, Biochemistry.

[31]  J. Chandrasekhar,et al.  Conformational interconversions in peptide beta-turns: analysis of turns in proteins and computational estimates of barriers. , 1998, Journal of molecular biology.

[32]  A study of conserved in-loop and out-of-loop glycine residues in the large subunit of ribulose bisphosphate carboxylase/oxygenase by directed mutagenesis. , 1998, Protein engineering.

[33]  D. Koshland Conformational changes: How small is big enough? , 1998, Nature Medicine.

[34]  H. A. Nagarajaram,et al.  Stereochemical punctuation marks in protein structures: glycine and proline containing helix stop signals. , 1998, Journal of molecular biology.

[35]  Dan S. Tawfik,et al.  Conformational changes affect binding and catalysis by ester-hydrolysing antibodies. , 1999, Journal of molecular biology.

[36]  W Li,et al.  Exploring the conformational diversity of loops on conserved frameworks. , 1999, Protein engineering.

[37]  M. Sternberg,et al.  An analysis of conformational changes on protein-protein association: implications for predictive docking. , 1999, Protein engineering.

[38]  A. Sali,et al.  Protein structure modeling for structural genomics , 2000, Nature Structural Biology.

[39]  Rafael Najmanovich,et al.  Side‐chain flexibility in proteins upon ligand binding , 2000, Proteins.

[40]  J A McCammon,et al.  Accommodating protein flexibility in computational drug design. , 2000, Molecular pharmacology.

[41]  U. Samanta,et al.  Assessing the role of tryptophan residues in the binding site. , 2001, Protein engineering.

[42]  Bruce Tidor,et al.  Optimization of binding electrostatics: Charge complementarity in the barnase‐barstar protein complex , 2001, Protein science : a publication of the Protein Society.

[43]  R Abagyan,et al.  High-throughput docking for lead generation. , 2001, Current opinion in chemical biology.

[44]  S. Hayward,et al.  Peptide‐plane flipping in proteins , 2001, Protein science : a publication of the Protein Society.

[45]  N. Sinha,et al.  Differences in electrostatic properties at antibody-antigen binding sites: implications for specificity and cross-reactivity. , 2002, Biophysical journal.

[46]  G. Hammes Multiple conformational changes in enzyme catalysis. , 2002, Biochemistry.

[47]  Heather A Carlson,et al.  Protein flexibility is an important component of structure-based drug discovery. , 2002, Current pharmaceutical design.

[48]  J. Koh Engineering selectivity and discrimination into ligand-receptor interfaces. , 2002, Chemistry & biology.

[49]  J. Berg,et al.  Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.

[50]  B. Ramakrishnan,et al.  Crystal structure of beta1,4-galactosyltransferase complex with UDP-Gal reveals an oligosaccharide acceptor binding site. , 2002, Journal of molecular biology.

[51]  Ruth Nussinov,et al.  Principles of docking: An overview of search algorithms and a guide to scoring functions , 2002, Proteins.

[52]  Pinak Chakrabarti,et al.  On residues in the disallowed region of the Ramachandran map. , 2002, Biopolymers.

[53]  N. Sinha,et al.  Protein structure to function via dynamics. , 2002, Protein and peptide letters.

[54]  L. Looger,et al.  Computational design of receptor and sensor proteins with novel functions , 2003, Nature.

[55]  S. Teague Implications of protein flexibility for drug discovery , 2003, Nature Reviews Drug Discovery.

[56]  J. Whisstock,et al.  Prediction of protein function from protein sequence and structure , 2003, Quarterly Reviews of Biophysics.

[57]  Janet M. Thornton,et al.  An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis , 2003, Bioinform..

[58]  William F. DeGrado Computational biology: Biosensor design , 2003, Nature.

[59]  R. Nussinov,et al.  Protein–protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[60]  Loren L Looger,et al.  Computational Design of a Biologically Active Enzyme , 2004, Science.

[61]  Y. Tse‐Dinh,et al.  Flexibility at Gly-194 Is Required for DNA Cleavage and Relaxation Activity of Escherichia coli DNA Topoisomerase I* , 2004, Journal of Biological Chemistry.

[62]  Philip E. Bourne,et al.  CE-MC: a multiple protein structure alignment server , 2004, Nucleic Acids Res..

[63]  Steven E Brenner,et al.  Structural genomics and structural biology: compare and contrast , 2004, Genome Biology.

[64]  Leslie A Kuhn,et al.  Side‐chain flexibility in protein–ligand binding: The minimal rotation hypothesis , 2005, Protein science : a publication of the Protein Society.

[65]  Michael Nilges,et al.  The impact of protein flexibility on protein–protein docking , 2004, Proteins.

[66]  Bruce Tidor,et al.  A computational method for the analysis and prediction of protein:phosphopeptide‐binding sites , 2005, Protein science : a publication of the Protein Society.

[67]  Y. Sasidhar,et al.  Insights into the role of the aromatic residue in galactose-binding sites: MP2/6-311G++** study on galactose- and glucose-aromatic residue analogue complexes. , 2005, Biochemistry.

[68]  B. Rost,et al.  Protein flexibility and rigidity predicted from sequence , 2005, Proteins.

[69]  J. Thornton,et al.  Conformational changes observed in enzyme crystal structures upon substrate binding. , 2005, Journal of molecular biology.