The blind search for the closed states of hinge-bending proteins

Proteins: Structure, Function and Genetics

Volumn 71, Issue 2, 2008, Pages 831-843

  Yesylevskyy, Semen O ^a   Kharkyanen, Valery N ^a   Demchenko, Alexander P ^b  

^a INSTITUTE OF HYDROBIOLOGY   (Ukraine)

^b PALLADIN INSTITUTE OF BIOCHEMISTRY   (Ukraine)

Author keywords

Domain identification; Domain motion; HCCP; Hinge bending proteins

Indexed keywords

HINGE BENDING PROTEIN; PROTEIN; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; AUTOANALYSIS; CLUSTER ANALYSIS; CORRELATION ANALYSIS; CRYSTAL STRUCTURE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN STRUCTURE; SIMULATION;

ALGORITHMS; ANIMALS; CALMODULIN; COMPUTER SIMULATION; DNA POLYMERASE BETA; HUMANS; LACTOFERRIN; MODELS, MOLECULAR; MONTE CARLO METHOD; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS;

EID: 41149105026     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21743     Document Type: Article

References (58)

1. Janin J, Wodak SJ. Protein modules and protein-protein interaction. Introduction. Adv Protein Chem 2002;61:1-8.
2. Janin J, Wodak SJ. Structural domains in proteins and their role in the dynamics of protein function. Prog Biophys Mol Biol 1983;42:21-78.
3. Bernstein BE, Michels PA, Hol WG. Synergistic effects of substrate-induced conformational changes in phosphoglycerate kinase activation. Nature 1997;385:275-278.
4. Park H, Hilsenbeck JL, Kim HJ, Shuttleworth WA, Park YH, Evans JN, Kang C. Structural studies of Streptococcus pneumoniae EPSP synthase in unliganded state, tetrahedral intermediate-bound state and S3p-Glp-bound state. Mol Microbiol 2004;51:963-971.
5. Oh BH, Pandit J, Kang CH, Nikaido K, Gokcen S, Ames GFL, Kim SH. Three-dimensional structures of the periplasmic lysine-,arginine-, ornithine-binding protein with and without a ligand. J BiolChem 1993;268:11348-11355.
6. Hsiao CD, Sun YJ, Rose J, Wang BC. The crystal structure of glutamine-binding protein from Escherichia coli. J Mol Biol 1996;262:225-242.
7. Nickitenko AV, Trakhanov S, Quiocho FA. 2 a resolution structure of dppa, a periplasmic dipeptide transport/chemosensory receptor. Biochemistry 1995;34:16585.
8. Craig R, Woodhead JL. Structure and function of myosin filaments. Curr Opin Struct Biol 2006;16:204-212.
9. Ponting CP, Russell RR. The natural history of protein domains. Annu Rev Biomol Struct 2002;31:45-71.
10. Yesylevskyy SO, Kharkyanen VN, Demchenko AP. The change of protein intradomain mobility on ligand binding, is it a commonly observed phenomenon? Biophys J 2006;91:3002-3013.
11. Yesylevskyy SO, Kharkyanen VN, Demchenko AP. Dynamic protein domains: identification, interdependence and stability. Biophys J 2006;91:670-685.
12. Yesylevskyy SO, Kharkyanen VN, Demchenko AP. Hierarchical clustering of the correlation patterns: new method of domain identification in proteins. Biophys Chem 2006;119:84-93.
13. Moschou EA, Bachas LG, Daunert S, Deo SK. Binding proteins: unraveling their analytical potential. Anal Chem 2006;78:6692-6700.
14. Auguin D, Barthe P, Auge-Senegas MT, Stern MH, Noguchi M, Roumestand C. Solution structure and backbone dynamics of the pleckstrin homology domain of the human protein kinase B (PKB/Akt). Interaction with inositol phosphates. J Biomol NMR 2004;28:137-155.
15. Bernado P, Fernandes MX, Jacobs DM, Fiebig K, Garcia de la Torre J, Pons M. Interpretation of NMR relaxation properties of Pinl, a two-domain protein, based on Brownian dynamic simulations. J Biomol NMR 2004;29:21-35.
16. Clore GM, Schwieters CD. Amplitudes of protein backbone dynamics and correlated motions in a small α/β protein: correspondence of dipolar coupling and heteronuclear relaxation measurements. Biochemistry 2004;43:10678-10691.
17. Ilin S, Hoskins A, Ohlenschlager O, Jonker HR, Schwalbe H, Wohnert J. Domain reorientation and induced fit upon RNA binding: solution structure and dynamics of ribosomal protein L11 from Thermotoga maritima. Chembiochem 2005;6:1611-1618.
18. Ragona L, Catalano M, Luppi M, Cicero D, Eliseo T, Foote J, Fogolari F, Zetta L, Molinari H. NMR dynamic studies suggest that allosteric activation regulates ligand binding in chicken liver bile acid-binding protein. J Biol Chem 2006;281:9697-9709.
19. Sakurai K, Goto Y. Dynamics and mechanism of the Tanford transition of bovine β-lactoglobulin studied using heteronuclear NMR spectroscopy. J Mol Biol 2006;356:483-496.
20. Thormann T, Soroka V, Nielbo S, Berezin V, Bock E, Poulsen FM. Backbone dynamics of the first, second, and third immunoglobulin modules of the neural cell adhesion molecule (NCAM). Biochemistry 2004;43:10364-10369.
21. Hayward S, Berendsen HJ. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins 1998;30:144-154.
22. Karplus M. Molecular dynamics simulations of biomolecules. Ace Chem Res 2002;35:321-322.
23. Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins 1998;33:417-429.
24. Hinsen K, Thomas A, Field MJ. Analysis of domain motions in large proteins. Proteins 1999;34:369-382.
25. Levitt M, Sander C, Stern PS. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J Mol Biol 1985;181:423-447.
26. Bahar I, Atilgan AR, Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 1997;2:173-181.
27. Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 2001;80:505-515.
28. Yildirim Y, Doruker P. Collective motions of RNA polymerases. Analysis of core enzyme, elongation complex and holoenzyme. J Biomol Struct Dyn 2004;22:267-280.
29. Keskin O. Comparison of full-atomic and coarse-grained models to examine the molecular fluctuations of c-AMP dependent protein kinase. J Biomol Struct Dyn 2002;20:333-345.
30. Doruker P, Atilgan AR, Bahar I. Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to α-amylase inhibitor. Proteins 2000;40:512-524.
31. Hayward S, Go N. Collective variable description of native protein dynamics. Annu Rev Phys Chem 1995;46:223-250.
32. Holm L, Sander C. Parser for protein folding units. Proteins 1994;19:256-268.
33. Wriggers W, Schulten K. Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins 1997;29:1-14.
34. Alexandrov N, Shindyalov I. PDP: protein domain parser. Bioinformatics 2003;19:429-430.
35. Fischer KF, Marqusee S. A rapid test for identification of autonomous folding units in proteins. J Mol Biol 2000;302:701-712.
36. Kundu S, Sorensen DC, Phillips GN, Jr. Automatic domain decomposition of proteins by a Gaussian Network Model. Proteins 2004;57:725-733.
37. Nichols WL, Rose GD, Ten Eyck LF, Zimm BH. Rigid domains in proteins: an algorithmic approach to their identification. Proteins 1995;23:38-48.
38. Tama F, Gadea FX, Marques O, Sanejouand YH. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins 2000;41:1-7.
39. Anselmi C, Bocchinfuso G, Scipioni A, De Santis P. Identification of protein domains on topological basis. Biopolymers 2001;58:218-229.
40. Armstrong N, Gouaux E. Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: crystal structures of the GluR2 ligand binding core. Neuron 2000;28:165-181.
41. Blaszczyk J, Li Y, Yan H, Ji X. Crystal structure of unligated guanylate kinase from yeast reveals GMP-induced conformational changes. J Mol Biol 2001;307:247-257.
42. Wriggers W, Mehler E, Pitici F, Weinstein H, Schulten K. Structure and dynamics of calmodulin in solution. Biophys J 1998;74:1622-1639.
43. Sawaya MR, Pelletier H, Kumar A, Wilson SH, Kraut J. Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism. Science 1994;264:1930-1935.
44. Pelletier H, Sawaya MR, Kumar A, Wilson SH, Kraut J. Structures of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP. Science 1994;264:1891-1903.
45. Norris GE, Anderson BF, Baker EN. Molecular replacement solution of the structure of apolactoferrin, a protein displaying large-scale conformational change. Acta Crystallogr 1991;47:998-1004.
46. Echols E, Milburn D, Gerstein M. MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res 2003;31:478-482.
47. Zhang C, Liu S, Zhou H, Zhou Y. An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci 2004;13:400-411.
48. Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002;11:2714-2726.
49. Miyazawa S, Jernigan RL. How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins? J Chem Phys 2005;122:024901.
50. Humphrey W, Dalke A, Schulten K. VMD - Visual Molecular Dynamics. J Mol Graphics 1996;14:33-38.
51. Bonvin AM. Flexible protein-protein docking. Curr Opin Struct Biol 2006;16:194-200.
52. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. Geometry-based flexible and symmetric protein docking. Proteins 2005;60:224-231.
53. Wolfson HJ, Shatsky M, Schneidman-Duhovny D, Drop O, Shulman-Peleg A, Ma B, Nussinov R. From structure to function: methods and applications. Curr Protein Pept Sci 2005;6:171-183.
54. Quiocho FA, Spurlino JC, Rodseth LE. Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport/chemosensory receptor. Structure 1997;5:997-1015.
55. Tama F, Sanejouand YH. Conformational change of proteins arising from normal mode calculations. Protein Eng 2001;14:1-6.
56. Keskin O, Durell SR, Bahar I, Jernigan RL, Covell DG. Relating molecular flexibility to function: a case study of tubulin. Biophys J 2002;83:663-680.
57. Halperin I, Ma B, Wolfson HJ, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 2002;47:409-443.
58. Bakker P, Furnham N, Blundell TL, DePristo MA. Conformer generation under restraints. Curr Opin Struct Biol 2006;16:160-165.