Incorporation of flexibility into rigid-body docking: Applications in rounds 3-5 of CAPRI

Proteins: Structure, Function and Genetics

Volumn 60, Issue 2, 2005, Pages 263-268

  Smith, Graham R ^a,c   Fitzjohn, Paul W ^a   Page, Christopher S ^a   Bates, Paul A ^a,b  

^a THE FRANCIS CRICK INSTITUTE   (United Kingdom)

^b IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^c INSTITUTE OF HUMAN GENETICS   (United Kingdom)

Author keywords

CAPRI; Molecular dynamics; Protein protein docking; Protein protein interactions; Rigid body cross docking

Indexed keywords

ANALYTIC METHOD; CONFERENCE PAPER; EXPERIMENT; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; RIGIDITY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; DIMERIZATION; ELECTROSTATICS; INTERNET; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR CONFORMATION; MUTATION; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 21644477228     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20568     Document Type: Conference Paper

References (42)

1. Wodak SJ, Méndez R. Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. Curr Opin Struct Biol 2004;14:1-8.
2. Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 2002;47:409-443.
3. Smith GR, Sternberg MJE. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002;12:28-35.
4. Jackson RM, Gabb HA, Sternberg MJE. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J Mol Biol 1998;276:265-285.
5. Zacharias M. Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci 2003;12: 1271-1282.
6. Fernández-Recio J, Totrov M, Abagyan R. ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins 2003;52:113-117.
7. Camacho CJ, Vajda S. Protein docking along smooth association pathways. Proc Natl Acad Sci USA 2001;98:10636-10641.
8. Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331:281-299.
9. Shatsky M, Nussinov R, Wolfson HJ. FlexProt: alignment of flexible protein structures without a predefinition of hinge regions. J Comput Biol 2004;11:83-106.
10. Fitzjohn PW, Bates PA. Guided docking: first step to locate potential binding sites. Proteins 2003;52:28-32.
11. Smith GR, Sternberg MJE, Bates PA. The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J Mol Biol 2005;345:1077-1101.
12. Dominguez C, Boelens R, Bonvin AMJJ. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 2003;125:1731-1737.
13. Grunberg R, Leckner J, Nilges M. Complementarity of structure ensembles in protein-protein binding. Structure (Camb) 2004;12: 2125-2136.
14. Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJE, Vajda S, Vakser I, Wodak SJ. CAPRI: a Critical Assessment of PRedicted Interactions. Proteins 2003;52:2-9.
15. Gabb HA, Jackson RM, Sternberg MJE. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 1997;272:106-120.
16. Moont G, Gabb HA, Sternberg MJE. Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 1999;35:364-373.
17. Bates PA, Kelley LA, MacCallum RM, Sternberg MJE. Enhancement of protein modelling by human intervention in applying the automatic prgrams 3D-JIGSAW and 3D-PSSM. Proteins 2001; Suppl 5:39-46.
18. Landgraf R, Xenarios I, Eisenberg D. Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J Mol Biol 2001;307:1487-1502.
19. Lindahl E, Hess B, van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Mod 2001;7: 306-317.
20. Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph 1996;14:33-38.
21. Goldstein H, Poole CP, Safko JL. Classical mechanics. Reading, MA: Addison-Wesley; 1992.
22. Press WH, Teukolsky SA, Vetterling WT, Flannery BP. Numerical recipes in FORTRAN-the art of scientific computing. Cambridge, UK: Cambridge University Press; 1988. p 490-602.
23. Robson B, Osguthorpe DJ. Refined models for computer simulation of protein folding applications to the study of conserved secondary structure and flexible hinge points during the folding of pancreatic trypsin inhibitor. J Mol Biol 1979;132:19-51.
24. Baumgartner R, Czisch M, Mayer U, Poschl E, Huber R, Timpl R, Holak TA. Structure of the nidogen binding LE module of the laminin gammal chain in solution. J Mol Biol 1996;257:658-668.
25. Miras I, Schaeffer F, Beguin P, Alzari PM. Mapping by site-directed mutagenesis of the region responsible for cohesin-dockerin interaction on the surface of the seventh cohesin domain of Clostridium thermocellum CipA. Biochemistry 2002;41:2115-2119.
26. Schaeffer F, Matuschek M, Guglielmi G, Miras I, Alzari PM, Beguin P. Duplicated dockerin subdomains of Clostridium thermocellum endoglucanase CelD bind to a cohesin domain of the scaffolding protein CipA with distinct thermodynamic parameters and a negative cooperativity. Biochemistry 2002;41:2106-2114.
27. Velge-Roussel F, Chardes T, Mevelec P, Brillard M, Hoebeke J, Bout D. Epitopic analysis of the Toxoplasma gondii major surface antigen SAG1. Mol Biochem Parasitol 1994;66:31-38.
28. Wu X, Tatchell K. Mutations in yeast protein phosphatase type 1 that affect targeting subunit binding. Biochemistry 2001;40:7410-7420.
29. Toth A, Kiss E, Herberg FW, Gergely P, Hartshorne DJ, Erdodi F. Study of the subunit interactions in myosin phosphatase by surface plasmon resonance. Eur J Biochem 2000;267:1687-1697.
30. Tahir TA, Berrin JG, Flatman R, Roussel A, Roepstorff P, Williamson G, Juge N. Specific characterization of substrate and inhibitor binding sites of a glycosyl hydrolase family 11 xylanase from Aspergillus niger. J Biol Chem 2002;277:44035-44043.
31. Juge N, Payan F, Williamson G. XIP-I, a xylanase inhibitor protein from wheat: a novel protein function. Biochim Biophys Acta 2004;1696:203-211.
32. Peretz D, Williamson RA, Kaneko K, Vergara J, Leclerc E, Schmitt-Ulms G, Mehlhorn IR, Legname G, Wormald MR, Rudd PM, Dwek RA, Burton DR, Prusiner SB. Antibodies inhibit prion propagation and clear cell cultures of prion infectivity. Nature 2001;412:739-743.
33. Bressanelli S, Stiasny K, Allison SL, Stura EA, Duquerroy S, Lescar J, Heinz FX, Rey FA. Structure of a flavivirus envelope glycoprotein in its low-pH-induced membrane fusion conformation. EMBO J 2004;23:728-738.
34. Modis Y, Ogata S, Clements D, Harrison SC. Structure of the dengue virus envelope protein after membrane fusion. Nature 2004;427:313-319.
35. Terrak M, Kerff F, Langsetmo K, Tao T, Dominguez R. Structural basis of protein phosphatase 1 regulation. Nature 2004;429:780-784.
36. Sansen S, De Ranter CJ, Gebruers K, Brijs K, Courtin CM, Delcour JA, Rabijns A. Structural basis for inhibition of Aspergillus niger xylanase by Triticum aestivum xylanase inhibitor-I. J Biol Chem 2004;279:36022-36028.
37. Rajamani D, Thiel S, Vajda S, Camacho CJ. Anchor residues in protein-protein interactions. Proc Natl Acad Sci USA 2004;101: 11287-11292.
38. Takagi J. [Complex between nidogen and laminin fragments reveals a paradigmatic beta-propeller interface]. Tanpakushitsu Kakusan Koso 2003;48:1920-1927.
39. Graille M, Zhou CZ, Receveur-Brechot V, Collinet B, Declerck N, van Tilbeurgh H. Activation of the LicT transcriptional antiterminator involves a domain swing/lock mechanism provoking massive structural changes. J Biol Chem 2005;280:14780-14789.
40. Carvalho AL, Dias FM, Prates JA, Nagy T, Gilbert HJ, Davies GJ, Ferreira LM, Romao MJ, Fontes CM. Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex. Proc Natl Acad Sci USA 2003;100:13809-13814.
41. Graille M, Ducancel F. Structure of the immunodominant epitope displayed by the surface antigen 1 (SAG1) of T. gondii complexed to a monoclonal antibody. 2005. Submitted for publication.
42. Eghiaian F, Grosclaude J, Lesceu S, Debey P, Doublet B, Treguer E, Rezaei H, Knossow M. Insight into the PrPC→PrPSc conversion from the structures of antibody-bound ovine prion scrapie-susceptibility variants. Proc Natl Acad Sci USA 2004;101:10254-10259.