Complementarity of structure ensembles in protein-protein binding

Structure

Volumn 12, Issue 12, 2004, Pages 2125-2136

  Grünberg, Raik ^a   Leckner, Johan ^a   Nilges, Michael ^a  

^a INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DIFFUSION; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SIMULATION;

MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 9944237833     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2004.09.014     Document Type: Article

References (55)

1. Abagyan R.A., Totrov M.M. Contact area difference (CAD). a robust measure to evaluate accuracy of protein models J. Mol. Biol. 268:1997;678-685
2. Abseher R., Nilges M. Efficient sampling in collective coordinate space. Proteins. 39:2000;82-88
3. Balsera M.A., Wriggers W., Oono Y., Schulten K. Principal component analysis and long time protein dynamics. J. Phys. Chem. 100:1996;2567-2572
4. Berger C., Weber-Bornhauser S., Eggenberger J., Hanes J., Pluckthun A., Bosshard H.R. Antigen recognition by conformational selection. FEBS Lett. 450:1999;149-153
5. Berman H.M., Battistuz T., Bhat T.N., Bluhm W.F., Bourne P.E., Burkhardt K., Feng Z., Gilliland G.L., Iype L., Jain S., et al. The Protein Data Bank. Acta Crystallogr. D Biol. Crystallogr. 58:2002;899-907
6. Betts M.J., Sternberg M.J. An analysis of conformational changes on protein-protein association. implications for predictive docking Protein Eng. 12:1999;271-283
7. Bosshard H.R. Molecular recognition by induced fit. how fit is the concept? News Physiol. Sci. 16:2001;171-173
8. Brooijmans N., Kuntz I.D. Molecular recognition and docking algorithms. Annu. Rev. Biophys. Biomol. Struct. 32:2003;335-373
9. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. Charmm. a program for macromolecular energy, minimization and dynamics calculations J. Comp. Chem. 4:1983;187-217
10. Brooks, C.L., III, Karplus, M., and Pettitt, B.M. (1988). Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics (New York: Wiley).
11. Brünger A. X-PLOR. A System for X-ray crystallography and NMR. 1992;Yale University Press, New Haven
12. Camacho C.J., Kimura S.R., DeLisi C., Vajda S. Kinetics of desolvation-mediated protein-protein binding. Biophys. J. 78:2000;1094-1105
13. Camacho C.J., Weng Z., Vajda S., DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophys. J. 76:1999;1166-1178
14. Caves L.S., Evanseck J.D., Karplus M. Locally accessible conformations of proteins. multiple molecular dynamics simulations of crambin Protein Sci. 7:1998;649-666
15. Chen R., Mintseris J., Janin J., Weng Z. A protein-protein docking benchmark. Proteins. 52:2003;88-91
16. Chothia C., Lesk A.M. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:1986;823-826
17. Dill K.A., Chan H.S. From Levinthal to pathways to funnels. Nat. Struct. Biol. 4:1997;10-19
18. Ehrlich L.P., Nilges M., Wade R. The impact of protein flexibility on protein-protein docking. Proteins. in press:2004
19. Fernandez-Recio J., Totrov M., Abagyan R. ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins. 52:2003;113-117
20. Fischer E. Einfluss der Configuration auf die Wirkung der Enzyme. Ber. Dt. Chem. Ges. 27:1894;2985-2993
21. Foote J., Milstein C. Conformational isomerism and the diversity of antibodies. Proc. Natl. Acad. Sci. USA. 91:1994;10370-10374
22. Frauenfelder H., Leeson D.T. The energy landscape in non-biological and biological molecules. Nat. Struct. Biol. 5:1998;757-759
23. Frauenfelder H., Sligar S.G., Wolynes P.G. The energy landscapes and motions of proteins. Science. 254:1991;1598-1603
24. Frisch C., Fersht A.R., Schreiber G. Experimental assignment of the structure of the transition state for the association of barnase and barstar. J. Mol. Biol. 308:2001;69-77
25. Gabdoulline R.R., Wade R.C. Protein-protein association. investigation of factors influencing association rates by brownian dynamics simulations J. Mol. Biol. 306:2001;1139-1155
26. Gabdoulline R.R., Wade R.C. Biomolecular diffusional association. Curr. Opin. Struct. Biol. 12:2002;204-213
27. Goh C.S., Milburn D., Gerstein M. Conformational changes associated with protein-protein interactions. Curr. Opin. Struct. Biol. 14:2004;104-109
28. Goodford P.J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 28:1985;849-857
29. Gordon H.L., Somorjai R.L. Fuzzy cluster analysis of molecular dynamics trajectories. Proteins. 14:1992;249-264
30. Gray J.J., Moughon S., Wang C., Schueler-Furman O., Kuhlman B., Rohl C.A., Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol. 331:2003;281-299
31. Halperin I., Ma B., Wolfson H., Nussinov R. Principles of docking. an overview of search algorithms and a guide to scoring functions Proteins. 47:2002;409-443
32. Janin J. The kinetics of protein-protein recognition. Proteins. 28:1997;153-161
33. Kimura S.R., Brower R.C., Vajda S., Camacho C.J. Dynamical view of the positions of key side chains in protein-protein recognition. Biophys. J. 80:2001;635-642
34. Koradi R., Billeter M., Wüthrich K. Molmol. a program for display and analysis of macromolecular structures J. Mol. Graph. 14:1996;51-55
35. Kirschner K., Eigen M., Bittman R., Voigt B. The binding of nicotinamide adenine dinucleotide to yeast glyceraldehyde-3-phosphate dehydrogenase. temperature-jump relaxation studies on the mechanism of an allosteric enzyme Proc. Natl. Acad. Sci. USA. 56:1966;1661-1667
36. Koshland D. Application of a theory of enzyme specifity to protein synthesis. Proc. Natl. Acad. Sci. USA. 44:1958;98-104
37. Kumar S., Ma B., Tsai C.J., Sinha N., Nussinov R. Folding and binding cascades. dynamic landscapes and population shifts Protein Sci. 9:2000;10-19
38. Kuntz I.D., Blaney J.M., Oatley S.J., Langridge R., Ferrin T.E. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161:1981;269-288
39. Lancet D., Pecht I. Kinetic evidence for hapten-induced conformational transition in immunoglobulin MOPC 460. Proc. Natl. Acad. Sci. USA. 73:1976;3549-3553
40. Leder L., Berger C., Bornhauser S., Wendt H., Ackermann F., Jelesarov I., Bosshard H.R. Spectroscopic, calorimetric, and kinetic demonstration of conformational adaptation in peptide-antibody recognition. Biochemistry. 34:1995;16509-16518
41. Lo Conte L., Chothia C., Janin J. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285:1999;2177-2198
42. Mendez R., Leplae R., De Maria L., Wodak S.J. Assessment of blind predictions of protein-protein interactions. current status of docking methods Proteins. 52:2003;51-67
43. Monod J., Wyman J., Changeux J.P. On the nature of allosteric transitions. a plausible model J. Mol. Biol. 12:1965;88-118
44. Northrup S.H., Erickson H.P. Kinetics of protein-protein association explained by Brownian dynamics computer simulation. Proc. Natl. Acad. Sci. USA. 89:1992;3338-3342
45. Ritchie D.W. Evaluation of protein docking prediction using Hex 3.1 in CAPRI rounds 1 and 2. Proteins. 52:2003;98-106
46. Ritchie D.W., Kemp G.J. Protein docking using spherical polar Fourier correlations. Proteins. 39:2000;178-194
47. Schneidman-Duhovny D., Inbar Y., Polak V., Shatsky M., Halperin I., Benyamini H., Barzilai A., Dror O., Haspel N., Nussinov R., et al. Taking geometry to its edge. fast unbound rigid (and hinge-bent) docking Proteins. 52:2003;107-112
48. Schrauber H., Eisenhaber F., Argos P. An analysis of amino acid side-chain conformations in globular proteins. J. Mol. Biol. 230:1993;592-612
49. Schreiber G. Kinetic studies of protein-protein interactions. Curr. Opin. Struct. Biol. 12:2002;41-47
50. Selzer T., Schreiber G. New insights into the mechanism of protein-protein association. Proteins. 45:2001;190-198
51. Smith G., Bates P.A. Test systems for a docking algorithm. http://www.bmm.icnet.uk/docking/systems.html:2002
52. Steinbach P.J., Loncharich R.J., Brooks B.R. The effects of environment and hydration on protein dynamics. a simulation study of myoglobin Chem. Phys. 158:1991;383-394
53. van Gunsteren W.F., Berendsen H.J.C. Algorithms for macromolecular dymaics and constraint dynamics. Mol. Phys. 34:1977;1311-1327
54. Vriend G. What if. a molecular modeling and drug design program J. Mol. Graph. 8:1990;52-56
55. Zhou H.X. Disparate ionic-strength dependencies of on and off rates in protein-protein association. Biopolymers. 59:2001;427-433