Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization

Protein Science

Volumn 16, Issue 12, 2007, Pages 2716-2725

  Lorenzen, Stephan ^a,b   Zhang, Yang ^a,c  

^a UNIVERSITY OF KANSAS   (United States)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

^c NONE   (United States)

Author keywords

Fast Fourier transformation; Protein protein docking; Refinement; Scoring; Smoothed potential

Indexed keywords

ARTICLE; ATOM; COMPLEX FORMATION; ELECTRIC POTENTIAL; ENERGY; FOURIER TRANSFORMATION; METHODOLOGY; MONTE CARLO METHOD; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RIGIDITY; SIMULATION;

ALGORITHMS; COMPUTER SIMULATION; MODELS, MOLECULAR; MONTE CARLO METHOD; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS;

EID: 36448981368     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.072847207     Document Type: Article

References (46)

1. Abagyan, R. and Totrov, M. 1994. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235: 983-1002.
2. Bastard, K., Prevost, C., and Zacharias, M. 2006. Accounting for loop flexibility during protein-protein docking. Proteins 62: 956-969.
3. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235-242.
4. Bernier-Villamor, V., Sampson, D.A., Matunis, M.J., and Lima, C.D. 2002. Structural basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin-conjugating enzyme Ubc9 and RanGAP1. Cell 108: 345-356.
5. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., and Karplus, M. 1983. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4: 187-217.
6. Camacho, C.J., Weng, Z., Vajda, S., and DeLisi, C. 1999. Free energy landscapes of encounter complexes in protein-protein association. Biophys. J. 76: 1166-1178.
7. Camacho, C.J., Ma, H., and Champ, P.C. 2006. Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions. Proteins 63: 868-877.
8. Chen, R., Li, L., and Weng, Z. 2003a. ZDOCK: An initial-stage protein-docking algorithm. Proteins 52: 80-87.
9. Chen, R., Mintseris, J., Janin, J., and Weng, Z. 2003b. A protein - protein docking benchmark. Proteins 52: 88-91.
10. Comeau, S.R., Gatchell, D.W., Vajda, S., and Camacho, C.J. 2004. ClusPro: An automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 20: 45-50.
11. Desterro, J.M., Thomson, J., and Hay, R.T. 1997. Ubch9 conjugates SUMO but not ubiquitin. FEBS Lett. 417: 297-300.
12. Dunbrack Jr., R.L. and Cohen, F.E. 1997. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci. 6: 1661-1681.
13. Fernandez-Recio, J., Totrov, M., and Abagyan, R. 2002. Soft protein-protein docking in internal coordinates. Protein Sci. 11: 280-291.
14. Fernandez-Recio, J., Totrov, M., and Abagyan, R. 2003. ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins 52: 113-117.
15. Gabb, H.A., Jackson, R.M., and Sternberg, M.J. 1997. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J. Mol. Biol. 272: 106-120.
16. Gray, J.J., Moughon, S., Wang, C., Schueler-Furman, O., Kuhlman, B., Rohl, C.A., and Baker, D. 2003. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol. 331: 281-299.
17. Gront, D., Kolinski, A., and Skolnick, J. 2000. Comparison of three Monte Carlo conformational search strategies for a protein-like homopolymer model: Folding thermodynamics and identification of low-energy structures. J. Chem. Phys. 113: 5065-5071.
18. Heifetz, A., Katchalski-Katzir, E., and Eisenstein, M. 2002. Electrostatics in protein-protein docking. Protein Sci. 11: 571-587.
19. Janin, J. 2005. Assessing predictions of protein-protein interaction: The CAPRI experiment. Protein Sci. 14: 278-283.
20. Janin, J., Henrick, K., Moult, J., Eyck, L.T., Sternberg, M.J., Vajda, S., Vakser, I., and Wodak, S.J. 2003. CAPRI: A critical assessment of predicted interactions. Proteins 52: 2-9.
21. Johnson, E.S. and Blobel, G. 1997. Ubc9p is the conjugating enzyme for the ubiquitin-like protein Smt3p. J. Biol. Chem. 272: 26799-26802.
22. Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.A., Aflalo, C., and Vakser, I.A. 1992. Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl. Acad. Sci. 89: 2195-2199.
23. Kirkpatrick, S., Gelatt Jr., C.D., and Vecchi, M.P. 1983. Optimization by simulated annealing. Science 220: 671-680.
24. Li, L., Chen, R., and Weng, Z. 2003. RDOCK: Refinement of rigid-body protein docking predictions. Proteins 53: 693-707.
25. Lin, D., Tatham, M.H., Yu, B., Kim, S., Hay, R.T., and Chen, Y. 2002. Identification of a substrate recognition site on Ubc9. J. Biol. Chem. 277: 21740-21748.
26. Lorber, D.M., Udo, M.K., and Shoichet, B.K. 2002. Protein-protein docking with multiple residue conformations and residue substitutions. Protein Sci. 11: 1393-1408.
27. Lorenzen, S. and Zhang, Y. 2007. Identification of near-native structures by clustering protein docking conformations. Proteins 68: 187-194.
28. Mandell, J.G., Roberts, V.A., Pique, M.E., Kotlovyi, V., Mitchell, J.C., Nelson, E., Tsigelny, I., and Ten Eyck, L.F. 2001. Protein docking using continuum electrostatics and geometric fit. Protein Eng. 14: 105-113.
29. Mendez, R., Leplae, R., Lensink, M.F., and Wodak, S.J. 2005. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 60: 150-169.
30. Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., Teller, A.H., and Teller, E. 1953. Equations of state calculations by fast computing machines. J. Chem. Phys. 21: 1087-1092.
31. Muller, S., Hoege, C., Pyrowolakis, G., and Jentsch, S. 2001. SUMO, ubiquitin's mysterious cousin. Nat. Rev. Mol. Cell Biol. 2: 202-210.
32. Murphy, J., Gatchell, D.W., Prasad, J.C., and Vajda, S. 2003. Combination of scoring functions improves discrimination in protein-protein docking. Proteins 53: 840-854.
33. Norel, R., Lin, S.L., Wolfson, H.J., and Nussinov, R. 1994. Shape complementarity at protein-protein interfaces. Biopolymers 34: 933-940.
34. Pichler, A., Knipscheer, P., Oberhofer, E., van Dijk, W.J., Korner, R., Olsen, J.V., Jentsch, S., Melchior, F., and Sixma, T.K. 2005. SUMO modification of the ubiquitin-conjugating enzyme E2-25K. Nat. Struct. Mol. Biol. 12: 264-269.
35. Riemann, R.N. and Zacharias, M. 2005. Refinement of protein cores and protein-peptide interfaces using a potential scaling approach. Protein Eng. Des. Sel. 18: 465-476.
36. Schueler-Furman, O., Wang, C., and Baker, D. 2005. Progress in protein - protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins 60: 187-194.
37. Schwarz, S.E., Matuschewski, K., Liakopoulos, D., Scheffner, M., and Jentsch, S. 1998. The ubiquitin-like proteins SMT3 and SUMO-1 are conjugated by the UBC9 E2 enzyme. Proc. Natl. Acad. Sci. 95: 560-564.
38. Swendsen, R.H. and Wang, J.S. 1986. Replica Monte Carlo simulation of spin glasses. Phys. Rev. Lett. 57: 2607-2609.
39. Tovchigrechko, A. and Vakser, I.A. 2005. Development and testing of an automated approach to protein docking. Proteins 60: 296-301.
40. Tovchigrechko, A. and Vakser, I.A. 2006. GRAMM-X public Web server for protein-protein docking. Nucleic Acids Res. 34: W310-W314. doi: 10.1093/nar/gki206.
41. Vakser, I.A. 1995. Protein docking for low-resolution structures. Protein Eng. 8: 371-377.
42. Vakser, I.A. 1996. Low-resolution docking: Prediction of complexes for underdetermined structures. Biopolymers 39: 455-464.
43. Zacharias, M. 2003. Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci. 12: 1271-1282.
44. Zacharias, M., Straatsma, T.P., and McCammon, J.A. 1994. Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration. J. Chem. Phys. 100: 9025-9031.
45. Zhang, C., Vasmatzis, G., Cornette, J.L., and DeLisi, C. 1997. Determination of atomic desolvation energies from the structures of crystallized proteins. J. Mol. Biol. 267: 707-726.
46. Zhang, Y., Kihara, D., and Skolnick, J. 2002. Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding. Proteins 48: 192-201.