SwarmDock and the use of normal modes in protein-protein Docking

International Journal of Molecular Sciences

Volumn 11, Issue 10, 2010, Pages 3623-3648

  Moal, Iain H ^a   Bates, Paul A ^a  

^a THE FRANCIS CRICK INSTITUTE   (United Kingdom)

Author keywords

CAPRI; Elastic network model; Normal mode analysis; Particle swarm optimization; Protein flexibility; PSO; RTB

Indexed keywords

IMMUNOGLOBULIN G1; INFLUENZA VIRUS HEMAGGLUTININ;

ANALYTIC METHOD; ANTIBODY COMBINING SITE; ANTIGEN BINDING; ARTICLE; BINDING KINETICS; BIOENERGY; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; LEARNING ALGORITHM; LINEAR SYSTEM; MOLECULAR DOCKING; MOLECULAR DYNAMICS; NORMAL MODE ANALYSIS; PROCESS MODEL; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; REGRESSION ANALYSIS; STATISTICAL MODEL; STRUCTURE ANALYSIS;

CAPRI; ELASTIC NETWORK MODEL; NORMAL MODE ANALYSIS; PARTICLE SWARM OPTIMISATION; PROTEIN FLEXIBILITY; PSO; RTB;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; HEMAGGLUTININ GLYCOPROTEINS, INFLUENZA VIRUS; IMMUNOGLOBULIN G; MICE; MOLECULAR DOCKING SIMULATION; MOLECULAR SEQUENCE DATA; PROTEIN BINDING;

EID: 77958133774     PISSN: None     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms11103623     Document Type: Article

References (83)

1. Katchalski-Katzir, E.; Shariv, I.; Eisenstein, M.; Friesem, A.A.; Aflalo, C.; Vakser, I.A. Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl. Acad. Sci. USA 1992, 89, 2195-2199.
2. Chen, R.; Weng, Z. Docking unbound proteins using hape complementarity, desolvation, and electrostatics. Proteins 2002, 47, 281-294.
3. Schneidman-Duhovny, D.; Inbar, Y.; Nussinov, R.; olfson, H.J. PatchDock and SymmDock: Servers for rigid and symmetric docking. Nucleic Acids Res. 2005, 33, W363-67.
4. Shentu, Z.; Al Hasan, M.; Bystroff, C.; Zaki, M.J. Context shapes: Efficient complementary shape matching for protein-protein docking. Proteins 2008, 70, 1056-1073.
5. Li, N.; Sun, Z.; Jiang, F. SOFTDOCK application to rotein-protein interaction benchmark and CAPRI. Proteins 2007, 69, 801-808.
6. Jackson, R.M.; Gabb, H.A.; Sternberg, M.J. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J. Mol. Biol. 1998, 276, 265-285.
7. Mandell, J.G.; Roberts, V.A.; Pique, M.E.; Kotlovyi, V.; Mitchell, J.C.; Nelson, E.; Tsigelny, I.; Ten Eyck, L.F. Protein docking using continuum electrostatics and geometric fit. Protein Eng. 2001, 14, 105-113.
8. Ritchie, D.W.; Kemp, G.J. Protein docking using spherical polar Fourier correlations. Proteins 2000, 39, 178-194.
9. Tovchigrechko, A.; Vakser, I.A. Development and testing of an automated approach to protein docking. Proteins 2005, 60, 296-301.
10. Zacharias, M. Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci. 2003, 12, 1271-1282.
11. Gardiner, E.J.; Willett, P.; Artymiuk, P.J. Protein docking using a genetic algorithm. Proteins 2001, 44, 44-56.
12. Smith, G.R.; Sternberg, M.J.; Bates, P.A. 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, 347, 1077-1101.
13. Grunberg, R.; Leckner, J.; Nilges, M. Complementarity of structure ensembles in protein-protein binding. Structure 2004, 12, 2125-2136.
14. Krol, M.; Chaleil, R.A.; Tournier, A.L.; Bates, P.A. Implicit flexibility in protein docking: Cross-docking and local refinement. Proteins 2007, 69, 750-757.
15. Krol, M.; Tournier, A.L.; Bates, P.A. Flexible relaxation of rigid-body docking solutions. Proteins 2007, 68, 159-169.
16. Dominguez, C.; Boelens, R.; Bonvin, A.M. HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 2003, 125, 1731-1737.
17. 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. 2003, 331, 281-299.
18. Comeau, S.R.; Gatchell, D.W.; Vajda, S.; Camacho, C.J. ClusPro: An automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 2004, 20, 45-50.
19. Camacho, C.J.; Gatchell, D.W. Successful discrimination of protein interactions. Proteins 2003, 52, 92-97.
20. Li, L.; Chen, R.; Weng, Z. RDOCK: Refinement of rigid-body protein docking predictions. Proteins 2003, 53, 693-707.
21. Andrusier, N.; Nussinov, R.; Wolfson, H.J. FireDock: Fast interaction refinement in molecular docking. Proteins 2007, 69, 139-159.
22. Fernndez-Recio, J.; Totrov, M.; Abagyan, R. ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins 2003, 52, 113-117.
23. Bastard, K.; Prvost, C.; Zacharias, M. Accounting for loop flexibility during protein-protein docking. Proteins 2006, 62, 956-969.
24. Schneidman-Duhovny, D.; Inbar, Y.; Nussinov, R.; Wolfson, H.J. Geometry-based flexible and symmetric protein docking. Proteins 2005, 60, 224-231.
25. Tirion, M.M. Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. Phys. Rev. Lett. 1996, 77, 1905-1908.
26. Bahar, I.; Atilgan, A.R.; Erman, B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des. 1997, 2, 173-181
27. Yang, L.W.; Eyal, E.; Chennubhotla, C.; Jee, J.; Gronenborn, A.M.; Bahar, I. Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions. Structure 2007, 15, 741-749.
28. Rueda, M.; Chacon, P.; Orozco, M. Thorough validation of protein normal mode analysis: A comparative study with essential dynamics. Structure 2007, 15, 565-575.
29. Yang, L.; Song, G.; Jernigan, R.L. How well can we understand large-scale protein motions using normal modes of elastic network models? Biophys. J. 2007, 93, 920-929.
30. Krebs, W.G.; Alexandrov, V.; Wilson, C.A.; Echols, N.; Yu, H.; Gerstein, M. Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic Proteins 2002, 48, 682-695.
31. Tama, F.; Sanejouand, Y.H. Conformational change of proteins arising from normal mode calculations. Protein Eng. 2001, 14, 1-6.
32. Atilgan, A.R.; Durell, S.R.; Jernigan, R.L.; Demirel, M.C.; Keskin, O.; Bahar, I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 2001, 80, 505-515.
33. Dobbins, S.E.; Lesk, V.I.; Sternberg, M.J. Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking. Proc. Natl. Acad. Sci. USA 2008, 105, 10390-10395.
34. Cui, Q.; Li, G.; Ma, J.; Karplus, M. A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase. J. Mol. Biol. 2004, 340, 345-372.
35. Petrone, P.; Pande, V.S. Can conformational change be described by only a few normal modes? Biophys. J. 2006, 90, 1583-1593.
36. Tama, F.; Miyashita, O.; Brooks, C.L. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J. Struct. Biol. 2004, 147, 315-326.
37. Mustard, D.; Ritchie, D.W. Docking essential dynamics eigenstructures. Proteins 2005, 60, 269-274.
38. Andrusier, N.; Mashiach, E.; Nussinov, R.; Wolfson, H.J. Principles of flexible protein-protein docking. Proteins 2008, 73, 271-289.
39. Bonvin, A.M. Flexible protein-protein docking. Curr. Opin. Struct. Biol. 2006, 16, 194-200.
40. May, A.; Zacharias, M. Accounting for global protein deformability during protein-protein and protein-ligand docking. Biochim. Biophys. Acta 2005, 1754, 225-231.
41. Rueda, M.; Bottegoni, G.; Abagyan, R. Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes. J. Chem. Inf. Model. 2009, 49, 716-725.
42. Zacharias, M.; Sklenar, H. Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to DNA minor groove ligand complex. J. Comp. Chem. 1999, 20, 287-300.
43. Lindahl, E.; Delarue, M. Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization. Nucleic Acids Res. 2005, 33, 4496-4506.
44. May, A.; Zacharias, M. Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: Evaluation on kinase inhibitor cross docking. J. Med. Chem. 2008, 51, 3499-3506.
45. Floquet, N.; Marechal, J.D.; Badet-Denisot, M.A.; Robert, C.H.; Dauchez, M.; Perahia, D. Normal mode analysis as a prerequisite for drug design: application to matrix metalloproteinases inhibitors. FEBS Lett. 2006, 580, 5130-5136.
46. Sander, T.; Liljefors, T.; Balle, T. Prediction of the receptor conformation for iGluR2 agonist binding: QM/MM docking to an extensive conformational ensemble generated using normal mode analysis. J. Mol. Graph. Model. 2008, 26, 1259-1268.
47. Cavasotto, C.N.; Kovacs, J.A.; Abagyan, R.A. Representing receptor flexibility in ligand docking through relevant normal modes. J. Am. Chem. Soc. 2005, 127, 9632-9640.
48. Kovacs, J.A.; Cavasotto, C.N.; Abagyan, R. Conformational Sampling of Protein Flexibility in Generalized Coordinates: Application to Ligand Docking. J. Comput. Theor. Nanosci. 2005, 2, 354-361.
49. May, A.; Zacharias, M. Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking. Proteins 2008, 70, 794-809.
50. Mashiach, E.; Nussinov, R.; Wolfson, H.J. FiberDock: Flexible induced-fit backbone refinement in molecular docking. Proteins 2010, 78, 1503-1519.
51. Hwang, H.; Pierce, B.; Mintseris, J.; Janin, J.; Weng, Z. Protein-protein docking benchmark version 3.0. Proteins 2008, 73, 705-709.
52. Canutescu, A.A.; Shelenkov, A.A.; Dunbrack, R.L. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci. 2003, 12, 2001-2014.
53. Rotkiewicz, P.; Skolnick, J. Fast procedure for reconstruction of full-atom protein models from reduced representations. J. Comput. Chem. 2008, 29, 1460-1465.
54. Kennedy, J.; Eberhart, R.C. Particle Swarm Optimization. In Proceedings of the IEEE International Conference on Neural Networks, Perth, Australia, 1995; Volume 4, pp. 1942-1948.
55. Solis, F.J.; Wets, R.J.B. Minimization by Random Search Techniques. Math. Oper. Res. 1981, 6, 19-30.
56. Sousa, T.; Silva, A.; Neves, A. Particle swarm based Data Mining Algorithms for classification tasks. Parallel Comput. 2004, 30, 767-783.
57. Xiao, X.; Dow, E.R.; Eberhart, R.; Miled, Z.B.; Oppelt, R.J. Gene Clustering Using Self-Organizing Maps and Particle Swarm Optimization. In Proceedings of the International Parallel and Distributed Processing Symposium, Nice, France 2003 pp.154b.
58. Rasmussen, T.K.; Krink, T. Improved Hidden Markov Model training for multiple sequence alignment by a particle swarm optimization-evolutionary algorithm hybrid. Bio Systems 2003, 72, 5-17.
59. Namasivayam, V.; Gunther, R. PSO@Autodock: A fast flexible molecular docking program based on Swarm intelligence. Chem. Biol. Drug Des. 2007, 70, 475-484.
60. Chen, H.M.; Liu, B.F.; Huang, H.L.; Hwang, S.F.; Ho, S.Y. SODOCK: Swarm optimization for highly flexible protein-ligand docking. J. Comput. Chem. 2007, 28, 612-623.
61. Janson, S.; Merkle, S.; Middendorf, M. Molecular docking with multi-objective Particle Swarm Optimization. Appl. Soft Comput. 2008, 8, 666-675
62. Li, X.; Moal, I.H.; Bates, P.A. Detection and Refinement of Encounter Complexes for Protein-Protein Docking: Taking Account of Macromolecular Crowding. Proteins 2010, doi: 10.1002/prot.22770.
63. Magnusson, U.; Chaudhuri, B.N.; Ko, J.; Park, C.; Jones, T.A.; Mowbray, S.L. Hinge-bending motion of D-allose-binding protein from Escherichia coli: Three open conformations. J. Biol. Chem. 2002, 277, 14077-14084.
64. Arnold, G.E.; Ornstein, R.L. Protein hinge bending as seen in molecular dynamics simulations of native and M61 mutant T4 lysozymes. Biopolymers 1997, 41, 533-544.
65. Boehr, D.D.; Nussinov, R.; Wright, P.E. The role of dynamic conformational ensembles in biomolecular recognition. Nat. Chem. Biol. 2009, 5, 789-796.
66. Isabet, T.; Montagnac, G.; Regazzoni, K.; Raynal, B.; El Khadali, F.; England, P.; Franco, M.; Chavrier, P.; Houdusse, A.; Menetrey, J. The structural basis of Arf effector specificity: The crystal structure of ARF6 in a complex with JIP4. EMBO J. 2009, 28, 2835-2845.
67. O'Neal, C.J.; Jobling, M.G.; Holmes, R.K.; Hol,W.G. Structural basis for the activation of cholera toxin by human ARF6-GTP. Science 2005, 309, 1093-1096.
68. Offman, M.N.; Tournier, A.L.; Bates, P.A. Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection. BMC Struct. Biol. 2008, 8, 34.
69. O'Shea, E.K.; Klemm, J.D.; Kim, P.S.; Alber, T. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 1991, 254, 539-544.
70. Katz, B.A.; Finer-Moore, J.; Mortezaei, R.; Rich, D.H.; Stroud, R.M. Episelection: Novel Ki approximately nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface. Biochemistry 1995, 34, 8264-8280.
71. Kurkcuoglu, O.; Jernigan, R.L.; Doruker, P. Loop motions of triosephosphate isomerase observed with elastic networks. Biochemistry 2006, 45, 1173-1182.
72. Brooks, B.R.; Janezic, D.; Karplus, M. Harmonic analysis of large systems. I. Methodology. J. Comp. Chem. 1995, 16, 1522-1542.
73. Tama, F.; Gadea, F.X.; Marques, O.; Sanejouand, Y.H. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins 2000, 41, 1-7.
74. Suhre, K.; Sanejouand, Y.H. ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res. 2004, 32, W610-W614.
75. Dongarra, J. Basic Linear Algebra Subprograms Technical Forum Standard. Int. J. High Perform. Appl. Supercomput. 2002, 16, 115-199.
76. Tama, F.; Gadea, F.X.; Marques, O.; Sanejouand, Y.H. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins 2000, 41, 1-7.
77. Li, G.; Cui, Q. A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca2+-ATPase. Biophys. J. 2002, 83, 2457-2474.
78. Durand, P.; Trinquier, G.; Sanejouand, Y.H. A new approach for determining low-frequency normal modes in macromolecules. Biopolymers 1994, 34, 759-771.
79. Durand, P. Direct determination of effective Hamiltonians by wave-operator methods. I. General formalism. Phys. Rev. A 1983, 28, 3184-3192
80. Marques, O.; Sanejouand, Y.H. Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins 1995, 23, 557-560.
81. Chen, R.; Mintseris, J.; Janin, J.; Weng, Z. A protein-protein docking benchmark. Proteins 2003, 52, 88-91.
82. Mendez, R.; Leplae, R.; de Maria, L.; Wodak, S.J. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 2003, 52, 51-67
83. MacKerell, A.D.; Bashford, D.; Bellott.; Dunbrack, R.L; Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. J. Phys. Chem. B 1998, 102, 3586-3616.