Protein-protein docking: From interaction to interactome

Biophysical Journal

Volumn 107, Issue 8, 2014, Pages 1785-1793

  Vakser, Ilya A ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN BINDING; PROTEOME;

AMINO ACID SEQUENCE; ANIMAL; CHEMISTRY; HUMAN; METABOLISM; MOLECULAR DOCKING; MOLECULAR GENETICS; PROCEDURES;

AMINO ACID SEQUENCE; ANIMALS; HUMANS; MOLECULAR DOCKING SIMULATION; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEOME;

EID: 84908263546     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2014.08.033     Document Type: Review

References (80)

1. K.E.B. Platzer, F.A. Momany, and H.A. Scheraga Conformational energy calculations of enzyme-substrate interactions. II. Computation of the binding energy for substrates in the active site of alpha-chymotrypsin Int. J. Pept. Protein Res. 4 1972 201 219
2. M.R. Pincus, S.S. Zimmerman, and H.A. Scheraga Prediction of three-dimensional structures of enzyme-substrate and enzyme-inhibitor complexes of lysozyme Proc. Natl. Acad. Sci. USA 73 1976 4261 4265
3. S.Y. Wodak, M.Y. Liu, and H.W. Wyckoff The structure of cytidilyl(2′,5′)adenosine when bound to pancreatic ribonuclease S J. Mol. Biol. 116 1977 855 875
4. M.R. Pincus, and H.A. Scheraga Conformational energy calculations of enzyme-substrate and enzyme-inhibitor complexes of lysozyme. 2. Calculation of the structures of complexes with flexible enzyme Macromolecules 12 1979 633 644
5. S.J. Wodak, and J. Janin Computer analysis of protein-protein interaction J. Mol. Biol. 124 1978 323 342
6. J. Greer, and B.L. Bush Macromolecular shape and surface maps by solvent exclusion Proc. Natl. Acad. Sci. USA 75 1978 303 307
7. E. Katchalski-Katzir, and I. Shariv I.A. Vakser Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques Proc. Natl. Acad. Sci. USA 89 1992 2195 2199
8. D. Fischer, and R. Norel R. Nussinov Surface motifs by a computer vision technique: searches, detection, and implications for protein-ligand recognition Proteins 16 1993 278 292
9. S. Vajda, D.R. Hall, and D. Kozakov Sampling and scoring: a marriage made in heaven Proteins 81 2013 1874 1884
10. I.A. Vakser, and C. Aflalo Hydrophobic docking: a proposed enhancement to molecular recognition techniques Proteins 20 1994 320 329
11. J.G. Mandell, and V.A. Roberts L.F. Ten Eyck Protein docking using continuum electrostatics and geometric fit Protein Eng. 14 2001 105 113
12. D. Kozakov, and R. Brenke S. Vajda PIPER: an FFT-based protein docking program with pairwise potentials Proteins 65 2006 392 406
13. J. Mintseris, and B. Pierce Z. Weng Integrating statistical pair potentials into protein complex prediction Proteins 69 2007 511 520
14. I.A. Vakser Main-chain complementarity in protein-protein recognition Protein Eng. 9 1996 741 744
15. I.A. Vakser, O.G. Matar, and C.F. Lam A systematic study of low-resolution recognition in protein-protein complexes Proc. Natl. Acad. Sci. USA 96 1999 8477 8482
16. G. Nicola, and I.A. Vakser A simple shape characteristic of protein-protein recognition Bioinformatics 23 2007 789 792
17. Q. Zhang, M. Sanner, and A.J. Olson Shape complementarity of protein-protein complexes at multiple resolutions Proteins 75 2009 453 467
18. P.J. Kundrotas, and I.A. Vakser Protein-protein alternative binding modes do not overlap Protein Sci. 22 2013 1141 1145
19. E. Trizac, Y. Levy, and P.G. Wolynes Capillarity theory for the fly-casting mechanism Proc. Natl. Acad. Sci. USA 107 2010 2746 2750
20. J. Liu, J.R. Faeder, and C.J. Camacho Toward a quantitative theory of intrinsically disordered proteins and their function Proc. Natl. Acad. Sci. USA 106 2009 19819 19823
21. X. Chu, and L. Gan J. Wang Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition Proc. Natl. Acad. Sci. USA 110 2013 E2342 E2351
22. M.G. Saunders, and G.A. Voth Coarse-graining of multiprotein assemblies Curr. Opin. Struct. Biol. 22 2012 144 150
23. M. Baaden, and S.J. Marrink Coarse-grain modelling of protein-protein interactions Curr. Opin. Struct. Biol. 23 2013 878 886
24. I.A. Vakser Long-distance potentials: an approach to the multiple-minima problem in ligand-receptor interaction Protein Eng. 9 1996 37 41
25. J.J. Gray, and S. Moughon D. Baker Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations J. Mol. Biol. 331 2003 281 299
26. I.A. Vakser Protein docking for low-resolution structures Protein Eng. 8 1995 371 377
27. A. Tovchigrechko, and I.A. Vakser How common is the funnel-like energy landscape in protein-protein interactions? Protein Sci. 10 2001 1572 1583
28. N. O'Toole, and I.A. Vakser Large-scale characteristics of the energy landscape in protein-protein interactions Proteins 71 2008 144 152
29. J. Hunjan, and A. Tovchigrechko I.A. Vakser The size of the intermolecular energy funnel in protein-protein interactions Proteins 72 2008 344 352
30. D. Douguet, and H.C. Chen I.A. Vakser DOCKGROUND resource for studying protein-protein interfaces Bioinformatics 22 2006 2612 2618
31. Y. Gao, and D. Douguet I.A. Vakser DOCKGROUND system of databases for protein recognition studies: unbound structures for docking Proteins 69 2007 845 851
32. H. Hwang, and T. Vreven Z. Weng Protein-protein docking benchmark version 4.0 Proteins 78 2010 3111 3114
33. U. Emekli, and D. Schneidman-Duhovny T. Haliloglu HingeProt: automated prediction of hinges in protein structures Proteins 70 2008 1219 1227
34. A.M. Ruvinsky, and T. Kirys I.A. Vakser Side-chain conformational changes upon Protein-Protein Association J. Mol. Biol. 408 2011 356 365
35. A.M. Ruvinsky, and T. Kirys I.A. Vakser Ensemble-based characterization of unbound and bound states on protein energy landscape Protein Sci. 22 2013 734 744
36. A.M. Ruvinsky, and I.A. Vakser Sequence composition and environment effects on residue fluctuations in protein structures J. Chem. Phys. 133 2010 155101
37. D. Beglov, and D.R. Hall S. Vajda Minimal ensembles of side chain conformers for modeling protein-protein interactions Proteins 80 2011 591 601
38. T. Kirys, and A.M. Ruvinsky I.A. Vakser Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding Proteins 80 2012 2089 2098
39. A. Tovchigrechko, C.A. Wells, and I.A. Vakser Docking of protein models Protein Sci. 11 2002 1888 1896
40. R. Elber, and M. Karplus A method for determining reaction paths in large molecules - application to myoglobin Chem. Phys. Lett. 139 1987 375 380
41. I. Anishchenko, and P.J. Kundrotas I.A. Vakser Protein models: the Grand Challenge of protein docking Proteins 82 2014 278 287
42. A.M. Ruvinsky, and I.A. Vakser Chasing funnels on protein-protein energy landscapes at different resolutions Biophys. J. 95 2008 2150 2159
43. I.A. Vakser Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex Proteins Suppl 1 1997 226 230
44. R. Sánchez, and A. Sali Advances in comparative protein-structure modelling Curr. Opin. Struct. Biol. 7 1997 206 214
45. J. Moult, and K. Fidelis A. Tramontano Critical assessment of methods of protein structure prediction (CASP)-round x Proteins 82 Suppl 2 2014 1 6
46. Y. Zhang, and I.A. Hubner J. Skolnick On the origin and highly likely completeness of single-domain protein structures Proc. Natl. Acad. Sci. USA 103 2006 2605 2610
47. P. Aloy, and H. Ceulemans R.B. Russell The relationship between sequence and interaction divergence in proteins J. Mol. Biol. 332 2003 989 998
48. P.J. Kundrotas, M.F. Lensink, and E. Alexov Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles Int. J. Biol. Macromol. 43 2008 198 208
49. J.P.G.L.M. Rodrigues, and A.S.J. Melquiond A.M.J.J. Bonvin Defining the limits of homology modeling in information-driven protein docking Proteins 81 2013 2119 2128
50. L. Lu, H. Lu, and J. Skolnick MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading Proteins 49 2002 350 364
51. A. Guerler, B. Govindarajoo, and Y. Zhang Mapping monomeric threading to protein-protein structure prediction J. Chem. Inf. Model. 53 2013 717 725
52. A. Szilagyi, and Y. Zhang Template-based structure modeling of protein-protein interactions Curr. Opin. Struct. Biol. 24 2014 10 23
53. S. Günther, and P. May R. Preissner Docking without docking: ISEARCH-prediction of interactions using known interfaces Proteins 69 2007 839 844
54. Q.C. Zhang, and D. Petrey B. Honig Structure-based prediction of protein-protein interactions on a genome-wide scale Nature 490 2012 556 560
55. A.W. Ghoorah, and M.D. Devignes D.W. Ritchie Spatial clustering of protein binding sites for template based protein docking Bioinformatics 27 2011 2820 2827
56. N. Tuncbag, and O. Keskin A. Gursoy Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement Proteins 80 2012 1239 1249
57. R. Sinha, P.J. Kundrotas, and I.A. Vakser Docking by structural similarity at protein-protein interfaces Proteins 78 2010 3235 3241
58. P.J. Kundrotas, and I.A. Vakser Global and local structural similarity in protein-protein complexes: implications for template-based docking Proteins 81 2013 2137 2142
59. M.F. Lensink, and S.J. Wodak Docking, scoring, and affinity prediction in CAPRI Proteins 81 2013 2082 2095
60. K. Khafizov, and C. Madrid-Aliste A. Fiser Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative Proc. Natl. Acad. Sci. USA 111 2014 3733 3738
61. P.J. Kundrotas, and Z. Zhu I.A. Vakser Templates are available to model nearly all complexes of structurally characterized proteins Proc. Natl. Acad. Sci. USA 109 2012 9438 9441
62. Y. Zhang, and J. Skolnick TM-align: a protein structure alignment algorithm based on the TM-score Nucleic Acids Res. 33 2005 2302 2309
63. S. Vajda, and I.A. Vakser J. Janin Modeling of protein interactions in genomes Proteins 47 2002 444 446
64. S. Liu, Y. Gao, and I.A. Vakser DOCKGROUND protein-protein docking decoy set Bioinformatics 24 2008 2634 2635
65. J.S. Dixon Evaluation of the CASP2 docking section Proteins Suppl 1 1997 198 204
66. M.N. Wass, A. David, and M.J.E. Sternberg Challenges for the prediction of macromolecular interactions Curr. Opin. Struct. Biol. 21 2011 382 390
67. I.A. Vakser Low-resolution structural modeling of protein interactome Curr. Opin. Struct. Biol. 23 2013 198 205
68. R. Mosca, and T. Pons P. Aloy Towards a detailed atlas of protein-protein interactions Curr. Opin. Struct. Biol. 23 2013 929 940
69. S.J. Wodak, and J. Vlasblom S. Pu Protein-protein interaction networks: the puzzling riches Curr. Opin. Struct. Biol. 23 2013 941 953
70. Z. Zhu, and A. Tovchigrechko I.A. Vakser Large-scale structural modeling of protein complexes at low resolution J. Bioinform. Comput. Biol. 6 2008 789 810
71. R. Mosca, and C. Pons P. Aloy Pushing structural information into the yeast interactome by high-throughput protein docking experiments PLOS Comput. Biol. 5 2009 e1000490
72. G. Kar, and O. Keskin A. Gursoy Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs J. Proteome Res. 11 2012 1196 1207
73. M. Levitt Nature of the protein universe Proc. Natl. Acad. Sci. USA 106 2009 11079 11084
74. P.J. Kundrotas, I.A. Vakser, and J. Janin Structural templates for modeling homodimers Protein Sci. 22 2013 1655 1663
75. P.J. Kundrotas, and I.A. Vakser Accuracy of protein-protein binding sites in high-throughput template-based modeling PLOS Comput. Biol. 6 2010 e1000727
76. R.B. Russell, and F. Alber A. Sali A structural perspective on protein-protein interactions Curr. Opin. Struct. Biol. 14 2004 313 324
77. H.X. Zhou, and P.A. Bates Modeling protein association mechanisms and kinetics Curr. Opin. Struct. Biol. 23 2013 887 893
78. P.L. Kastritis, and A.M.J.J. Bonvin Molecular origins of binding affinity: seeking the Archimedean point Curr. Opin. Struct. Biol. 23 2013 868 877
79. M. Feig, and Y. Sugita Variable interactions between protein crowders and biomolecular solutes are important in understanding cellular crowding J. Phys. Chem. B 116 2012 599 605
80. D. Kozakov, and K. Li S. Vajda Encounter complexes and dimensionality reduction in protein-protein association eLife 3 2014 e01370