Predicting 3D structures of transient protein-protein complexes by homology

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1764, Issue 9, 2006, Pages 1498-1511

  Kundrotas, Petras J ^a   Alexov, Emil ^a  

^a CLEMSON UNIVERSITY   (United States)

Author keywords

Domain structure; Homology modeling; Protein protein complex; Sequence similarity; Structural superimposition; Structure prediction

Indexed keywords

ARTICLE; COMPLEX FORMATION; DATA BASE; METHODOLOGY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

ALGORITHMS; DATABASES, PROTEIN; GENOMICS; MODELS, MOLECULAR; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 33748453562     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2006.08.002     Document Type: Article

References (63)

1. Smith G.R., and Sternberg M.J.E. Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol. 12 (2002) 28-35
2. McCammon J.A. Theory of biomolecular recognition. Curr. Opin. Struct. Biol. 8 (1998) 245-249
3. Topf M., and Sali A. Combining electron microscopy and comparative modeling. Curr. Opin. Chem. Biol. 15 (2005) 578-585
4. Lu L., Lu H., and Skolnick J. MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 15 (2005) 350-364
5. Aloy P., and Russell R.B. InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics 19 (2003) 161-162
6. Fields S., and Song O. A novel genetic system to detect protein-protein interactions. Nature 340 (1989) 245-246
7. Uetz P. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403 (2000) 623
8. Cavin A., Bosche M., Krause R., Grandi P., Marcioch M., Bauer A., Schultz J., Rick J., and Cruciat C. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415 (2002) 141-147
9. Zhu H., Bildin M., Bangham R., Casamayor H.D.A., Bertone P., Lan N., Jansen R., Bidlingmaier S., and Houfek T. Global analysis of protein activities using proteome chips. Science 293 (2001) 2101-2105
10. Valencia A., and Pazos F. Computational methods for the prediction of protein interactions. Curr. Opin. Struc. Biol. 12 (2002) 368-373
11. Szilagyi A., Grimm V., Arakaki A., and Skolnick J. Prediction of physical protein-protein interactions. Phys. Biol. 2 (2005) 1-16
12. Aloy P., Bottcher B., Ceulemans H., Leutwein C., Mellwig C., Fischer S., Gavin A.C., Bork P., Superti-Furga G., Serrano L., and Russell R.B. Structure-based assembly of protein complexes in yeast. Science 303 (2004) 2026-2029
13. Stelzl U., Worm U., Lalowski M., Haenig C., Brembeck F., Goehler H., Stroedicke M., Zenkner M., Schoenherr A., Koeppen S., Timm J., Mintzlaff S., Abraham C., Bock N., Kietzmann S., Goedde A., Toksoz E., Droege A., Krobisch S., Korn B., Brichmeier W., Lehrach H., and Wanker E. A human protein-protein interaction network: a resource for annotating the proteome. Cell 122 (2005) 957-968
14. Rual J., Venkatesan K., Hao T., Hirozane-Kishikawa T., Dricot A., Li N., Berriz G., Gibbons F., Dreze M., Ayivi-Guedehoussou N., Klitgord N., Simon C., Boxem M., Milstein S., Rosenberg J., Goldberg D., Zhang L., Wong S., Franklin G., Li S., Alabala J., LLim J., Fraughton C., Llamosas E., Cevik S., Bex C., Lamesch P., Sikorski R., Vandenhaute J., Zoghbi H., Smoyar A., Bosak S., Sequerra R., Doucette-Stamm L., Cusick M., Hill D., Roth F., and Vidal M. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437 (2005) 1173-1178
15. Vakser I. Evaluation of GRAMM Low-Resolution Docking Methodology on the Hemagglutin-Antibody Complex. Proteins 1 (1997) 226-230
16. Tovchigrechko A., Wells C., and Vakser I. Docking of protein models. Prot. Sci. 11 (2002) 1888-1896
17. Chen R., Li L., and Weng Z. ZDOCK: An Initial-Stage Protein-Docking Algorithm. Proteins 52 (2003) 80-87
18. Norel R., Lin S., Wolfson H., and Nussinov R. Shape complimentarity at protein-protein interfaces. Biopolymers 34 (1994) 933-940
19. Norel R., Sheinerman F., Petrey D., and Honig B. Electrostatic contribution to protein-protein interactions: Fast energetic filters for docking and their physical basis. Prot. Sci. 10 (2001) 2147-2161
20. Morris G., Goodsell D., Halliday R., Huey R., Hart W., Belew R., and Olson A. Automated Docking Using a Lamarckian Genetic Algorithm and Empirical Binding Free Energy Function. J. Comp. Chem. 19 (1998) 1639-1662
21. Comeau S., Vajda S., and Camacho C. Performance of the first protein docking server ClusPro in CAPRI rounds 3-5. Proteins 60 (2005) 239-244
22. Fernandes-Recio J., Totrov M., and Abagyan R. ICM-DISCO Docking by Global Energy Optimization with Fully Flexible Side-Chains. Proteins 52 (2003) 113-117
23. Schueler-Furman O., Wang C., and Baker D. Progress in protein-protein docking: atomic resolution in the predictions in the CAPRI experiment using RosattaDock with an improved treatment of the side-chain flexibility. Proteins 60 (2005) 187-194
24. Carter P., Lesk V., Islam S., and Sternberg M. protein-protein docking using 3D-Dock in rounds 3,4 of CAPRI. Proteins 60 (2005) 281-288
25. Schneidman-Duhovny D., Inbar Y., Nussinov R., and Wolfson R. Geometry-based flexible and symmetric protein docking. Proteins 60 (2005) 224-231
26. Gohlke H., Kiel C., and Case D. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J. Mol. Biol. 330 (2003) 891-913
27. Mendez R., Leplae R., Lensink M., and Wodak S. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 60 (2005) 150-169
28. Vajda S., Vakser I., Steinberg M., and Janin J. Modeling of Protein Interactions in Genomes. Proteins 47 (2002) 444-446
29. Janin J. The targets of CAPRI rounds 3-5. Proteins 60 (2005) 170-175
30. Pieper U., Eswar N., Braberg H., Madhusudhan M.S., Davis F.P., Stuart A.C., Mirkovic N., Rossi A., Marti-Renom M.A., Fiser A., Webb B., Greenblatt D., Huang C.C., Ferrin T.E., and Sali A. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 32 (2004) D217-D222
31. Davis F.P., and Sali A. PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics 21 (2005) 1901-1907
32. Aloy P., and Russell R.B. Interrogating protein interaction networks through structural biology. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 5896-5901
33. Grimm V., Zhang Y., and Skolnick J. Benchmarking of dimeric threading and structure refinement. Proteins 63 (2006) 457-465
34. Berman H., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. TheProtein Data Bank. Nucleic Acids Res. 28 (2000) 235-242
35. Sridharan S., Nicholls A., and Honig B. A new vertex algorithm to calculate solvent accessible surface areas. Biophys. J. 61 (1992) A174
36. Li W., Jaroszewski L., and Godzik A. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 17 (2001) 282-283
37. Szilagyi A., Grimm V., Arakaki A.K., and Skolnick J. Prediction of physical protein-protein interactions. Phys. Biol. 2 (2005) S1-S16
38. Alexandrov N., and Shindyalov I. PDP: protein domain parser. Bioinformatics 19 (2003) 429-430
39. Murzin A.G., Brenner S.E., Hubbard T., and Chothia C. SCOP: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures. J. Mol. Biol. 247 (1995) 536-540
40. Orengo C., Michie A., Jones S., Jones D., Swindells M., and Thornton J. CATH-A hierarchic classification of protin domain structures. Structure 5 (1997) 1093-1108
41. Sonnhammer E.L.L., Eddy S.R., and Durbin R. Pfam: A Comprehensive Database of Protein Families Based on Seed Alignments. Protein 28 (1997) 405-420
42. Gong S., Park C., Choi H., Ko J., Jang I., Lee J., Bolser D.M., Oh D., Kim D.S., and Bhak J. A protein domain interaction interface database: InterPare. BMC Bioinformatics 6 (2005)
43. Stein A., Russell R.B., and Aloy P. 3Did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res. 33 (2005) D413-D417
44. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs. Nuclei Acids Res. 25 (1997) 3389-3402
45. Henikoff S., and Henikoff J. Performance evaluation of amino acid substitution matrices. Proteins 17 (1993) 49-61
46. Aloy P., and Russell R.B. Structural systems biology: modelling protein interactions. Nat. Rev., Mol. Cell Biol. 7 (2006) 188-197
47. Russell R.B., Alber F., Aloy P., Davis F.P., Korkin D., Pichaud M., Topf M., and Sali A. A structural perspective on protein-protein interactions. Curr. Opin. Struct Biol. 14 (2004) 313-324
48. Petrey D., Xiang Z., Tang C., Xie L., Gimpelev M., Mitros T., Soto C., Goldsmith-Fischman S., Kernytsky A., Schlessinger A., Koh I., Alexov E., and Honig B. Uning Multiple Structure Alignments, Fast Model Builing, and Energetic Analysis in Fold Recognition and Homology Modeling. Proteins 53 (2003) 430-435
49. Yang A., and Honig B. An Integrated Approach to the Analysis and Modeling of Protein Sequences and Structures. I. Protein Structural Alignment and a Qualitative Measure for Protein Structural Distance. J. Mol. Biol. 301 (2000) 665-678
50. Aloy P., Ceulemans H., Stark A., and Russell R.B. The relationship between sequence and interaction divergence in proteins. J. Mol. Biol. 332 (2003) 989-998
51. Tang C., Xie L., Koh I., Posy S., Alexov E., and Honig B. On the Role of Structure and Sequence Information for Remote Homology Detection and Sequence Alignment: New Methods Using Hybrid Sequence Profiles. J. Mol. Biol. 334 (2003) 1043-1062
52. Nicholls A., Sharp K.A., and Honig B. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct. Funct. Genet. 11 (1991) 281-296
53. Aloy P., Pichaud M., and Russell R.B. Protein complexes: structure prediction challenges for the 21st century. Curr. Opin. Struct. Biol. 15 (2005) 15-22
54. Jones S., and Thornton J. Prediction of protein-protein Interaction Sites using Patch Analysis. J. Mol. Biol. 272 (1997) 113-143
55. Valdar W., and Thornton J. protein-protein Interfaces: Analysis of Amino Acid Concervation in Homodimers. Proteins 42 (2001) 108-124
56. Pazos F., and Valencia A. In Silico Two-Hybrid System for the Selection of Physically Interacting Protein Pairs. Proteins 47 (2002) 219-227
57. Pazos F., Helmer-Citterich M., Ausiello G., and Valencia A. Correlated Mutations Contain Information About protein-protein Interactions. J. Mol. Biol. 271 (1997) 511-523
58. Lichtarge O., and Sowa M. Evolutionary predictions of binding surfaces and interactions. Curr. Opin. Struct. Biol. 12 (2002) 21-27
59. Glaser F., Steinberg D., Vakser I., and Ben-Tal N. Residue Frequencies and Pairing Preferences at protein-protein Interfaces. Proteins 43 (2001) 89-102
60. Wang B., Chen P., Huang D., Li J., Lok T., and Lyu M. Predicting protein interaction sites from residue spatial sequence profile and evolution rate. FEBS Lett. 580 (2006) 380-384
61. Chung J., Wang W., and Bourne P. Exploiting sequence and structure homologs to identify protein-protein binding sites. Proteins 62 (2006) 630-640
62. Ofran Y., and Rost B. Predicted protein-protein interaction sites from local sequence information. FEBS Lett. 544 (2003) 236-239
63. Fernandes-Recio J., Totrov M., Skorodumov C., and Abagyan R. Optimal Docking Area: A New Method for Predicting protein-protein Interaction Site. Proteins 57 (2005) 400-413