Prediction of interface residues in protein-protein complexes by a consensus neural network method: Test against NMR data

Proteins: Structure, Function and Genetics

Volumn 61, Issue 1, 2005, Pages 21-35

  Chen, Huiling ^a   Zhou, Huan Xiang ^a,b  

^a DREXEL UNIVERSITY   (United States)

^b Florida State University   (United States)

Author keywords

Interface prediction; Neural network; Protein complexes; Protein docking; Protein protein interaction

Indexed keywords

CYTOCHROME B5; CYTOCHROME C; HISTONE H3; IMMUNOGLOBULIN G; PROTEIN; PROTEIN P47; PROTEIN P97; PROTEIN UBC9; SOLVENT; SUMO 1 PROTEIN; THROMBIN; THROMBOMODULIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; ARTIFICIAL NEURAL NETWORK; BINDING SITE; HYDROPHOBICITY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SURFACE PROPERTY; X RAY CRYSTALLOGRAPHY;

BINDING SITES; MEMBRANE PROTEINS; MODELS, MOLECULAR; NEURAL NETWORKS (COMPUTER); NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN BINDING; PROTEIN STRUCTURE, QUATERNARY;

EID: 24344484686     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20514     Document Type: Article

References (68)

1. Ito T, Chiba T, Osawa R, Yoshida M, Hattori M, Sasaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 2000;98:4569-4574.
2. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000;403:623-627.
3. Lichtarge O, Sowa ME, Philippi A. Evolutionary traces of functional surfaces along the G protein signaling pathway. Methods Enzymol 2001;344:536-556.
4. Sowa ME, He W, Slep KC, Kercher MA, Lichtarge O, Wensel TG. Prediction and confirmation of a site critical for effector regulation of RGS domain activity. Nat Struct Biol 2001;8:234-237.
5. Zhou H-X. Improving the understanding of human genetic disease through predictions of protein structures and protein-protein interaction sites. Curr Med Chem 2004;11:539-549.
6. Dominguez C, Boelens R, Bonvin AMJJ. HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 2003;125:1731-1737.
7. Zhou H-X, Shan Y. Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins 2001;44:336-343.
8. Jones S, Thornton JM. Principles of protein-protein interactions. Proc Natl Acad Sci USA 1996;93:13-20.
9. Jones S, Thornton JM. Analysis of protein-protein interaction sites using surface patches. J Mol Biol 1997;272:121-132.
10. Jones S, Thornton JM. Prediction of protein-protein interaction sites using patch analysis. J Mol Biol 1997;272:133-143.
11. Conte LL, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999;285:2177-2198.
12. Hu Z, Ma B, Wolfson H, Nussinov R. Conservation of polar residues as hot spots at protein interfaces. Proteins 2000;39:331-342.
13. Valdar WSJ, Thornton JM. Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins 2001;42:108-124.
14. Glaser F, Steinberg DM, Vakser IA, Ben-Tal N. Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 2001;43:89-102.
15. Armon A, Graur D, Ben-Tal N. Consurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol 2001;307:447-463.
16. Landgraf R, Xenarios L, Eisenberg D. Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J Mol Biol 2001;307:1487-1502.
17. Pupko T, Bell RE, Mayrose I, Glaser F, Ben-Tal N. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 2002;18:S71-S77.
18. Madabushi S, Yao H, Marsh M, Kristensen DM, Philippi A, Sowa ME, Lichtarge O. 2002. Structural clusters of evolutionary trace residues are statistically significant and common in proteins. J Mol Biol 316:139-154.
19. Lichtarge O, Sowa ME. Evolutionary predictions of binding surfaces and interactions. Curr Opin Struct Biol 2002;12:21-27.
20. Ofran Y, Rost B. Analysing six types of protein-protein interfaces. J Mol Biol 2003;325:377-387.
21. Nooren IMA, Thornton JM. Structural characterization and functional significance of transient protein-protein interactions. J Mol Biol 2003;325:991-1018.
22. Yao H, Kristensen DM, Mihalek I, Sowa ME, Shaw C, Kimmel M, Kavraki L, et al. An accurate, sensitive, and scalable method to identify functional sites in protein structures. J Mol Biol 2003;326: 255-261.
23. Ma B, Elkayam T, Wolfson H, Nussinov R. Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci USA 2003;100:5772-5777.
24. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25: 3389-3402.
25. Rost B, Sander C. Progress of ID protein structure prediction at last. Proteins 1995;23:295-300.
26. Jones D. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
27. Shan Y, Wang G, Zhou H-X. Fold recognition and accurate query-template alignment by a combination of PSI-BLAST and threading. Proteins 2001;42:23-37.
28. Minakuchi Y, Satou K, Konagaya A, Ito T. Prediction of protein-protein interaction sites using support vector machines. Genome Informatics 2002;13:322-323.
29. Fariselli P, Pazos F, Valencia A, Casadio R. Prediction of protein-protein interaction sites in heterocomplexes with neural networks. Eur J Biochem 2002;269:1356-1361.
30. Ofran Y, Rost B. Predicted protein-protein interaction sites from local sequence information. FEBS Lett 2003;544:236-239.
31. Koike A, Takagi T. Prediction of protein-protein interaction sites using support vector machines. Protein Eng Des Sel 2004;17:165-173.
32. Neuvirth H, Raz R, Schreiber G. ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 2004;338:181-199.
33. Yan CH, Honavar V, Dobbs D. Identification of interface residues in protease-inhibitor and antigen-antibody complexes: a support vector machine approach. Neural Comput Appl 2004;13:123-129.
34. Janin J, Henrick K, Moult J, Eyck LT, Sternberg M, Vajda S, Vakser I, et al. CAPRI: a critical assessment of predicted interactions. Proteins 2003;52:2-9.
35. Chen R, Mintseris J, Janin J, Weng Z. A protein-protein docking benchmark. Proteins 2003;52:88-91.
36. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
37. Fuentes-Prior P, Iwanaga Y, Huber R, Pagila R, Rumennik G, Seto M, Morser J, Light DR, Bode W. Structural basis for the anticoagulant activity of the thrombin-thrombomodulin complex. Nature 2000;404:518-525.
38. Deisenhofer J. Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-A resolution. Biochemistry 1981;20:2361-2370.
39. Vassylyev DG, Takeda S, Wakatsuki S, Maeda K, Maeda Y. Crystal structure of troponin C in complex with troponin I fragment at 2.3-Å resolution. Proc Natl Acad Sci USA 1998;95: 4847-4852.
40. Dreveny I, Kondo H, Uchiyama K, Shaw A, Zhang X, Freemont PS. Structural basis of the interaction between the AAA ATPase p97/VCP and its adaptor protein p47. EMBO J 2004;23:1030-1039.
41. Jacobs SA, Khorasanizadeh S. Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science 2002;295: 2080-2083.
42. Nielsen PR, Nietlispach D, Mott HR, Callaghan J, Bannister A, Kouzarides T, Murzin AG, Murzina NV, Laue ED. Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9. Nature 2002;416:103-107.
43. Shao W, Im SC, Zuiderweg ER, Waskell L. Mapping the binding interface of the cytochrome b5-cytochrome c complex by nuclear magnetic resonance. Biochemistry 2003;42:14774-14784.
44. Wood MJ, Benitez BAS, Komives EA. Solution structure of the smallest cofactor-active fragment of thrombomodulin. Nat Struct Biol 2000;7:200-204.
45. Yuan X, Shaw A, Zhang X, Kondo H, Lally J, Freemont PS, Matthews S. Solution structure and interaction surface of the C-terminal domain from p47: a major p97-cofactor involved in SNARE disassembly. J Mol Biol 2001;311:255-263.
46. Takeda S, Yamashita A, Maeda K, Maeda Y. Structure of the core domain of human cardiac troponin in the Ca(2+)-saturated form. Nature 2003;424:35-41.
47. Li MX, Saude EJ, Wang X, Pearlstone JR, Smillie LB, Sykes BD. Kinetic studies of calcium and cardiac troponin I peptide binding to human cardiac troponin C using NMR spectroscopy. Eur Biophys J 2002;31:245-256.
48. Gasmi-Seabrook GMC, Howarth JW, Finley N, Abusamhadneh E, Gaponenko V, Brito RMM, Solaro RJ, Rosevear PR. Solution structures of the C-terminal domain of cardiac troponin C free and bound to the N-terminal domain of cardiac troponin I. Biochemistry 1999;38:8313-8322.
49. Mercier P, Li MX, Sykes BD. Role of the structural domain of troponin C in muscle regulation: NMR studies of Ca2+ binding and subsequent interactions with regions 1-40 and 96-115 of troponin I. Biochemistry 2000;39:2902-2911.
50. Jacobs SA, Taverna SD, Zhang Y, Briggs SD, Li J, Eissenberg JC, Allis CD, Khorasanizadeh S. Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J 2001;20:5232-5241.
51. Takahashi H, Nakanishi T, Kami K, Arata Y, Shimada I. A novel NMR method for determining the interfaces of large protein-protein complexes. Nat Struct Biol 2000;7:220-223.
52. Liu Q, Jin C, Liao X, Shen Z, Chen DJ, Chen Y. The binding interface between an E2 (UBC9) and a ubiquitin homologue (UBL1). J Biol Chem 1999;274:16979-16987.
53. Tatham MH, Kim S, Yu B, Jaffray E, Song J, Zheng Z, Rodriguez MS, Hay RT, Chen Y. Role of an N-terminal site of Ubc9 in SUMO-1, -2, and -3 binding and conjugation. Biochemistry 2003; 42:9959-9969.
54. Zushi M, Gomi K, Honda G, Kondo S, Yamamoto S, Hayashi T, Suzuki K. Aspartic acid 349 in the fourth epidermal growth factor-like structure of human thrombomodulin plays a role in its Ca(2+)-mediated binding to protein C. J Biol Chem 1991;266: 19886-19889.
55. Nagashima M, Lundh E, Leonard JC, Morser J, Parkinson JF. Alanine-scanning mutagenesis of the epidermal growth factor-like domains of human thrombomodulin identifies critical residues for its cofactor activity. J Biol Chem 1993;268:2888-2892.
56. Lentz SR, Chen Y, Sadler JE. Sequences required for thrombomodulin cofactor activity within the fourth epidermal growth factor-like domain of human thrombomodulin. J Biol Chem 1993; 268:15312-15317.
57. Yang L, Rezaie AR. The fourth epidermal growth factor-like domain of thrombomodulin interacts with the basic exosite of protein C. J Biol Chem 2003;278:10484-10490.
58. Wodak SJ, Janin J. Computer analysis of protein-protein interactions. J Mol Biol 1978;124:323-342.
59. van Dijk ADJ, de Vries SJ, Dominguez C, Chen H, Zhou H-X, Bonvin AMJJ. Data-driven docking: HADDOCK's adventures in CAPRI. Proteins 2005;60:232-238.
60. Carvalho AL, Dias FM, Prates JA, Nagy T, Gilbert HJ, Davies GJ, Ferreira LM, Romao MJ, Fontes CM. Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex. Proc Natl Acad Sci USA 2003;100:13809-13814.
61. Terrak M, Kerff F, Langsetmo K, Tao T, Dominguez R. Structural basis of protein phosphatase 1 regulation. Nature 2004;429:780-784.
62. Graille M, Mora L, Buckingham RH, van Tilbeurgh H, de Zamaroczy M. Structural inhibition of the colicin D tRNase by the tRNA-mimicking immunity protein. EMBO J 2004;23:1474-1482.
63. Bressanelli S, Stiasny K, Allison SL, Stura EA, Duquerroy S, Lescar J, Heinz FX, Rey FA. Structure of a flavivirus envelope glycoprotein in its low-pH-induced membrane fusion conformation. EMBO J 2004;23:728-738.
64. Sansen S, de Ranter CJ, Gebruers K, Brijs K, Courtin CM, Delcour JA, Rabijns A. Structural basis for inhibition of Aspergillus niger xylanase by triticum aestivum xylanase inhibitor-I. J Biol Chem 2004;279:36022-36028.
65. Eghiaian F, Grosclaude J, Lesceu S, Debey P, Doublet B, Treguer E, Rezaei H, Knossow M. Insight into the PrPC→PrPSc conversion from the structures of antibody-bound ovine prion scrapie-susceptibility variants. Proc Natl Acad Sci USA 2004;101:10254-10259.
66. Jacobs SA, Taverna SD, Zhang Y, Briggs SD, Li J, Eissenberg JC, Allis CD, Khorasanizadeh S. Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J 2001;20:5232-5241.
67. Liu Q, Jin C, Liao X, Shen Z, Chen DJ, Chen Y. The binding interface between an E2 (UBC9) and a ubiquitin homologue (UBL1). J Biol Chem 1999;274:16979-16987.
68. Tatham MH, Kim S, Yu B, Jaffray E, Song J, Zheng Z, Rodriguez MS, Hay RT, Chen Y. Role of an N-terminal site of Ubc9 in SUMO-1, -2, and -3 binding and conjugation. Biochemistry 2003; 42:9959-9969.