Oligomeric protein structure networks: Insights into protein-protein interactions

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Brinda, K V ^a   Vishveshwara, Saraswathi ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

DISSOCIATION CONSTANT; EXPERIMENTAL VERIFICATION; HYDROPHOBIC INTERACTIONS; INTERACTION STRENGTH; NON-COVALENT INTERACTION; PROTEIN ASSOCIATIONS; PROTEIN-PROTEIN ASSOCIATIONS; PROTEIN-PROTEIN INTERACTIONS;

AMINO ACIDS; ASSOCIATION REACTIONS; COMPLEX NETWORKS; DISSOCIATION; HYDROGEN BONDS; OLIGOMERS;

PROTEINS;

AMINO ACID; AROMATIC COMPOUND; MONOMER; OLIGOMER; ARGININE; PROTEIN; PROTEIN BINDING; TYROSINE;

ALANINE SCANNING ENERGETICS DATA BASE; AMINO ACID ANALYSIS; AMINO ACID SEQUENCE; ARTICLE; CORRELATION ANALYSIS; COVALENT BOND; CRYSTAL STRUCTURE; GENE MUTATION; GENE TARGETING; HYDROGEN BOND; HYDROPHILICITY; INFORMATION PROCESSING; PREDICTION; PROTEIN DATABASE; PROTEIN ENGINEERING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; ANIMAL; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CLUSTER ANALYSIS; HUMAN; KINETICS; MUTATION; PROCEDURES; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEOMICS; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

ANIMALS; ARGININE; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; HUMANS; HYDROGEN BONDING; KINETICS; MODELS, MOLECULAR; MUTATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEIN INTERACTION MAPPING; PROTEINS; PROTEOMICS; THERMODYNAMICS; TYROSINE;

EID: 29244487908     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-296     Document Type: Article

References (59)

1. Janin J & Wodak SJ. Structural basis for macromolecular recognition. In Protein modules and protein-protein interactions. Advances in protein chemistry. Harcourt publishers Ltd., 2002.
2. Russel 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., 2004, 14: 313-324.
3. Valencia A. & Pazos F. Computational methods for prediction of protein interactions. Curr. Opin. Struct. Biol., 2002, 12: 368-372.
4. Jones S. & Thornton J.M. Analysis and classification of protein-protein interactions from a structural perspective. In Protein-Protein Recognition (Kleanthous, C., ed.), Oxford University Press, Oxford, 2000.
5. Janin J. Kinetics and thermodynamics of protein-protein interactions. In Protein-Protein Recognition (Kleanthous, C., ed.), Oxford University Press, Oxford, 2000.
6. Smith G.R. & Sternberg M.J. Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol., 2002, 12: 28-35.
7. Glaser F., Steinberg D.M., Vakser I.A. & Ben-Tal N. Residue frequencies and pairing preferences at protein-protein interfaces. Proteins: Struct. Funct. Genet., 2001, 43: 89-102.
8. Lawrence M.C. & Colman P.M. Shape complementarity at protein/protein interfaces. J. Mol. Biol., 1993, 234: 946-950.
9. Gabb H. A. Jackson R. M. & Sternberg M. J. Modeling protein docking using shape complementarity, electrostatics and biochemical information. J. Mol. Biol., 1997, 272: 106-120.
10. Jones S. & Thornton J.M. Analysis of protein-protein interaction sites using surface patches. J. Mol. Biol., 1997, 272: 121-132.
11. Jones S. & Thornton J.M. Principles of protein-protein interactions. Proc. Natl. Acad. Sci. USA, 1996, 93: 13-20.
12. Miller S., Lesk A.M., Janin J. and Chothia C. The accessible surface area and stability of oligomeric proteins. Nature, 1987, 328: 834-836.
13. Lo Conte L., Chothia C. & Janin J. The atomic structure of protein-protein recognition sites. J. Mol. Biol., 1999, 285: 2177-2198.
14. Chakrabarti P, Janin J. Dissecting protein-protein recognition sites. Proteins: Struct. Funct. Genet., 2002, 47(3): 334-43.
15. Bahadur RP, Chakrabarti P, Rodier F, Janin J. Dissecting subunit interfaces in homodimeric proteins. Proteins: Struct. Funct. Genet., 2003, 53(3): 708-19.
16. Fernandez and H. A. Scheraga. Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc. Natl. Acad. Sci. USA, 2003, 100(1): 113-118.
17. Xu D., Tsai C. J. and Nussinov R. Hydrogen bonds and salt bridges across protein-protein interfaces. Protein Engg., 1997, 10: 999-1012.
18. Young L., Jernigan R.L. & Covell D.G. A role of surface hydrophobicity in protein-protein recognition. Protein Sci., 1994, 3: 717-729.
19. Tsai C.J., Lin S. L., Wolfson H. J. & Nussinov R. Study of protein-protein interfaces: a statistical analysis of the hydrophobic effect. Protein Sci., 1997, 6: 53-64.
20. Li Y., Huang Y., Swaminathan C.P., Smith-Gill S.J. & Mariuzza R.A. Magnitude of the hydrophobic effect at central versus peripheral sites in protein-protein interfaces. Structure, 2005, 13(2): 297-307.
21. Shanahan H.P. & Thornton J.M. Amino acid architecture and the distribution of polar atoms on the surfaces of proteins. Biopolymers, 2005, 78(6): 318-28.
22. Valdar W. S. J. & Thornton J. M. Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins: Struct. Funct. Genet., 2001, 42: 108-124.
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. Landgraf R., Xenarios I. and Eisenberg D. Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J. Mol. Biol., 2001, 307: 1487-1502.
25. Lichtarge O., Bourne H. R. & Cohen F. E. An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol., 1996, 257: 342-358.
26. Keskin O., Ma B. and Nussinov R. Hot regions in protein-protein interactions: the organization and contribution of structurally conserved hot spot residues. J. Mol. Biol., 2005, 345(5): 1281-94.
27. Bogan A. A. & Thorn K. S. Anatomy of hot spots in protein interfaces. J. Mol. Biol., 1998, 280(1): 1-9.
28. Kortemme T. & Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl. Acad. Sci. USA, 2002, 99: 14116-14121.
29. Ying G., Wang R. & Lai L. Structure based method for analyzing protein-protein interfaces. J. Mol. Model., 2004, 10(1): 44-54.
30. Haliloglu T., Keskin O. and Nussinov R. How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. Biophys. J., 2005, 88(3): 1552-9.
31. Ofran Y. & Rost B. Analyzing six types of protein-protein interfaces. J. Mol. Biol., 2003, 325: 377-387.
32. De S., Krishnadev O., Srinivasan N. & Rekha N. Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different. BMC Struct. Biol., 2005. [Epub ahead of print].
33. Bahadur R. P., Chakrabarti P., Rodier F. and Janin J. A dissection of specific and non-specific protein-protein interfaces. J. Mol. Biol., 2004, 336: 943-955.
34. Levy Y., Wolynes P. G. & Onuchic J. N. Protein topology determines binding mechanism. Proc. Natl. Acad. Sci. USA, 2004, 101(2): 511-516.
35. Janin J., Henrick K., Moult J., Eyck L. T., Sternberg M. J., Vajda S., Vakser I. & Wodak S. J. CAPRI: a Critical Assessment of PRedicted Interactions. Proteins: Struct. Funct. Genet., 2003, 52: 2-9.
36. Brinda K.V., Kannan N., Vishveshwara S. Analysis of homodimeric protein interfaces by graph-spectral methods. Protein Engg., 2002, 4: 265-77.
37. Del Sol A. & O'meara P. Small-world network approach to identify key residues in protein-protein interaction. Proteins: Struct. Funct. Bioinf., 2005, 58(3): 672-82.
38. Del Sol A., Fujihashi H. and O'meara P. Topology of small-world networks of protein-protein complex structures. Bioinformatics, 2005, 21(8): 1311-5.
39. Brinda K. V., Mitra N., Surolia A. & Vishveshwara S. Determinants of quaternary association in legume lectins. Protein Sci., 2004, 13: 1735-1749.
40. Kannan N., Preethi C., Ghosh P., Vishveshwara S. and Chatterji D. Stabilizing interactions in the dimer interface of α-subunit in Escherichia coli RNA polymerase: A graph spectral and point mutation study. Protein Sci., 2001, 10: 46-54.
41. Ramesh K. Sistla, Brinda K. V. and Saraswathi Vishveshwara. Identification of Domains and Domain Interface Residues in Multidomain Proteins from Graph Spectral Method, Proteins: Struct. Funct. Bioinfo., 2005, 59(3): 616-626.
42. Barabasi AL. Linked: The new science of networks. Persues Publishing, Cambridge, Massachusetts, 2002.
43. Vendruscolo M., Paci E., Dobson C.M. and Karplus M. Three key residues form a critical contact network in a protein folding transition state. Nature, 2001, 409: 641-645.
44. Vendruscolo M., Dokholyan N.V., Paci E. and Karplus M. Small-world view of the amino acids that play a key role in protein folding. Phys. Rev. E, 2002, 65: 061910.
45. Dokholyan N.V., Li L., Ding F. and Shakhnovich E.I. Topological determinants of protein folding. Proc. Natl. Acad. Sci. USA, 2002, 99(13): 8637-8641.
46. Atilgan A.R., Akan P. and Baysal C. Small-world communication of residues and significance for protein dynamics. Biophys. J., 2004, 86: 85-91.
47. Greene L.H. and Higman V.A. Uncovering network systems within protein structures. J. Mol. Biol., 2003, 334: 781-791.
48. Brinda K.V. and Vishveshwara S. A network representation of protein structures: implications to protein stability. Biophys. J., 2005, in press.
49. Sathyapriya R. and Vishveshwara S. Short hydrogen bonds in proteins. FEBS J., 2005, 272: 1819-1832.
50. Nooren I.M.A. and Thornton J.M. Structural characterization and functional significance of transient protein-protein interactions. J. Mol. Biol., 2003, 325: 991-1018.
51. Schnittman S.M., Lane H.C., Roth J., Burrows A., Folks T.M., Kehrl J.H., Koenig S., Berman P. and Fauci A.S. Characterization of GP120 binding to CD4 and an assay that measures ability of sera to inhibit this binding. J. Immunol. 1988, 141(12): 4181-6.
52. Lascols O., Cherqui G., Capeau J., Caron M. and Picard J. Alteration by concanavalin A of the slow dissociable component in the human growth hormone-receptor interaction. Horm. Metab. Res., 1986, 18(8): 512-6.
53. Thorn K.S. and Bogan A.A. ASEdb: A database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics, 2001, 17(3): 284-285.
54. Castro M.J. and Anderson S. Alanine point mutations in the reactive regions of bovine pancreatic trypsin inhibitor: effects on the kinetics and thermodynamics of binding to beta-trypsin and alpha-chymotrypsin. Biochemistry, 1996, 35(35): 11435-46.
55. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N. and Bourne P.E. The Protein Data Bank. Nucleic Acids Res., 2000, 28: 235-242.
56. Henrick K. & Thornton J.M. PQS: A protein quaternary structure file server. Trends in Biochem. Sci., 1998, 23(9): 358-61.
57. Hubbard S. J. NACCESS: program for calculating accessibilities. Department of Biochemistry and Molecular Biology. University college of London, 1992.
58. Kannan N. & Vishveshwara S. Identification of side-chain clusters in protein structures by a graph spectral method. J. Mol. Biol., 1999, 292 (2): 441-64.
59. West D.B. Introduction to Graph theory. Prentice-Hall of India Private Limited. 2000.