Structural interface parameters are discriminatory in recognising near-native poses of protein-protein interactions

PLoS ONE

Volumn 9, Issue 2, 2014, Pages

  Malhotra, Sony ^a   Sankar, Kannan ^a   Sowdhamini, Ramanathan ^a  

^a TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

HETERODIMER; HOMODIMER; PROTEIN; PROTEIN BINDING;

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; DIMERIZATION; HYDROPHOBICITY; MOLECULAR DOCKING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SCORING SYSTEM; SURFACE PROPERTY; CHEMISTRY; METABOLISM; PRINCIPAL COMPONENT ANALYSIS; PROTEIN MULTIMERIZATION; PROTEIN TERTIARY STRUCTURE;

ALGORITHMS; MOLECULAR DOCKING SIMULATION; PRINCIPAL COMPONENT ANALYSIS; PROTEIN BINDING; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 84895485085     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0080255     Document Type: Article

References (27)

1. Sali A, Glaeser R, Earnest T, Baumeister W (2003) From words to literature in structural proteomics. Nature 422: 216-225. doi:10.1038/ nature01513. (Pubitemid 36362759)
2. Makino S, Kuntz ID (1997) Automated flexible ligand docking method and its application for database search. Journal of Computational Chemistry 18: 1812-1825. doi:10.1002/(SICI)1096-987X(19971115)18:14〈1812::AID- JCC10〉3.0.CO;2-H.
3. Sousa SF, Fernandes PA, Ramos MJ (2006) Protein-ligand docking: current status and future challenges. Proteins 65: 15-26. doi:10.1002/prot.21082. (Pubitemid 44320611)
4. Chen R, Li L, Weng Z (2003) ZDOCK: an initial-stage protein-docking algorithm. Proteins 52: 80-87. (Pubitemid 36648854)
5. Garzon JI, Lopéz-Blanco JR, Pons C, Kovacs J, Abagyan R, et al. (2009) FRODOCK: a new approach for fast rotational protein-protein docking. Bioinformatics 25: 2544-2551. doi:10.1093/bioinformatics/btp447.
6. Tovchigrechko A, Vakser IA (2006) GRAMM-X public web server for protein-protein docking. Nucleic Acids Research 34: W310-W314. doi:10.1093/nar/gkl206. (Pubitemid 44529784)
7. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267: 727-748. doi:10.1006/jmbi.1996.0897. (Pubitemid 27170693)
8. Duan Y, Reddy BVB, Kaznessis YN (2005) Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions. Protein science 14: 316-328. (Pubitemid 40194583)
9. Gottschalk K-E, Neuvirth H, Schreiber G (2004) A novel method for scoring of docked protein complexes using predicted protein-protein binding sites. Protein Eng Des Sel 17: 183-189. doi:10.1093/protein/gzh021. (Pubitemid 38477745)
10. Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, et al. (1992) Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proceedings of the National Academy of Sciences 89: 2195-2199.
11. Xue LC, Jordan RA, El-Manzalawy Y, Dobbs D, Honavar V (2013) DockRank: ranking docked conformations using partner-specific sequence homology based protein interface prediction. Proteins. doi:10.1002/prot.24370.
12. Bahadur RP, Chakrabarti P, Rodier F, Janin J (2003) Dissecting subunit interfaces in homodimeric proteins. Proteins 53: 708-719. doi:10.1002/prot. 10461. (Pubitemid 37352183)
13. Zhanhua C, Gan JG-K, Lei L, Sakharkar MK, Kangueane P (2005) Protein subunit interfaces: heterodimers versus homodimers. Bioinformation 1: 28-39.
14. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Research 28: 235-242. doi:10.1093/nar/28.1.235. (Pubitemid 30047768)
15. Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res 38: W529-W533. doi:10.1093/nar/gkq399.
16. Alva V, Syamala Devi DP, Sowdhamini R (2008) COILCHECK: an interactive server for the analysis of interface regions in coiled coils. Protein Pept Lett 15: 33-38. (Pubitemid 351206473)
17. Tsai CJ, Nussinov R (1997) Hydrophobic folding units at protein-protein interfaces: implications to protein folding and to protein-protein association. Protein Sci 6: 1426-1437. doi:10.1002/pro.5560060707.
18. Tsai CJ, Lin SL, Wolfson HJ, Nussinov R (1996) Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences. Crit Rev Biochem Mol Biol 31: 127-152. doi:10.3109/10409239609106582. (Pubitemid 26138958)
19. Tsai CJ, Lin SL, Wolfson HJ, Nussinov R (1997) Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect. Protein Sci 6: 53-64. (Pubitemid 27045243)
20. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J Chem Theory Comput 4: 435-447. doi:10.1021/ct700301q.
21. Yang Y, Zhou Y (2008) Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions. Protein Sci 17: 1212-1219. doi:10.1110/ps.033480.107. (Pubitemid 351930918)
22. Mashiach E, Schneidman-Duhovny D, Andrusier N, Nussinov R, Wolfson HJ (2008) FireDock: a web server for fast interaction refinement in molecular docking. Nucleic Acids Res 36: W229-232. doi:10.1093/nar/gkn186.
23. Ho Y-SJ, Burden LM, Hurley JH (2000) Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor. The EMBO Journal 19: 5288-5299. doi:10.1093/emboj/19.20.5288.
24. Martinez SE, Bruder S, Schultz A, Zheng N, Schultz JE, et al. (2005) Crystal structure of the tandem GAF domains from a cyanobacterial adenylyl cyclase: modes of ligand binding and dimerization. Proc Natl Acad Sci USA 102: 3082-3087. doi:10.1073/pnas.0409913102. (Pubitemid 40299919)
25. Martinez SE, Wu AY, Glavas NA, Tang X-B, Turley S, et al. (2002) The two GAF domains in phosphodiesterase 2A have distinct roles in dimerization and in cGMP binding. Proc Natl Acad Sci USA 99: 13260-13265. doi:10.1073/pnas. 192374899.
26. Jung HJ, Kim S, Kim YJ, Kim M-K, Kang SG, et al. (2012) Dissection of the dimerization modes in the DJ-1 superfamily. Mol Cells 33: 163-171. doi:10.1007/s10059-012-2220-6.
27. Lobanov MY, Shoemaker BA, Garbuzynskiy SO, Fong JH, Panchenko AR, et al. (2009) ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder. Nucleic Acids Research 38: Issue Suppl. 1 D283-D287.