A PDB-wide, evolution-based assessment of protein-protein interfaces

BMC Structural Biology

Volumn 14, Issue 1, 2014, Pages

  Baskaran, Kumaran ^a   Duarte, Jose M ^a,b   Biyani, Nikhil ^a   Bliven, Spencer ^a,c,d   Capitani, Guido ^a  

^a PAUL SCHERRER INSTITUTE   (Switzerland)

^b ETH ZURICH   (Switzerland)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Biological interfaces; Crystal contacts; EPPIC; PDB; PISA; Protein protein interfaces

Indexed keywords

DIMER; PROTEIN; PROTEIN BINDING;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; ERROR; MEASUREMENT ACCURACY; MOLECULAR EVOLUTION; NUCLEAR MAGNETIC RESONANCE; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN DATA BANK; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION; PROTEIN PROTEIN INTERFACE; PROTEIN STRUCTURE; SENSITIVITY AND SPECIFICITY; SOFTWARE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CONSERVED SEQUENCE; METABOLISM; PROCEDURES; PROTEIN SECONDARY STRUCTURE;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 84988711021     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/s12900-014-0022-0     Document Type: Article

References (22)

1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The protein data bank. Nucleic Acids Res 2000, 28:235-242, [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=102472&tool=pmcentrez&rendertype=abstract]
2. Schärer Ma, Grütter MG, Capitani G: CRK: An evolutionary approach for distinguishing biologically relevant interfaces fromcrystal contacts. Proteins: Struct Funct Bioinformatics 2010, [http://doi.wiley.com/10.1002/prot.22787]
3. Duarte JM, Srebniak A, Schärer Ma, Capitani G: Protein interface classification by evolutionary analysis. BMC Bioinformatics 2012, 13:334, [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid= 3556496&tool=pmcentrez&rendertype=abstract]
4. Duarte JM, Biyani N, Baskaran K, Capitani G: An analysis of oligomerization interfaces in transmembrane proteins. BMC Struct Biol 2013, 13:21. [http://www.ncbi.nlm.nih.gov/pubmed/24134166]
5. Ivan G, Szabadka Z, Grolmusz V: A hybrid clustering of protein binding sites. Febs J 2010, 277(6):1494-1502. [http://www.ncbi.nlm.nih.gov/pubmed/20148971]
6. Janin J: Specific versus non-specific contacts in protein crystals. Nat Struct Biol 1997, [http://ukpmc.ac.uk/abstract/MED/9406542]
7. The UniProt Consortium: Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res 2013, 41(Database issue):D43-7, [http://www.ncbi.nlm.nih.gov/pubmed/23161681]
8. Ponstingl H, Kabir T, Thornton JM: Automatic inference of protein quaternary structure from crystals. J Appl Cryst 2003, 36(5):1116-1122, [http://scripts.iucr.org/cgi-bin/paper?S0021889803012421]
9. Krissinel E, Henrick K: Inference of macromolecular assemblies from crystalline state. JMol Biol 2007, [http://www.sciencedirect.com/science/article/pii/S0022283607006420]
10. Xu Q, Canutescu Aa, Wang G, Shapovalov M, Obradovic Z, Dunbrack RL: Statistical analysis of interface similarity in crystals of homologous proteins. JMol Biol 2008, 381(2):487-507, [http://www.pubmedcentral. nih.gov/articlerender.fcgi?artid=2573399&tool=pmcentrez&rendertype= abstract]
11. Xu Q, Dunbrack RL: The protein common interface database (ProtCID)-a comprehensive database of interactions of homologous proteins in multiple crystal forms. Nucleic Acids Res 2011, 39(Database issue):D761-70, [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3013667&tool=pmcentrez&rendertype=abstract]
12. Monod J, Wyman J, Changeux JP: On the nature of allosteric transitions: A plausiblemodel. JMol Biol 1965, 12:88-118, [http://linkinghub.elsevier.com/retrieve/pii/S0022283665802856]
13. Levy ED, Teichmann S: Structural, evolutionary, and assembly principles of protein oligomerization. Prog Mol Biol Transl Sci 2013, 117:25-51, [http://dx.doi.org/10.1016/B978-0-12-386931-9.00002-7]
14. Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, McCoy A, et al.: Overview of the CCP4 suite and current developments. Acta Crystallogr Section D: Biol Crystallogr 2011, 67(4):235-242.
15. Krissinel E: Macromolecular complexes in crystals and solutions. Acta Crystallogr Section D 2011, 67(4):376-385, [http://dx.doi.org/10.1107/S0907444911007232]
16. Bahadur RP, Chakrabarti P, Rodier F, Janin J: A dissection of specific and non-specific protein-protein interfaces. JMol Biol 2004, 336(4):943-955.
17. Dauter Z, Wlodawer A, Minor W, Jaskolski M, Rupp B: Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining. IUCrJ 2014, 1(3):179-193, [http://dx.doi.org/10.1107/S2052252514005442]
18. Levy ED, Pereira-Leal JB, Chothia C, Teichmann SA: 3D Complex: A structural classification of protein complexes. PLoS Comput Biol 2006, 2(11):e155, [http://dx.plos.org/10.1371%2Fjournal.pcbi.0020155]
19. Levy ED: PiQSi: protein quaternary structure investigation. Struct (London, England: 1993) 2007, 15(11):1364-7, [http://www.ncbi.nlm.nih.gov/pubmed/17997962]
20. Poupon A, Janin J: Analysis and prediction of protein quaternary structure. Methods Mol Biol Clifton Nj 2010, 609:349-364, [http://www.springerlink.com/index/10.1007/978-1-60327-241-4-20]
21. Banatao DR, Cascio D, Crowley CS, Fleissner MR, Tienson HL, Yeates TO: An approach to crystallizing proteins by synthetic symmetrization. Proc Nat Acad Sci USA 2006, 103(44):16230-16235, [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1637565&tool= pmcentrez&rendertype=abstract] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1637565/]
22. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucliec Acids Res 1997, 25(17):3389-3402, [http://dx.doi.org/10.1093/nar/25.17.3389]