Evolution of oligomeric state through geometric coupling of protein interfaces

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 21, 2012, Pages 8127-8132

  Perica, Tina ^a   Chothia, Cyrus ^a   Teichmann, Sarah A ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

Homomeric complexes; Protein complex evolution; Protein geometry

Indexed keywords

BACTERIAL PROTEIN; INTERLEUKIN 8; OLIGOMER; PROTEIN PYRR; TRIOSEPHOSPHATE ISOMERASE; UNCLASSIFIED DRUG;

ALLOSTERISM; ARTICLE; COMPLEX FORMATION; GEOMETRY; HUMAN; MOLECULAR EVOLUTION; MYCOBACTERIUM; NONHUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION; THERMOTOGA MARITIMA;

AMINO ACID SEQUENCE; BACILLUS SUBTILIS; BACTERIA; BACTERIAL PROTEINS; CONSERVED SEQUENCE; DIMERIZATION; EVOLUTION, MOLECULAR; INTERLEUKIN-8; MODELS, CHEMICAL; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; MULTIPROTEIN COMPLEXES; MYCOBACTERIUM TUBERCULOSIS; PENTOSYLTRANSFERASES; PHYLOGENY; PROTEIN STRUCTURE, QUATERNARY; REPRESSOR PROTEINS; THERMOTOGA MARITIMA; TRIOSE-PHOSPHATE ISOMERASE;

EID: 84861450634     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1120028109     Document Type: Article

References (39)

1. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW (2002) Evolutionary rate in the protein interaction network. Science 296:750-752. (Pubitemid 34442006)
2. Chothia C, Janin J (1975) Principles of protein-protein recognition. Nature 256:705-708.
3. Janin J, Bahadur RP, Chakrabarti P (2008) Protein-protein interaction and quaternary structure. Q Rev Biophys 41:133-180.
4. Lo Conte L, Chothia C, Janin J (1999) The atomic structure of protein-protein recognition sites. J Mol Biol 285:2177-2198. (Pubitemid 29078179)
5. Nooren IMA, Thornton JM (2003) Diversity of protein-protein interactions. EMBO J 22:3486-3492. (Pubitemid 36898326)
6. Mintseris J,Weng Z (2005) Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci USA 102:10930-10935. (Pubitemid 41105970)
7. Levy ED (2010) A simple definition of structural regions in proteins and its use in analyzing interface evolution. J Mol Biol 403:660-670.
8. Clackson T, Wells JA (1995) A hot spot of binding energy in a hormone-receptor interface. Science 267:383-386.
9. Bogan A, Thorn K (1998) Anatomy of hot spots in protein interfaces. J Mol Biol 280:1-9. (Pubitemid 28312802)
10. Ma B, Elkayam T, Wolfson H, Nussinov R (2003) Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci USA 100:5772-5777. (Pubitemid 36576883)
11. Rajamani D, Thiel S, Vajda S, Camacho CJ (2004) Anchor residues in protein-protein interactions. Proc Natl Acad Sci USA 101:11287-11292. (Pubitemid 39038339)
12. Guharoy M, Chakrabarti P (2010) Conserved residue clusters at protein-protein interfaces and their use in binding site identification. BMC Bioinformatics 11:286.
13. Akiva E, Itzhaki Z, Margalit H (2008) Built-in loops allow versatility in domaindomain interactions: Lessons from self-interacting domains. Proc Natl Acad Sci USA 105:13292-13297.
14. Hashimoto K, Panchenko AR (2010) Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states. Proc Natl Acad Sci USA 107:20352-20357.
15. Teichmann SA (2002) The constraints protein-protein interactions place on sequence divergence. J Mol Biol 324:399-407.
16. Kim WK, Henschel A, Winter C, SchroederM (2006) The many faces of protein-protein interactions: A compendium of interface geometry. PLoS Comput Biol 2:e124.
17. Keskin O, Nussinov R (2005) Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways. Protein Eng Des Sel 18:11-24. (Pubitemid 40516987)
18. Zhang QC, Petrey D, Norel R, Honig BH (2010) Protein interface conservation across structure space. Proc Natl Acad Sci USA 107:10896-10901.
19. Dayhoff JE, Shoemaker BA, Bryant SH, Panchenko AR (2010) Evolution of protein binding modes in homooligomers. J Mol Biol 395:860-870.
20. Aloy P, Ceulemans H, Stark A, Russell RB (2003) The relationship between sequence and interaction divergence in proteins. J Mol Biol 332:989-998. (Pubitemid 37108793)
21. Han JH, Kerrison N, Chothia C, Teichmann SA (2006) Divergence of interdomain geometry in two-domain proteins. Structure 14:935-945.
22. Levy ED, Pereira-Leal JB, Chothia C, Teichmann SA (2006) 3D complex: a structural classification of protein complexes. PLoS Comput Biol 2:e155.
23. Kühner S, et al. (2009) Proteome organization in a genome-reduced bacterium. Science 326:1235-1240.
24. Levy ED, Boeri Erba E, Robinson CV, Teichmann SA (2008) Assembly reflects evolution of protein complexes. Nature 453:1262-1265. (Pubitemid 351913589)
25. Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536-540.
26. Chakrabarti P, Janin J (2002) Dissecting protein-protein recognition sites. Proteins 47:334-343. (Pubitemid 34438683)
27. Karanicolas J, et al. (2011) A de novo protein binding pair by computational design and directed evolution. Mol Cell 42:250-260.
28. Best RB, Lindorff-Larsen K, DePristo MA, Vendruscolo M (2006) Relation between native ensembles and experimental structures of proteins. Proc Natl Acad Sci USA 103:10901-10906. (Pubitemid 44148392)
29. Perica T, Chothia C (2010) Ubiquitin-molecular mechanisms for recognition of different structures. Curr Opin Struct Biol 20:367-376.
30. Maes D, et al. (1999) The crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima: A comparative thermostability structural analysis of ten different TIM structures. Proteins 37:441-453. (Pubitemid 29519733)
31. Mainfroid V, et al. (1996) Three hTIM mutants that provide new insights on why TIM is a dimer. J Mol Biol 257:441-456. (Pubitemid 26114045)
32. Cansu S, Doruker P (2008) Dimerization affects collective dynamics of triosephosphate isomerase. Biochemistry 47:1358-1368. (Pubitemid 351198712)
33. Turnbough CL, Jr, Switzer RL (2008) Regulation of pyrimidine biosynthetic gene expression in bacteria: repression without repressors. Microbiol Mol Biol Rev 72:266-300 table of contents.
34. Fernandez EJ, Lolis E (2002) Structure, function, and inhibition of chemokines. Annu Rev Pharmacol Toxicol 42:469-499. (Pubitemid 34160533)
35. de Lima Morais DA, et al. (2011) SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Res 39:D427-434.
36. Fleishman SJ, et al. (2011) Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 332:816-821.
37. Grueninger D, et al. (2008) Designed protein-protein association. Science 319:206-209.
38. Hardy JA, Wells JA (2009) Dissecting an allosteric switch in caspase-7 using chemical and mutational probes. J Biol Chem 284:26063-26069.
39. Lesk AM, ed. (1986) Integrated access to sequence and structural data. Biosequences: Perspectives and User Services in Europe pp 23-28.