Structure, function and evolution of multidomain proteins

Current Opinion in Structural Biology

Volumn 14, Issue 2, 2004, Pages 208-216

  Vogel, Christine ^a   Bashton, Matthew ^a   Kerrison, Nicola D ^a   Chothia, Cyrus ^a   Teichmann, Sarah A ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

PDB; Protein Data Bank; RMSD; Root mean square deviation; SCOP; SH; Src homology; Structural Classification of Proteins; WHD; Winged helix domain

Indexed keywords

AMINO TERMINAL SEQUENCE; CARBOXY TERMINAL SEQUENCE; GENOMICS; GEOMETRY; HUMAN; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW; SEQUENCE HOMOLOGY;

COMPUTER SIMULATION; EVOLUTION, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; SOFTWARE;

EID: 1842861592     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2004.03.011     Document Type: Review

References (68)

1. Murzin A.G., Brenner S.E., Hubbard T., Chothia C. SCOP - a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 247:1995;536-540.
2. Andreeva A., Howorth D., Brenner S.E., Hubbard T.J., Chothia C., Murzin A.G. SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res. 32:2004;D226-D229.
3. Chothia C. Proteins - 1000 families for the molecular biologist. Nature. 357:1992;543-544.
4. Orengo C.A., Jones D.T., Thornton J.M. Protein superfamilies and domain superfolds. Nature. 372:1994;631-634.
5. Coulson A.F., Moult J. A unifold, mesofold, and superfold model of protein fold use. Proteins. 46:2002;61-71.
6. Gough J., Karplus K., Hughey R., Chothia C. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol. 313:2001;903-919.
7. Madera M., Vogel C., Kummerfeld S.K., Chothia C., Gough J. The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res. 32:2004;D235-D239 The SUPERFAMILY database provides assignments of the over 1200 domain superfamilies, as defined in the SCOP database, to proteins using highly sensitive hidden Markov models. Close to 60% of all proteins have at least one match and one half of all residues are covered by assignments. The database is located at http://www.supfam.org and updated twice a year. SUPERFAMILY is now part of InterPro.
8. Kelley L.A., MacCallum R.M., Sternberg M.J. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol. 299:2000;499-520.
9. Buchan D.W., Rison S.C., Bray J.E., Lee D., Pearl F., Thornton J.M., Orengo C.A. Gene3D: structural assignments for the biologist and bioinformaticist alike. Nucleic Acids Res. 31:2003;469-473.
10. Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Barrell D., Bateman A., Binns D., Biswas M., Bradley P., Bork P.et al. The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res. 31:2003;315-318 InterPro is a metaserver that combines several domain assignment servers, including PRINTS, PROSITE, Pfam, ProDom, SMART, TIGRFAMs and also SUPERFAMILY, and integrates information on protein families, domains and functional sites.
11. Teichmann S.A., Park J., Chothia C. Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc Natl Acad Sci USA. 95:1998;14658-14663.
12. Gerstein M. How representative are the known structures of the proteins in a complete genome? A comprehensive structural census. Fold Des. 3:1998;497-512.
13. Lynch M., Conery J.S. The evolutionary fate and consequences of duplicate genes. Science. 290:2000;1151-1155.
14. Muller A., MacCallum R.M., Sternberg M.J. Structural characterization of the human proteome. Genome Res. 12:2002;1625-1641 This large-scale study of the human and three other eukaryote proteomes, as well as several bacterial and archaeal proteomes, focuses on domain superfamilies rather than whole proteins. The authors describe the duplication and expansion of specific domain superfamilies in the human genome compared with other organisms. They also discuss transmembrane and disease-related proteins, and domain superfamilies in the human genome.
15. Wolf Y.I., Karev G., Koonin E.V. Scale-free networks in biology: new insights into the fundamentals of evolution? Bioessays. 24:2002;105-109.
16. Qian J., Luscombe N.M., Gerstein M. Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. J Mol Biol. 313:2001;673-681.
17. Wuchty S. Scale-free behavior in protein domain networks. Mol Biol Evol. 18:2001;1694-1702.
18. Hill E., Broadbent I.D., Chothia C., Pettitt J. Cadherin superfamily proteins in Caenorhabditis elegans and Drosophila melanogaster. J Mol Biol. 305:2001;1011-1024.
19. Vogel C., Teichmann S.A., Chothia C. The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity. Development. 130:2003;6317-6328.
20. Chervitz S.A., Aravind L., Sherlock G., Ball C.A., Koonin E.V., Dwight S.S., Harris M.A., Dolinski K., Mohr S., Smith T.et al. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science. 282:1998;2022-2028.
21. Aravind L., Subramanian G. Origin of multicellular eukaryotes - insights from proteome comparisons. Curr Opin Genet Dev. 9:1999;688-694.
22. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W.et al. Initial sequencing and analysis of the human genome. Nature. 409:2001;860-921.
23. Kaessmann H., Zollner S., Nekrutenko A., Li W.H. Signatures of domain shuffling in the human genome. Genome Res. 12:2002;1642-1650.
24. Patthy L. Genome evolution and the evolution of exon-shuffling - a review. Gene. 238:1999;103-114.
25. Enright A.J., Iliopoulos I., Kyrpides N.C., Ouzounis C.A. Protein interaction maps for complete genomes based on gene fusion events. Nature. 402:1999;86-90.
26. Marcotte E.M., Pellegrini M., Thompson M.J., Yeates T.O., Eisenberg D. A combined algorithm for genome-wide prediction of protein function. Nature. 402:1999;83-86.
27. Snel B., Bork P., Huynen M. Genome evolution. Gene fusion versus gene fission. Trends Genet. 16:2000;9-11.
28. Yanai I, Wolf YI, Koonin EV: Evolution of gene fusions: horizontal transfer versus independent events. Genome Biol 2002, 3:research0024.
29. Apic G., Huber W., Teichmann S.A. Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination. J Struct Funct Genomics. 4:2003;67-78.
30. Vogel C, Berzuini C, Bashton M, Gough J, Teichmann SA: Supra-domains - evolutionary units larger than single protein domains. J Mol Biol 2004, in press.
31. Apic G., Gough J., Teichmann S.A. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol. 310:2001;311-325.
32. Liu Y, Gerstein M, Engelman DM: Evolutionary use of domain recombination: a distinction between membrane and soluble proteins. Proc Natl Acad Sci USA 2004, in press.
33. Park J., Lappe M., Teichmann S.A. Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J Mol Biol. 307:2001;929-938.
34. Harrison S.C. Variation on an Src-like theme. Cell. 112:2003;737-740 This review presents a good example of domains that reappear in different domain contexts: the SH3, SH2 and kinase domains recombine with various other domains in signal transduction multidomain proteins.
35. Pawson T., Nash P. Assembly of cell regulatory systems through protein interaction domains. Science. 300:2003;445-452 This review illustrates the modularity of proteins in a colourful manner. It describes the reuse of protein interaction domains, such as SH2 and SH3 domains and others, in the regulation of different cellular processes. The authors focus on the properties of single domains, but also point out the increase in dimensionality of functions and interactions when domains are combined to form multidomain proteins.
36. Chothia C., Gough J., Vogel C., Teichmann S.A. Evolution of the protein repertoire. Science. 300:2003;1701-1703.
37. Bashton M., Chothia C. The geometry of domain combination in proteins. J Mol Biol. 315:2002;927-939 This study presents a detailed analysis of the structures of proteins containing Rossmann fold domains in combination with other domain superfamilies. It demonstrates that, in all the cases studied, the N- to C-terminal order of the domains is conserved because the proteins have descended from a common ancestor. For pairs of proteins in the PDB in which the order is reversed, the interface and functional relationships of the domains are altered.
38. Coin L., Bateman A., Durbin R. Enhanced protein domain discovery by using language modeling techniques from speech recognition. Proc Natl Acad Sci USA. 100:2003;4516-4520 The technique presented in this paper formalises the use of domain associations for the improvement of domain assignment to protein sequences. In analogy to speech recognition methods that use context information to improve recognition of words, assignment of domains is improved using information on their domain combination context in multidomain proteins.
39. Hegyi H., Gerstein M. Annotation transfer for genomics: measuring functional divergence in multi-domain proteins. Genome Res. 11:2001;1632-1640.
40. Aloy P., Russell R.B. Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA. 99:2002;5896-5901 The authors describe a method to assess the likelihood of an interface forming between two proteins when the components are modelled on complexes of known structure.
41. Prabu M.M., Suguna K., Vijayan M. Variability in quaternary association of proteins with the same tertiary fold: a case study and rationalization involving legume lectins. Proteins. 35:1999;58-69.
42. Spahn C.M., Beckmann R., Eswar N., Penczek P.A., Sali A., Blobel G., Frank J. Structure of the 80S ribosome from saccharomyces cerevisiae - tRNA-ribosome and subunit-subunit interactions. Cell. 107:2001;373-386.
43. Beckmann R., Spahn C.M., Eswar N., Helmers J., Penczek P.A., Sali A., Frank J., Blobel G. Architecture of the protein-conducting channel associated with the translating 80S ribosome. Cell. 107:2001;361-372.
44. Aloy P., Ciccarelli F.D., Leutwein C., Gavin A.C., Superti-Furga G., Bork P., Bottcher B., Russell R.B. A complex prediction: three-dimensional model of the yeast exosome. EMBO Rep. 3:2002;628-635.
45. Aloy P., Ceulemans H., Stark A., Russell R.B. The relationship between sequence and interaction divergence in proteins. J Mol Biol. 332:2003;989-998 Using RMSD as a simple measure to compare interactions between domains, the authors found that homologues with more than 30% sequence identity usually conserve the geometry of their interaction.
46. Serres M.H., Goswami S., Riley M. GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins. Nucleic Acids Res. 32:2004;D300-D302.
47. Harris M.A., Clark J., Ireland A., Lomax J., Ashburner M., Foulger R., Eilbeck K., Lewis S., Marshall B., Mungall C.et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32:2004;D258-D261.
48. Mewes H.W., Amid C., Arnold R., Frishman D., Guldener U., Mannhaupt G., Munsterkotter M., Pagel P., Strack N., Stumpflen V.et al. MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res. 32:2004;D41-D44.
49. Tatusov R.L., Fedorova N.D., Jackson J.D., Jacobs A.R., Kiryutin B., Koonin E.V., Krylov D.M., Mazumder R., Mekhedov S.L., Nikolskaya A.N.et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 4:2003;41.
50. Bairoch A. The ENZYME database in 2000. Nucleic Acids Res. 28:2000;304-305.
51. Todd A.E., Orengo C.A., Thornton J.M. Evolution of protein function, from a structural perspective. Curr Opin Chem Biol. 3:1999;548-556.
52. Todd A.E., Orengo C.A., Thornton J.M. Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol. 307:2001;1113-1143.
53. Bartlett G.J., Borkakoti N., Thornton J.M. Catalysing new reactions during evolution: economy of residues and mechanism. J Mol Biol. 331:2003;829-860 A detailed analysis of catalytic sites and residues in homologous enzymes of different function reveals the economy of evolution: the residue types, functions and mechanistic steps are frequently conserved.
54. Brenner S.E. Target selection for structural genomics. Nat Struct Biol. 7(suppl):2000;967-969.
55. Kriventseva E.V., Koch I., Apweiler R., Vingron M., Bork P., Gelfand M.S., Sunyaev S. Increase of functional diversity by alternative splicing. Trends Genet. 19:2003;124-128.
56. Lespinet O., Wolf Y.I., Koonin E.V., Aravind L. The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 12:2002;1048-1059.
57. Letunic I., Goodstadt L., Dickens N.J., Doerks T., Schultz J., Mott R., Ciccarelli F., Copley R.R., Ponting C.P., Bork P. Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 30:2002;242-244.
58. Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S.R., Griffiths-Jones S., Howe K.L., Marshall M., Sonnhammer E.L. The Pfam protein families database. Nucleic Acids Res. 30:2002;276-280.
59. Geer L.Y., Domrachev M., Lipman D.J., Bryant S.H. CDART: protein homology by domain architecture. Conserved Domain Architecture Retrieval Tool. Genome Res. 12:2003;1619-1623.
60. Marchler-Bauer A., Panchenko A.R., Shoemaker B.A., Thiessen P.A., Geer L.Y., Bryant S.H. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res. 30:2002;281-283.
61. Pohl E., Holmes R.K., Hol W.G. Crystal structure of the iron-dependent regulator (IdeR) from Mycobacterium tuberculosis shows both metal binding sites fully occupied. J Mol Biol. 285:1999;1145-1156.
62. Pohl E., Goranson-Siekierke J., Choi M.K., Roosild T., Holmes R.K., Hol W.G. Structures of three diphtheria toxin repressor (DtxR) variants with decreased repressor activity. Acta Crystallogr. 57:2001;619-627.
63. 2+ reveals mechanism of antibiotic resistance. J Mol Biol. 247:1995;260-280.
64. Schumacher M.A., Miller M.C., Grkovic S., Brown M.H., Skurray R.A., Brennan R.G. Structural mechanisms of QacR induction and multidrug recognition. Science. 294:2001;2158-2163.
65. Xu Y., Heath R.J., Li Z., Rock C.O., White S.W. The FadR.DNA complex. Transcriptional control of fatty acid metabolism in Escherichia coli. J Biol Chem. 276:2001;17373-17379.
66. Wah D.A., Hirsch J.A., Dorner L.F., Schildkraut I., Aggarwal A.K. Structure of the multimodular endonuclease FokI bound to DNA. Nature. 388:1997;97-100.
67. Liu S., Widom J., Kemp C.W., Crews C.M., Clardy J. Structure of human methionine aminopeptidase-2 complexed with fumagillin. Science. 282:1998;1324-1327.
68. Boeckmann B., Bairoch A., Apweiler R., Blatter M.C., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O'Donovan C., Phan I.et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31:2003;365-370.