Exploiting protein structure data to explore the evolution of protein function and biological complexity

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 361, Issue 1467, 2006, Pages 425-440

  Marsden, Russell L ^a   Ranea, Juan A G ^a   Sillero, Antonio ^a   Redfern, Oliver ^a   Yeats, Corin ^a   Maibaum, Michael ^a   Lee, David ^a   Addou, Sarah ^a   Reeves, Gabrielle A ^a   Dallman, Timothy J ^a   Orengo, Christine A ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Evolution; Function; Genome analysis; Protein structure

Indexed keywords

BACTERIUM; COMPLEXITY; GENOME; METABOLISM; PROTEIN;

BACTERIA (MICROORGANISMS);

PROTEIN;

ALGORITHM; BIOLOGY; CHEMISTRY; FACTUAL DATABASE; METABOLISM; MOLECULAR EVOLUTION; PROTEIN CONFORMATION; REVIEW;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; EVOLUTION, MOLECULAR; PROTEIN CONFORMATION; PROTEINS;

EID: 33646348740     PISSN: 09628436     EISSN: None     Source Type: Journal    
DOI: 10.1098/rstb.2005.1801     Document Type: Article

References (84)

1. Alfarano, C. et al. 2005 The biomolecular interaction network database and related tools 2005 update. Nucleic Acids Res., D418-D424. 33 Database issue.
2. Aloy, P., Stark, A., Hadley, C. & Russell, R. B. 2003 Predictions without templates: new folds, secondary structure and contacts in CASP5. Proteins 53, 436-456. (doi:10.1002/prot.10546)
3. Andreeva, A., Howorth, D., Brenner, S. E., Hubbard, T. J., Chothia, C. & Murzin, A. G. 2004 SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res. 32, D226-D229. (doi:10.1093/nar/ gkh039)
4. Apic, G., Gough, J. & Teichmann, S. A. 2001 Domain combinations in archaeal, eubacterial and eukaryotic proteins. J. Mol. Biol. 310, 311-325. (doi:10.1006/jmbi. 2001.4776)
5. Apweiler, R. et al. 2004 UniProt: the universal protein knowledgebase. Nucleic Acids Res. 32, D115-D119. (doi:10.1093/nar/gkh131)
6. Bateman, A. et al. 2004 The Pfam protein families database. Nucleic Acids Res. 32, D138-141. (doi:10.1093/nar/gkh121)
7. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. & Wheeler, D. L. 2005 Genbank. Nucleic Acids Res. 33, D34-D38. (doi:10.1093/nar/gki063)
8. Bray, J. E., Marsden, R. L., Rison, S. C., Savchenko, A., Edwards, A. M., Thornton, J. & Orengo, C. A. 2004 A practical and robust sequence search strategy for structural genomics target selection. Bioinformatics 20, 2288-2295. (doi:10.1093/bioinformatics/bth240)
9. Brenner, S. E. 2001 A tour of structural genomics. Nat. Rev. Genet. 2, 801-809. (doi:10.1038/35093574)
10. Buchan, D. W., Shepherd, A. J., Lee, D., Pearl, F. M., Rison, S. C., Thornton, J. M. & Orengo, C. A. 2002 Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database. Genome Res. 12, 503-514. (doi:10.1101/gr.213802)
11. Burley, S. K. 2000 An overview of structural genomics. Nat. Rev. Genet. 2, 801-809.
12. Chothia, C. & Lesk, A. M. 1986 The relation between the divergence of sequence and structure in proteins. EMBO J. 5, 823-826.
13. Chothia, C., Gough, J., Vogel, C. & Teichmann, S. A. 2003 Evolution of the protein repertoire. Science 300, 1701-1703. (doi:10.1126/science.1085371)
14. Corpet, F., Servant, F., Gouzy, J. & Kahn, D. 2000 ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res. 28, 267-269. (doi:10.1093/nar/28.1.267)
15. Deshpande, N. et al. 2005 The RCSB protein data bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res. 33, D233-D237. (doi:10.1093/nar/gki057)
16. Durbin, R., Eddy, S., Krogh, A. & Mitchison, G. 1998 Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge, UK: Cambridge University Press.
17. Eddy, S. R. 1998 Profile hidden Markov models. Bioinformatics 14, 755-763. (doi:10.1093/bioinformatics/14.9.755)
18. Enright, A. J., Van Dongen, S. & Ouzounis, C. A. 2002 An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30, 1575-1584. (doi:10.1093/nar/30.7.1575)
19. Enright, A. J., Kunin, V. & Ouzounis, C. A. 2003 Protein families and TRIBES in genome sequence space. Nucleic Acids Res. 31, 4632-4638. (doi:10.1093/nar/gkg495)
20. Fleming, K., Muller, A., MacCallum, R. M. & Sternberg, M. J. 2004 3D GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes. Nucleic Acids Res. 32, D245-D250. (doi:10.1093/nar/gkh064)
21. Frishman, D. et al. 2003 The Pedant genome database. Nucleic Acids Res. 31, 207-211. (doi:10.1093/nar/gkg005)
22. Gibrat, J. F., Madej, T. & Bryant, S. H. 1996 Surprising similarities in structure comparison. Curr. Opin. Struct. Biol. 6, 377-385. (doi:10.1016/S0959-440X(96)80058-3)
23. Gough, J., Karplus, K., Hughey, R. & Chothia, C. 2001 Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J. Mol. Biol. 313, 903-919. (doi:10.1006/jmbi.2001.5080)
24. Grant, A., Lee, D. & Orengo, C. 2004 Progress towards mapping the universe of protein folds. Genome Biol. 5, 107. (doi:10.1186/gb-2004-5-5-107)
25. Griffiths-Jones, S. & Bateman, A. 2002 The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs. Bioinformatics 18, 1243-1249. (doi:10.1093/bioinformatics/18.9. 1243)
26. Harrison, A., Pearl, F., Mott, R., Thornton, J. & Orengo, C. 2002 Quantifying the similarities within fold space. J. Mol. Biol. 323, 909-926. (doi:10.1016/S0022-2836 (02)00992-0)
27. Horowitz, N. H. 1945 On the evolution of biochemical synthesis. Proc. Natl Acad. Sci. USA 31, 153-157.
28. Jensen, R. A. 1976 Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 30, 409-425. (doi:10. 1146/annurev.mi.30.100176.002205)
29. Jones, D. T. 1999 GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287, 797-815. (doi:10.1006/jmbi.1999.2583)
30. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y. & Hattori, M. 2004 The KEGG resources for deciphering the genome. Nucleic Acids Res. 32, D277-D280. (doi:10. 1093/nar/gkh063)
31. Karplus, K., Barrett, C. & Hughey, R. 1998 Hidden Markov models for detecting remote protein homologies. Bioinformatics 14, 846-856. (doi:10.1093/bioinformatics/14.10.846)
32. Kelley, L., MacCallum, R. & Sternberg, M. 2000 Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299, 499-522. (doi:10. 1006/jmbi.2000.3741)
33. Kolodny, R., Koehl, P. & Levitt, M. 2005 Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J. Mol. Biol. 346, 1173-1188. (doi:10.1016/j.jmb.2004.12.032)
34. Koonin, E. 2003 Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat. Rev. Microbiol. 1, 127-136. (doi:10.1038/ nrmicro751)
35. Koonin, E. V., Wolf, Y. I. & Karev, G. P. 2002 The structure of the protein universe and genome evolution. Nature 420, 218-223. (doi:10.1038/ nature01256)
36. Krause, A., Stoye, J. & Vingron, M. 2000 The SYSTERS protein sequence cluster set. Nucleic Acids Res. 28, 270-272. (doi:10.1093/nar/28.1.270)
37. Kurland, C. G., Canback, B. & Berg, O. G. 2003 Horizontal gene transfer: a critical view. Proc. Natl Acad. Sci. USA 100, 9658-9662. (doi:10.1073/pnas.1632870100)
38. Lee, D., Grant, A., Marsden, R. L. & Orengo, C. 2005 Identification and distribution of protein families in 120 completed genomes using Gene3D. Proteins Struct. Funct. Bioinform. 59, 603-615.
39. Liu, J. & Rost, B. 2001 Comparing function and structure between entire proteomes. Protein Sci. 10, 1970-1979. (doi:10.1110/ps.10101)
40. Madera, M., Vogel, C., Kummerfeld, S. K., Chothia, C. & Gough, J. 2004 The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res. 32, D235-D239. (doi:10.1093/nar/gkh117)
41. Marsden, R. L., Lee, D., Maibaum, M., Yeats, C. & Orengo, C. A. 2006 Comprehensive analysis of 203 structural genomics with provides structural genomics with new insights into protein family space. Nucleic Acids Res. Submitted.
42. McGuffin, L. J., Street, S., Sorensen, S. A. & Jones, D. T. 2004 The genomic threading database. Bioinformatics 20, 131-132. (doi:10.1093/ bioinformatics/btg387)
43. Mira, A., Ochman, H. & Moran, N. A. 2001 Deletion bias and the evolution of bacterial genomes. Trends Genet. 10, 589-596. (doi:10.1016/S0168- 9525(01)02447-7)
44. Mitchell, E. M., Artymiuk, P. J., Rice, D. & Willett, P. 1990 Use of techniques derived from graph theory to compare secondary structure motifs in proteins. J. Mol. Biol. 212, 151-166. (doi:10.1016/0022-2836(90)90312-A)
45. Mulder, N. J. et al. 2003 The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res. 31, 315-318. (doi:10.1093/nar/ gkg046)
46. Nagl, S. 2003 Profile based methods for sequence analysis. In Bioinformatics genes, proteins & computers (ed. C. A. Orengo, D. T. Jones & J. M. Thornton). Oxford, UK: BIOS.
47. Orengo, C. A. & Thornton, J. M. In press. Protein families and their evolution-a structural perspective.
48. Orengo, C. A., Flores, T. P., Taylor, W. R. & Thornton, J. M. 1993 Identification and classification of protein fold families. Protein Eng. 6, 485-500.
49. Orengo, C. A., Jones, D. T. & Thornton, J. M. 1994 Protein superfamilies and domain superfolds. Nature 372, 631-634. (doi:10.1038/372631a0)
50. Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells, M. B. & Thornton, J. M. 1997 CATH-a hierarchical classification of protein domain structures. Structure 5, 1093-1108. (doi:10.1016/S0969-2126(97)00260-8)
51. Orengo, C. A., Sillitoe, I., Reeves, G. & Pearl, F. M. 2001 Review: what can structural classifications reveal about protein evolution? J. Struct. Biol. 134, 145-165. (doi:10. 1006/jsbi.2001.4398)
52. Park, J., Karplus, K., Barrett, C., Hughey, R., Haussler, D., Hubbard, T. & Chothia, C. 1998 Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol. 284, 1201-1210. (doi:10.1006/jmbi.1998.2221)
53. Pearl, F. M. et al. 2001 A rapid classification protocol for the CATH domain database to support structural genomics. Nucleic Acids Res. 29, 223-227. (doi:10.1093/nar/29.1.223)
54. Pearl, F. et al. 2005 The CATH domain structure database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res. 33, D247-D251. (doi:10.1093/nar/gki024)
55. Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D. & Yeates, T. O. 1999 Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA 96, 4285-4288. (doi:10.1073/pnas.96.8.4285)
56. Ranea, J. A., Buchan, D. W., Thornton, J. M. & Orengo, C. A. 2004 Evolution of protein superfamilies and bacterial genome size. J. Mol. Biol. 336, 871-887. (doi:10.1016/j.jmb.2003.12.044)
57. Ranea, J. A., Buchan, D. W. A., Thornton, J. M. & Orengo, C. A. 2005 Factory economics can explain optimum genome size in bacteria. Trends Genet. 21, 21-25. (doi:10. 1016/j.tig.2004.11.014)
58. Redfern, O., Bennett, C. & Orengo, C. 2004 Structural classifications of proteins. In Bioinformatics encyclopaedia (ed. R. Apweiler). London: Wiley.
59. Redfern, O., Bennett, C. & Orengo, C. 2005 Survey of current protein family databases. J. Chromatogr. A 815, 97-107. (doi:10.1016/j.jchromb.2004.11. 010)
60. Reeves, G. A., Dallman, T., Redfern, O. & Orengo, C. A. In preparation. Structural diversity of domain superfamilies in the CATH database.
61. Rison, S., Teichmann, S. & Thornton, J. 2002 Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli. J. Mol. Biol. 318, 911-932. (doi:10.1016/S0022-2836(02) 00140-7)
62. Rost, B. 1997 Protein structures sustain evolutionary drift. Fold. Des. 2, S19-S24. (doi:10.1016/S1359-0278(97)00059-X)
63. Sali, A. 1998 100,000 protein structures for the biologist. Nat. Struct. Biol. 5, 1029-1032. (doi:10.1038/4136)
64. Salwinski, L., Miller, C. S., Smith, A. J., Pettit, F. K., Bowie, J. U. & Eisenberg, D. 2004 The database of interacting proteins: 2004 update. Nucleic Acids Res. 32, D449-D451. (doi:10.1093/nar/gkh086)
65. Sasson, O., Vaaknin, A., Fleischer, H., Portugaly, E., Bilu, Y., Linial, N. & Linial, M. 2003 ProtoNet: navigating the hierarchical clustering of the protein space. Nucleic Acids Res. 31, 348-352. (doi:10.1093/nar/gkg096)
66. Shindyalov, I. N. & Bourne, P. E. 1998 Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 11, 739-747. (doi:10.1093/protein/11.9.739)
67. Sillitoe, I. & Orengo, C. 2003 Protein structure comparison. In Bioinformatics genes, proteins & computers (ed. C. A. Orengo, D. T. Jones & J. M. Thornton). Oxford, UK: BIOS.
68. Sillitoe, I., Dibley, M., Bray, J., Addou, S. & Orengo, C. 2005 Assessing strategies for improved superfamily recognition. Protein Sci. 14, 1800-1810.
69. Tatusov, R. L. et al. 2001 The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29, 22-28. (doi:10.1093/nar/29.1.22)
70. Taylor, W. R. & Orengo, C. A. 1989 Protein structure alignment. J. Mol. Biol. 208, 1-22. (doi:10.1016/0022-2836(89)90084-3)
71. Teichmann, S. A. & Babu, M. M. 2004 Gene regulatory growth by duplication. Nat. Genet. 36, 492-496. (doi:10. 1038/ng1340)
72. Todd, A. E., Orengo, C. A. & Thornton, J. M. 2001 Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307, 1113-1143. (doi:10.1006/jmbi.2001.4513)
73. Todd, A. E., Orengo, C. A. & Thornton, J. M. 2002 Plasticity of enzyme active sites. Trends Biochem. Sci. 27, 419-426. (doi:10.1016/S0968- 0004(02)02158-8)
74. Todd, A. E., Marsden, R. L., Thornton, J. M. & Orengo, C. A. 2005 Progress of structural genomics initiatives: an analysis of solved target structures. J. Mol. Biol. 348, 1235-1260. (doi:10.1016/j.jmb.2005.03.037)
75. Van Dongen, S. 2000 Graph clustering by flow simulation. Ph.D. thesis, University of Utrecht. (http://www.library. uu.nl/digiarchief/dip/diss/1895620/ inhoud.htm)
76. Velankar, S., McNeil, P., Mittard-Runte, V., Suarez, A., Barrell, D., Apweiler, R. & Henrick, K. 2005 E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Res. 33, D262-D265. (doi:10.1093/nar/gki058)
77. Venter, J. C. et al. 2004 Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66-74. (doi:10.1126/science.1093857)
78. Vogel, C., Teichmann, S. A. & Chothia, C. 2003 The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity. Development 130, 6317-6328. (doi:10.1242/dev.00848)
79. Vogel, C., Bashton, M., Kerrison, N. D., Chothia, C. & Teichmann, S. A. 2004a Structure, function and evolution of multidomain proteins. Curr. Opin. Struct. Biol. 14, 208-216. (doi:10.1016/j.sbi.2004.03.011)
80. Vogel, C., Berzuini, C., Bashton, M., Gough, J. & Teichmann, S. A. 2004b Supra domains: evolutionary units larger than single domain protein domains. J. Mol. Biol. 336, 809-823. (doi:10.1016/j.jmb.2003.12.026)
81. Webb, E. C. 1992 Enzyme nomenclature, Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology. New York: Academic Press.
82. Woese, C. 1998 The universal ancestor. Proc. Natl Acad. Sci. USA 95, 6854-6859. (doi:10.1073/pnas.95.12.6854)
83. Yona, G. & Levitt, M. 2002 Within the twilight zone: a senstive profile-profile comparison tool based on information theory. J. Mol. Biol. 315, 1257-1275. (doi:10. 1006/jmbi.2001.5293)
84. Zanzoni, A., Montecchi-Palazzi, L., Quondam, M., Ausiello, G., Helmer-Citterich, M. & Cesareni, G. 2002 MINT: a Molecular INTeraction database. FEBS Lett. 513, 135-140. (doi:10.1016/S0014-5793(01)03293-8)