Protein families and their evolution - A structural perspective

Annual Review of Biochemistry

Volumn 74, Issue , 2005, Pages 867-900

  Orengo, Christine A ^a   Thornton, Janet M ^b  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

Bioinformatics; Comparative genomics; Protein classifications

Indexed keywords

GENOMIC DNA;

BACTERIUM; BIOINFORMATICS; COMPARATIVE GENOMIC HYBRIDIZATION; EUKARYOTE; GENE SEQUENCE; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN STRUCTURE; REVIEW; STRUCTURE ANALYSIS;

ANIMALS; BACTERIAL PROTEINS; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; GENOME; HUMANS; IMMUNOGLOBULINS; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; PROTEOME;

EID: 22244450719     PISSN: 00664154     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biochem.74.082803.133029     Document Type: Review

References (107)

1. Apic G, Gough J, Teichmann SA. 2001. J. Mol. Biol. 310:311-25
2. Chothia C, Gough J, Vogel C, Teichmann SA. 2003. Science 300:1701-3
3. Vogel C, Bashton M, Kerrison ND, Chothia C, Teichmann SA. 2004. Curr. Opin. Struct. Biol. 14:208-16
4. Lee D, Grant A, Buchan D, Orengo CA. 2003. Curr. Opin. Struct. Biol. 13:359-69
5. Chothia C, Lesk AM. 1986. EMBO J. 5:823-26
6. Orengo CA, Sillitoe I, Reeves G, Pearl FM. 2001. J. Struct. Biol. 134:145-65
7. Redfern O, Bennett C, Orengo CA. 2005. In Bioinformatics Encyclopaedia, ed. R Apweiler. New York: Wiley
8. Orengo CA. 1999. Protein Sci. 8:699-715
9. Redfern O, Grant A, Maibaum M, Orengo CA. 2005. J. Chromotogr. B 815:97-107
10. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, et al. 2003. Nucleic Acids Res. 31:315-18
11. Vogel C, Teichmann SA, Chothia C. 2004. Development 130:6317-28
12. Ranea JA, Buchan DW, Thornton JM, Orengo CA. 2004. J. Mol. Biol. 336:871-87
13. Ranea JAG, Buchan DWA, Thornton JM, Orengo CA. 2005. Trends Genet. 21:21-25
14. 13a. Dayhoff MO, ed. 1965. Atlas of Protein Sequence and Structure. Washington, DC: Natl. Biomed. Res. Foundation
15. Branden C, Tooze J. 1991. In Introduction to Protein Structure. New York/London: Garland
16. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. 1997. Structure 5:1093-108
17. Murzin AG, Brenner SE, Hubbard T, Chothia C. 2000. J. Mol. Biol. 247:536-40
18. Todd A. 2003. In Bioinformatics: Genes, Proteins and Computers, ed. CA Orengo, DT Jones, JM Thornton, eds, pp. 151-74. Oxford, UK: BIOS
19. Needleman SB, Wunsch CD. 1970. J. Mol. Biol. 48:443-53
20. Smith TF, Waterman MS. 1981. J. Mol. Biol. 147:195-97
21. Orengo CA. 2003. See Ref. 17, pp. 29-48
22. Pearson WR, Lipman DJ. 1988. Proc. Natl. Acad. Sci. USA 85:2444-48
23. Altschul SF, Madden TL, Schärfer AA, Zhang J, Zhang Z, et al. 1997. Nucleic Acids Res. 25:3389-402
24. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. 2000. Nucleic Acids Res. 28:235-42
25. 23a. Feng DF, Doolittle RF. 1996. Methods Enzymol. 266:368-82
26. Nagl S. 2003. See Ref. 17, pp. 65-79
27. Altschul S. 2001. Nucleic Acids Res. 29:2994-3005
28. Attwood TK, Bradley P, Flower DR, Gaulton A, Maudling N, et al. 2003. Nucleic Acids Res. 31:400-2
29. Eddy SR. 1998. Bioinformatics 14:755-63
30. Karplus K, Barrett C, Hughey R. 1998. Bioinformatics 14:846-56
31. Gough J, Karplus K, Hughey R, Chothia C. 2001. J. Mol. Biol. 313:903-19
32. Jones DT, Taylor WR, Thornton JM. 1992. Nature 358:86-89
33. Bowie JU, Luthy R, Eisenberg D. 1991. Science 253:164-70
34. Jones DT. 2003. See Ref. 17, pp. 135-150
35. McGuffin LJ, Street S, Sorensen SA, Jones DT. 2004. Bioinformatics 20:131-32
36. Fleming K, Muller A, MacCallum RM, Sternberg MJ. 2004. Nucleic Acids Res. 32:D245-50
37. Pawlowski K, Rychlewski L, Zhang B, Godzik A. 2001. J. Struct. Biol. 134:219-31
38. Park J, Karplus K, Barrett C, Hughey R, Haussler D, et al. 1998. J. Mol. Biol. 284:1201-10
39. Sillitoe I, Orengo C. 2003. See Ref. 17, pp. 81-101
40. Taylor WR, Orengo CA. 1989. J. Mol. Biol. 208:1-22
41. Sali A, Blundell TL. 1990. J. Mol. Biol. 212:403-28
42. Holm L, Sander C. 1993. J. Mol. Biol. 233:123-38
43. Russell RB, Barton GJ. 1992. Proteins 14:309-23
44. Mitchell EM, Artymiuk PJ, Rice DW, Willett P. 1990. J. Mol. Biol. 212:151-66
45. Harrison A, Pearl F, Mott R, Thornton J, Orengo CA. 2002. J. Mol. Biol. 323:909-26
46. Krissinel E, Henrick K. 2003. Proc. Int. Conf. Mol. Struct. Biol., Vienna, 5th, Sept. 3-7, ed. AJ Kungl, PJ Kungl, p. 88
47. Shindyalov IN, Bourne PE. 1998. Proton Eng. 11:739-47
48. Jones S, Stewart M, Michie AD, Swindells M, Orengo CA, Thornton JM. 1997. Protein Sci. 7:233-42
49. Holm L, Sander C. 1994. Proteins 19:256-68
50. Swindells MB. 1995. Protein Sci. 4:103-12
51. Siddiqui AS, Barton GJ. 1995. Protein Sci. 4:872-84
52. Taylor WR. 1999. Protein Eng. 12:203-16
53. Wernisch L, Hunting M, Wodak SJ. 1999. Proteins 35:338-52
54. Dietmann S, Park J, Notredame C, Heger A, Lappe M, Holm L. 2001. Nucleic Acids Res. 29:55-57
55. Madej T, Gibrat JF, Bryant SH. 1995. Proteins 23:356-69
56. Liu J, Rost B. 2004. Proteins 55:678-88
57. Heger A, Holm L. 2003. J. Mol. Biol. 328:749-67
58. Enright AJ, Ouzounis CA. 2000. Bioinformatics 16:451-57
59. Lee D, Grant A, Marsden R, Orengo CA. 2005. Proteins. In press
60. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, et al. 2004. Nucleic Acids Res. 32:D138-41
61. Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, et al. 2004. Nucleic Acids Res. 32:D142-44
62. Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, et al. 2001. Nucleic Acids Res. 29:41-43
63. Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. 2004. Nucleic Acids Res. 32:D226-29
64. Pearl FM, Bennett CF, Bray JE, Harrison AP, Martin N, et al. 2003. Nucleic Acids Res. 31:D452-55
65. Orengo CA, Jones DT, Thornton JM. 1994. Nature 372:631-34
66. Brenner SE, Chothia C, Hubbard TJ. 1997. Curr. Opin. Struct. Biol. 7:369-76
67. Pearl F, Orengo CA. 2003. See Ref. 17, pp. 102-19
68. Shakhnovich B, Dokholyan N, DeLisi C, Shakhnovich E. 2003. J. Mol. Biol. 326:1-9
69. Nagano N, Orengo CA, Thornton JM. 2002. J. Mol. Biol. 321:741-65
70. Lupas AN, Ponting CP, Russell RB. 2001. J. Struct. Biol. 134:191-203
71. Grishin NV. 2001. J. Struct. Biol. 134:167-85
72. Koppensteiner WA, Lackner P, Wiederstein M, Sippl M. 2000. J. Mol. Biol. 296:1139-52
73. Hadley C, Jones DT. 1999. Struct. Fold Des. 7:1099-112
74. Chothia C. 1992. Nature 357:543-44
75. Coulson AFW, Moult J. 2002. Proteins 46:61-71
76. Wolf EI, Grishin NV, Koonin EV. 2000. J. Mol. Biol. 299:897-905
77. Zhang C, DeLisi C. 1998. J. Mol. Biol. 284:1301-5
78. Grant A, Lee D, Orengo CA. 2004. Genome Biol. 5:107
79. Yang S, Doolittle R, Bourne PE. 2004. Inst. Struct. Mol. Biol., July 29-30, Glasgow, UK
80. Koonin E. 2003. Nat. Rev. Microbiol. 1:127-36
81. Abeln S, Deane CM. 2004. Inst. Struct. Mol. Biol., July 29-30, Glasgow, UK
82. Enright AJ, Kunin V, Ouzounis CA. 2003. Nucleic Acids Res. 31:4632-38
83. Krause A, Vingron M. 1998. Bioinformatics 14:430-38
84. Sasson O, Vaaknin A, Fleischer H, Portugaly E, Bilu Y, et al. 2003. Nucleic Acids Res. 31:348-52
85. Tatusov RL, Koonin EV, Lipman DJ. 1997. Science 278:631-37
86. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, et al. 2003. BMC Bioinform. 4:41
87. Rost B. 2002. Curr. Opin. Struct. Biol. 12:409-16
88. Todd AE, Orengo CA, Thornton JM. 2001. J. Mol. Biol. 307:1113-43
89. Deleted in proof
90. Todd AE, Orengo CA, Thornton JM. 2002. Trends Biochem. Sci. 27:419-26
91. Devos D, Valencia A. 2000. Proteins 41:98-107
92. Todd A. 2003. See Ref. 17, pp. 151-74
93. Todd A. 2004. In Proteomics Protocols Handbook, ed. J Walker, pp. 805-34. Totowa, NJ: Humana
94. Vogel C, Berzuini C, Bashton M, Gough J, Teichmann S. 2004. J. Mol. Biol. 336:809-23
95. Bashton M, Chothia C. 2002. J. Mol. Biol. 315:927-39
96. Rison S, Teichmann S, Thornton J. 2002. J. Mol. Biol. 318:911-32
97. Alves R, Chaleil R, Sternberg M. 2002. J. Mol. Biol. 320:751-70
98. Horowitz NH. 1945. Proc. Natl. Acad. Sci. USA 31:153-57
99. Jensen RA. 1976. Annu. Rev. Microbiol. 30:409-25
100. Bork P, Orengo C. 2004. Curr. Opin. Struct. Biol. 14:261-63
101. Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA. 2004. Curr. Opin. Struct. Biol. 14:283-91
102. Teichmann SA, Babu MM. 2004. Nat. Genet. 36:492-96
103. Woese C. 2002. Proc. Natl. Acad. Sci. USA 99:8742-47
104. Thornton J. 2003. See Ref. 17, pp. XIII-XIV
105. Rufino SD, Blundell TL. 1994. J. Comput. Aided Mol. Des. 8:5-27
106. Huynen MA, van Nimwegen E. 1998. Mol. Biol. Evol. 15:583-89
107. Quian J, Luscombe NM, Gerstein M. 2001. J. Mol. Biol. 313:673-81