Protein domain organisation: Adding order

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Kummerfeld, Sarah K ^a,b   Teichmann, Sarah A ^b  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DEGREE OF CLUSTERING; FUNCTIONAL RELATIONSHIP; GRAPH REPRESENTATION; PHYLOGENETIC CONSERVATION; PROTEIN-PROTEIN INTERACTIONS; RECOMBINATION EVENTS; STATISTICAL SIGNIFICANCE; STRUCTURAL CONSTRAINTS;

DIRECTED GRAPHS; GENES;

PROTEINS;

PROTEIN;

ALGORITHM; ANIMAL; ARTICLE; CHEMISTRY; GENOME; HUMAN; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE;

ALGORITHMS; ANIMALS; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; GENOME; HUMANS; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 62849100176     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-39     Document Type: Article

References (32)

1. Brenner SE Hubbard T Murzin A Chothia C Gene duplications in the H. influenzae genome Nature 1995, 378:140 10.1038/378140a0 7477316
2. Teichmann SA Park J Chothia C Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements Proc Natl Acad Sci USA 1998, 95:14658-14663 24505 9843945 10.1073/pnas.95.25.14658
3. Apic G Gough J Teichmann SA An insight into domain combinations Bioinformatics 2001, 17(Suppl 1):S83-S89 11472996
4. Murzin AG Brenner SE Hubbard T Chothia C SCOP: A structural classification of proteins database for the investigation of sequences and structures J Mol Biol 1995, 247(4):536-540 7723011
5. Orengo C Thornton J Protein families and their evolution-a structural perspective Annual Review of Biochemistry 2005, 74:867-900 10.1146/ annurev.biochem.74.082803.133029 15954844
6. Koonin EV Wolf YI Karev GP The structure of the protein universe and genome evolution Nature 2002, 420(6912):218-223 10.1038/nature01256 12432406
7. Muller A MacCallum RM Sternberg MJE Structural characterization of the human proteome Genome Res 2002, 12(11):1625-1641 187559 12421749 10.1101/ gr.221202
8. Gerrard DT Bornberg-Bauer E doMosaic - Analysis of the mosaic-like domain arrangements in proteins Informatica 2003, 27:15-20
9. Apic G Huber W Teichmann SA Multi-domain protein families and domain pairs: Comparison with known structures and a random model of domain recombination J Struct Funct Genomics 2003, 4(2-3):67-78 10.1023/ A:1026113408773 14649290
10. Vogel C Berzuini C Bashton M Gough J Teichmann S Supra-domains: evolutionary units larger than single protein domains J Mol Biol 2004, 336:809-23 10.1016/j.jmb.2003.12.026 15095989
11. Gough J Convergent evolution of domain architectures (is rare) Bioinformatics 2005, 21(8):1464-1471 10.1093/bioinformatics/bti204 15585523
12. Bashton M Chothia C The geometry of domain combination in proteins J Mol Biol 2002, 315(4):927-939 10.1006/jmbi.2001.5288 11812158
13. Forslund K Henricson A Hollich V Sonnhammer EL Domain tree-based analysis of protein architecture evolution Mol Biol Evol 2008, 25:254-64 10.1093/molbev/msm254 18025066
14. Basu MK Carmel L Rogozin IB Koonin EV Evolution of protein domain promiscuity in eukaryotes Genome Res 2008, 18(3):449-61 2259109 18230802 10.1101/gr.6943508
15. Weiner JBBE 3rd Moore AD Just how versatile are domains? BMC Evol Biol 2008, 8:285 2588589 18854028 10.1186/1471-2148-8-285
16. Wuchty S Scale-free behavior in protein domain networks Mol Biol Evol 2001, 18:1694-702 11504849
17. Ye Y Godzik A Comparative analysis of protein domain organization Genome Res 2004, 14:343-353 535408 14993202 10.1101/gr.1610504
18. Weiner J Beaussart F Bornberg-Bauer E Domain deletions and substitutions in the modular protein evolution FEBS J 2006, 273(9):2037-47 10.1111/ j.1742-4658.2006.05220.x 16640566
19. Przytycka T Davis G Song N Durand D Graph theoretical insights into evolution of multidomain proteins J Comput Biol 2006, 13(2):351-63 1815482 16597245 10.1089/cmb.2006.13.351
20. Wuchty S Almaas E Evolutionary cores of domain co-occurrence networks BMC Evol Biol 2005, 5:24 1079808 15788102 10.1186/1471-2148-5-24
21. Cohen-Gihon I Nussinov R Sharan R Comprehensive analysis of co-occurring domain sets in yeast proteins BMC Genomics 2007, 8:161 1919370 17562021 10.1186/1471-2164-8-161
22. Qian J Luscombe NM Gerstein M Protein family and fold occurrence in genomes: Power-law behaviour and evolutionary model J Mol Biol 2001, 313(4):673-81 10.1006/jmbi.2001.5079 11697896
23. Dokholyan NV Shakhnovich B Shakhnovich EI Expanding protein universe and its origin from the biological Big Bang Proc Natl Acad Sci USA 2002, 99(22):14132-6 137849 12384571 10.1073/pnas.202497999
24. 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 2001, 313(4):903-919 10.1006/ jmbi.2001.5080 11697912
25. Barabasi A Albert R Emergence of scaling in random networks Science 1999, 286:509-512 10.1126/science.286.5439.509 10521342
26. Newman ME Strogatz SH Watts DJ Random graphs with arbitrary degree distributions and their applications Physical review E, Statistical, nonlinear, and soft matter physics 2001, 64(2 Pt 2):026118 11497662
27. Bollobas B Borgs C Chayes J Riordan O Directed scale-free graphs Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms Society for Industrial and Applied Mathematics 2003 132-139
28. Watts DJ Strogatz SH Collective dynamics of 'small-world' networks Nature 1998, 393:440-442 10.1038/30918 9623998
29. Apic G Gough J Teichmann SA Domain combinations in archaeal, eubacterial and eukaryotic proteomes J Mol Biol 2001, 310(2):311-325 10.1006/ jmbi.2001.4776 11428892
30. Todd AE Orengo CA Thornton JM Evolution of function in protein superfamilies, from a structural perspective J Mol Biol 2001, 307(4):1113-1143 10.1006/jmbi.2001.4513 11286560
31. Kanehisa M Goto S KEGG: Kyoto Encyclopedia of Genes and Genomes Nucleic Acids Res 2000, 28:27-30 102409 10592173 10.1093/nar/28.1.27
32. Pawson T Nash P Assembly of cell regulatory systems through protein interaction domains Science 2003, 300(5618):445-452 10.1126/ science.1083653 12702867