Graph theoretical insights into evolution of multidomain proteins

Journal of Computational Biology

Volumn 13, Issue 2, 2006, Pages 351-363

  Przytycka, Teresa ^a   Davis, George ^b   Song, Nan ^b   Durand, Dannie ^b  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

Chordal graphs; Dollo parsimony; Domain overlap graph; Helly property; Multidomain proteins; Protein evolution

Indexed keywords

MULTIDOMAIN PROTEIN; PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; CONFERENCE PAPER; MOLECULAR EVOLUTION; PARSIMONY ANALYSIS; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; THEORETICAL STUDY;

AMINO ACIDS; ANIMALS; BINDING SITES; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; HUMANS; MICE; MODELS, THEORETICAL; PHYLOGENY; PROTEIN-TYROSINE KINASES; PROTEINS;

EID: 33646001426     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2006.13.351     Document Type: Conference Paper

References (36)

1. Apic, G., Gough, J., and Teichmann, S.A. 2001. Domain combinations in archaeal, eubacterial, and eukaryotic proteomes. J. Mol. Biol. 310, 311-325.
2. Apic, G., Huber, W., and Teichmann, S.A. 2003. Multi-domain protein families and domain pairs: Comparison with known structures and a random model of domain recombination. J. Struct. Funct. Genomics 4, 67-78.
3. Barabasi, A.-L., and Albert, R. 1999. Emergence of scaling in random networks. Science 286, 509-512.
4. Bashton, M., and Chothia, C. 2002. The geometry of domain combination in proteins. J. Mol. Biol. 315, 927-939.
5. Bateman, A., Birney, E., Durbin, R., Eddy, S.R., Howe, K.L., and Sonnhammer, E.L. 2000. The Pfam protein families database. Nucl. Acids Res. 28, 263-266.
6. Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.-C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O'Donovan, C., Phan, I., Pilbout, S., and Schneider, M. 2003. The SWISS-PROT protein knowledge base and its supplement TrEMBL in 2003. Nucl. Acids Res. 31, 365-370.
7. Bollobas, B. 2001. Random Graph Theory, Cambridge University Press, London.
8. Buneman, P. 1974. A characterisation of rigid circuit graphs. Discrete Math. 9, 205-212.
9. Camin, J.H., and Sokal, R.R. 1965. A method for deducting branching sequences in phytogeny. Evolution 19, 311-326.
10. Cheek, S., Zhang, H., and Grishin, N.V. 2002. Sequence and structure classification of kinases. J. Mol. Biol. 320, 855-881.
11. Danzer, L., Grunbaum, B., and Klee, V. 1963. Helly's theorem and its relatives. Convexity, AMS 7, 101-180.
12. Day, W., Johnson, D., and Sankoff, D. 1986. The computational complexity of inferring rooted phytogenies by parsimony. Math. Biosci. 81, 33-42.
13. Farris, J.S. 1977. Phylogenetic analysis under Dollo's law. Syst. Zool. 26, 77-88.
14. Felsenstein, J. 2004. Inferring Phylogenies, Sinauer Associates, Sunderland, MA.
15. Gavril, F. 1974. The intersection graphs of subtrees in trees are exactly the chordal graphs. J. Comb. Theory (B) 16, 47-56.
16. Geer, L.Y., Domrachev, M., Lipman, D.J., and Bryant, S.H. 2002. CDART: Protein homology by domain architecture. Genome Res. 12, 1619-1623.
17. Gerstein, M. 1998. How representative are the known structures of the proteins in a complete genome? A comprehensive structural census. Fold Des. 3, 497-512.
18. Golumbic, M. 1980. Algorithmic Graph Theory and Perfect Graphs, Academic Press, New York.
19. Gu, J., and Gu, X. 2003. Natural history and functional divergence of protein tyrosine kinases. Gene 317, 49-57.
20. Gusfield, D. 1991. Efficient methods for inferring evolutionary history. Networks 21, 19-28.
21. Hanks, S.K. 2003. Genomic analysis of the eukaryotic protein kinase superfamily: A perspective. Genome Biol. 4, 111.
22. Heger, A., and Holm, L., 2003. Exhaustive enumeration of protein domain families. J. Mol. Biol. 328, 749-767.
23. Krause, A., Stoye, J., and Vingron, M. 2000. The SYSTERS protein sequence cluster set. Nucl. Acids Res. 28, 270-272.
24. Kummerfeld, S., Vogel, C., Madera, M., and Teichmann, S.A. 2004. Evolution of multi-domain proteins by gene fusion and fission. ISMB 2004.
25. Letunic, I., Goodstadt, L., Dickens, N.J., Doerks, T., Schultz, J., Mott, R., Ciccarelli, F., Copley, R.R., Ponting, C.P., and Bork, P. 2002. Recent improvements to the SMART domain-based sequence annotation resource. Nucl. Acids Res. 31, 242-244.
26. Liu, Y., Gerstein, M., and Engelman, D.M. 2004. Evolutionary use of domain recombination: A distinction between membrane and soluble proteins. Proc. Natl. Acad. Sci. USA, 3495-3497.
27. Long, M. 2001. Evolution of novel genes. Curr. Opin. Genet. Dev. 11, 673-680.
28. Marcotte, F.M., Pellegrini, M., Ng, H.L., Rice, D.W., Yeates, T.O., and Eisenberg, D. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science 285, 751-753.
29. Mehlhorn, K., and Naher, S. 1999. The LEDA Platform of Combinatorial and Geometric Computing, Cambridge University Press, London.
30. Patthy, L. 1999. Genome evolution and the evolution of exon-shuffling-A review. Gene 238, 103-114.
31. Robinson, D.R., Wu, Y.M., and Lin, S.F. 2000. The protein tyrosine kinase family of the human genome. Oncogene 19, 5548-5558.
32. Snel, B., Bork, P., and Huynen, M. 2002. Genome evolution gene fusion versus gene fission. Trends Genet. 16, 9-11.
33. Teichmann, S.A., Park, J., and Chothia, C. 1998. Structural assignments to the mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc. Natl. Acad. Sci. USA 95, 14658-14663.
34. Wuchty, S. 2001. Scale-free behavior in protein domain networks. Mol. Biol. Evol. 18, 1694-1702.
35. Yanai, I., Wolf, Y.I., and Koonin, E.V. 2002. Evolution of gene fusions: Horizontal transfer versus independent events. Genome Biol. 3. Research:0024.
36. Yona, G., Linial, N., and Linial, M. 1999. Protomap: Automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space. Proteins: Structure, Function and Genetics 37, 360-378.