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Reconstructing Domain Compositions of Ancestral Multi-domain Proteins

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4205))

Abstract

A model for the evolution of multidomain proteins should encompass not only sequence divergence but also domain duplications and recombination of domains. Given a set of contemporary multidomain proteins from different species together with a species tree, in this paper, we suggest a model for constructing the domain compositions of ancestral multi-domain proteins considering the above evolutionary events.

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References

  1. Apic, G., Gough, J., Teichmann, S.A.: An insight into domain combinations. Suppl. Bioinformatics 89, S83–S89 (2001)

    Google Scholar 

  2. 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. Journal of Structural and Functional Genomics 4, 67–78 (2003)

    Article  Google Scholar 

  3. Aroul-Selvam, R.: Tim Hubbard and Rajkumar Sasidharan: Domain Insertions in Protein Structures. J. Mol. Biol. 338, 633–641 (2004)

    Article  Google Scholar 

  4. Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L., Studholme, D.J., Yeats, C., Eddy, S.R.: The Pfam protein families database. Nucleic Acids Res. 32, 138–141 (2004)

    Article  Google Scholar 

  5. Asa, K.: Björklund, Diana Ekman, Sara Light, Johannes Frey-Skött and Arne Elofsson: Domain Rearrangements in Protein Evolution. J. Mol. Biol. 353, 911–923 (2005)

    Article  Google Scholar 

  6. Felsenstein, J.: Phylogenies from molecular sequences: Inference and reliability. Annu. Rev. Genet. 22, 521–565 (1988)

    Article  Google Scholar 

  7. Fitch, W., Margoliash, E.: Construction of phylogenetic trees. Science 155, 279–284 (1967)

    Article  Google Scholar 

  8. Islam, S.A., Luo, J., Sternberg, M.J.E.: Identification and analysis of domains in proteins. Protein Engineering 8(6), 513–526 (1995)

    Article  Google Scholar 

  9. Kirkpatrick, S., Galatt, C.D., Vecchi, M.P.: Optimization by Simulated Annealing. Science 220, 4598, 671–680 (1983)

    Article  MathSciNet  Google Scholar 

  10. Kummerfeld, S.K., Vogel, C., Madera, M., Pacold, M., Teichmann, S.A.: Evolution of Multi-domain Proteins by Gene Fusion and Fission. In: Proceedings of ISMB 2004 (2004)

    Google Scholar 

  11. Kummerfeld, S.K., Teichmann, S.A.: Relative rate of gene fusion and fission in multi-domain proteins. Trends. in Genetics 21(1), 25–30 (2005)

    Article  Google Scholar 

  12. Letunic, I., Copley, R.R., Pils, B., Pinkert, S., Schultz, J., Bork, P.: SMART 5: domains in the context of genomes and networks. Nucleic Acids Res. 34, 257–260 (2006)

    Article  Google Scholar 

  13. Murzin, A.G., Brenner, S., Hubbard, T., Chotia, C.: SCOP: the structural classification of proteins database. J. Mol. Biol. 247, 536–540 (1995)

    Google Scholar 

  14. Nei, M.: Molecular Evolution Genetics. Columbia University Press, New York (1987)

    Google Scholar 

  15. Orengo, C.A., Thornton, J.M.: Protein Families and their Evolution–A Structural Perspective. Anni. Rev. Biochem. 74, 867–900 (2005)

    Article  Google Scholar 

  16. Page, R.D.M.: Maps between trees and cladistic analysis of historical associations among genes, organisms and areas. Syst. Zool. 43, 58–77 (1994)

    Google Scholar 

  17. Pasek, S., Risler, J.-L., Brézellec, P.: Gene Fusion/Fission is a major contributor to evolution of multi-domain bacterial proteins. Bioinformatics (to appear, 2006)

    Google Scholar 

  18. Pearl, F.M., Bennett, C.F., Bray, J.E., Harrison, A.P., Martin, N., Shepherd, A., Sillitoe, I., Thornton, K., Orengo, C.A.: The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Research 31(1), 452–455 (2003)

    Article  Google Scholar 

  19. Przytycka, T., Davis, G., Song, N., Durand, D.: Graph theoretical insights into evolution of multidomain proteins. J. Computational Biology 13(2), 351–363 (2006)

    Article  MathSciNet  Google Scholar 

  20. Weiner III, J., Beaussart, F., Bornberg-Bauer, E.: Domain deletions and substitutions in the modular protein evolution. The FEBS journal 273, 2037–2047 (2006)

    Article  Google Scholar 

  21. Weiner III, J., Bornberg-Bauer, E.: Evolution of Circular Permutations in Multidomain Proteins. Molecular Biology and Evolution 23(4), 734–743 (2006)

    Article  Google Scholar 

  22. Christine Vogel, M., Bashton, N.D., Kerrison, C., Chotia, S.A.: Teichmann: Structure, function and evolution of multidomain proteins. Current Opinion in Structural Biology 14, 208–216 (2004)

    Article  Google Scholar 

  23. Vogel, C., Berzuini, C., Bashton, M., Gough, J., Teichmann, S.A.: Supra-domains: Evolutionary Units larger than Single Protein Domains. J. Mol. Biol. 336, 809–823 (2004)

    Article  Google Scholar 

  24. Vogel, C., Teichmann, S.A., Pereira-Leal, J.: The Relationship Between Domain Duplication and Recombination. J. Mol. Biol. 346, 355–365 (2005)

    Article  Google Scholar 

  25. Ye, Y., Godzik, A.: Comparative Analysis of Protein Domain Organization. Genome Research 14, 343–353 (2004)

    Article  Google Scholar 

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© 2006 Springer-Verlag Berlin Heidelberg

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Behzadi, B., Vingron, M. (2006). Reconstructing Domain Compositions of Ancestral Multi-domain Proteins. In: Bourque, G., El-Mabrouk, N. (eds) Comparative Genomics. RCG 2006. Lecture Notes in Computer Science(), vol 4205. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11864127_1

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  • DOI: https://doi.org/10.1007/11864127_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-44529-6

  • Online ISBN: 978-3-540-44530-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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