Protein structure and evolutionary history determine sequence space topology

Genome Research

Volumn 15, Issue 3, 2005, Pages 385-392

  Shakhnovich, Boris E ^a   Deeds, Eric ^b   Delisi, Charles ^a   Shakhnovich, Eugene ^c  

^a BOSTON UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

^c HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARTICLE; ENTROPY; GENE MUTATION; GENETIC VARIABILITY; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; THERMODYNAMICS; AMINO ACID SEQUENCE; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; GENETICS; MOLECULAR GENETICS; MUTATION;

AMINO ACID SEQUENCE; EVOLUTION, MOLECULAR; MODELS, GENETIC; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; THERMODYNAMICS;

EID: 15544390249     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.3133605     Document Type: Article

References (40)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, Z., Miller W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
2. Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., Bucher, P., Cerutti, L., Corpet, F., Croning, M.D., et al. 2000. InterPro-An integrated documentation resource for protein families, domains and functional sites. Bioinformatics 16: 1145-1150.
3. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., et al. 2000. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25: 25-29.
4. Baker, D. and Sali, A. 2001. Protein structure prediction and structural genomics. Science 294: 93-96.
5. Bashford, D., Chothia, C., and Lesk, A.M. 1987. Determinants of a protein fold. Unique features of the globin amino acid sequences. J Mol. Biol. 196: 199-216.
6. Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O'Donovan, C., Phan, I., et al. 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31: 365-370.
7. Deeds, E.J., Dokholyan, N.V., and Shakhnovich, E.I. 2003. Protein evolution within a structural space. Biophys. J. 85: 2962-2972.
8. Dietmann, S., Park, J., Notredame, C., Heger, A., Lappe, M., and Holm, L. 2001. A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucleic Acids Res. 29: 55-57.
9. Dokholyan, N.V., Shakhnovich, B., and Shakhnovich, E.I. 2002. Expanding protein universe and its origin from the biological Big Bang. Proc. Natl. Acad. Sci. 99: 14132-14136.
10. England, J.L. and Shakhnovich, E.I. 2003. Structural determinant of protein designability. Phys. Rev. Lett. 90: 218101.
11. England, J.L., Shakhnovich, B.E., and Shakhnovich, E.I. 2003. Natural selection of more designable folds: A mechanism for thermophilic adaptation. Proc. Natl. Acad. Sci. 100: 8727-8731.
12. Finkelstein, A.V. and Ptitsyn, O.B. 1987. Why do globular proteins fit the limited set of folding patterns? Prog. Biophys. Mol. Biol. 50: 171-190.
13. Finkelstein, A.V., Gutin, A.M., and Badretdinov, A. 1995. Boltzmann-like statistics of protein architectures. Origins and consequences. Subcell. Biochem. 24: 1-26.
14. Govindarajan, S. and Goldstein, R.A. 1996. Why are some proteins structures so common? Proc. Natl. Acad. Sci. 93: 3341-3345.
15. Grzybowski, B.A., Ishchenko, A.V., Shimada, J., and Shakhnovich, E.I. 2002. From knowledge-based potentials to combinatorial lead design in silico. Acc. Chem. Res. 35: 261-269.
16. Hegyi, H. and Gerstein, M. 2001. Annotation transfer for genomics: Measuring functional divergence in multi-domain proteins. Genome Res. 11: 1632-1640.
17. Holm, L. and Sander, C. 1993. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233: 123-138.
18. Holm, L. and Sander, C. 1998. Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics 14: 423-429.
19. Huynen, M.A. and van Nimwegen, E. 1998. The frequency distribution of gene family sizes in complete genomes. Mol. Biol. Evol. 15: 583-589.
20. Koehl, P. and Levitt, M. 2002. Protein topology and stability define the space of allowed sequences. Proc. Natl. Acad. Sci. 99: 1280-1285.
21. Koonin, E.V., Wolf, Y.I., and Karev, G.P. 2002. The structure of the protein universe and genome evolution. Nature 420: 218-223.
22. Landau, L.D., Lifshitz, E.M., and Pitaevskii, L.P. 1978. Statistical physics. Pergamon Press, Oxford, New York.
23. Lespinet, O., Wolf, Y.I., Koonin, E.V., and Aravind, L. 2002. The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 12: 1048-1059.
24. Li, H., Helling, R., Tang, C., and Wingreen, N. 1996. Emergence of preferred structures in a simple model of protein folding. Science 273: 666-669.
25. Manning, G., Plowman, G.D., Hunter, T., and Sudarsanam, S. 2002. Evolution of protein kinase signaling from yeast to man. Trends Biochem. Sci. 27: 514-520.
26. Miller, J., Zeng, C., Wingreen, N.S., and Tang, C. 2002. Emergence of highly designable protein-backbone conformations in an off-lattice model. Proteins 47: 506-512.
27. Mirkin, B.G., Fenner, T.I., Galperin, M.Y., and Koonin, E.V. 2003. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol. Biol. 3: 2.
28. Orengo, C.A., Todd, A.E., and Thornton, J.M. 1999. From protein structure to function. Curr. Opin. Struct. Biol. 9: 374-382.
29. Orengo, C.A., Pearl, F.M., and Thornton, J.M. 2003. The CATH domain structure database. Methods Biochem. Anal. 44: 249-271.
30. Ponting, C.P. and Russell, R.R. 2002. The natural history of protein domains. Annu. Rev. Biophys. Biomol. Struct. 31: 45-71.
31. Qian, J., Luscombe, N.M., and Gerstein, M. 2001. Protein family and fold occurrence in genomes: Power-law behaviour and evolutionary model. J. Mol. Biol. 313: 673-681.
32. Shakhnovich, E.I. 1998. Protein design: A perspective from simple tractable models. Fold Des. 3: R45-R58.
33. Sonnhammer, E.L., Eddy, S.R., Birney, E., Bateman, A., and Durbin, R. 1998. Pfam: Multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res. 26: 320-322.
34. Taverna, D.M. and Goldstein, R.A. 2000. The distribution of structures in evolving protein populations. Biopolymers 53: 1-8.
35. Teichmann, S.A., Chothia, C., and Gerstein, M. 1999. Advances in structural genomics. Curr. Opin. Struct. Biol. 9: 390-399.
36. Tiana, G., Shakhnovich, B.E., Dokholyan, N.V., and Shakhnovich, E.I. 2004. Imprint of evolution on protein structures. Proc. Natl. Acad. Sci. 101: 2846-2851.
37. Vitkup, D., Melamud, E., Moult, J., and Sander, C. 2001. Completeness in structural genomics. Nat. Struct. Biol. 8: 559-566.
38. Westbrook, J., Feng, Z., Chen, L., Yang, H., and Berman, H.M. 2003. The Protein Data Bank and structural genomics. Nucleic Acids Res. 31: 489-491.
39. Wolynes, P.G. 1996. Symmetry and the energy landscapes of biomolecules. Proc. Natl. Acad. Sci. 93: 14249-14255.
40. Yanai, I., Camacho, C.J., and DeLisi, C. 2000. Predictions of gene family distributions in microbial genomes: Evolution by gene duplication and modification. Phys. Rev. Lett. 85: 2641-2644.