Divergent evolution of a structural proteome: Phenomenological models

Biophysical Journal

Volumn 92, Issue 3, 2007, Pages 701-716

  Roland, C Brian ^a   Shakhnovich, Eugene I ^b  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

STRUCTURAL PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CONVERGENT EVOLUTION; EVOLUTIONARY ALGORITHM; MOLECULAR DYNAMICS; MUTATIONAL ANALYSIS; NONHUMAN; PHENOMENOLOGY; PROKARYOTE; PROTEIN DOMAIN; PROTEIN STRUCTURE;

PROKARYOTA;

EID: 33846782884     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.081265     Document Type: Article

References (21)

1. Koonin, E. V., Y. I. Wolf, and G. P. Karev. 2002. The structure of the protein universe and genome evolution. Nature. 420:218-223.
2. Gerstein, M. 1997. A structural census of genomes: comparing bacterial, eukaryotic, and archael genomes in terms of protein structure. J. Mol. Biol. 274:562-576.
3. Qian, J., N. M. Luscombe, and M. Gerstein. 2001. Protein family and fold occurance in genomes: power-law behavior and evolutionary model. J. Mol. Biol. 313:673-681.
4. Murzin, A. G., S. E. Brenner, T. J. Hubbard, and C. Chothia. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:536-540.
5. Lo Conte, L., B. Ailey, T. J. Hubbard, S. E. Brenner, A. G. Murzin, and C. Chothia. 2000. SCOP: a structural classification of proteins database. Nucl. Acids Res. 28:257-259.
6. Holm, L., and C. Sander. 1996. Mapping the protein universe. Science. 273:595-602.
7. Li, H., R. Tellig, C. Tang, and N. Wingreen. 1996. Emergence of preferred structures in a simple model of protein folding. Science. 273:666-669.
8. Dokholyan, N. V., B. Shakhnovich, and E. I. Shakhnovich. 2002. Expanding protein universe and its origin from the biological Big Bang. Proc. Natl. Acad. Sci. USA. 99:14132-14136.
9. Holm, L., and C. Sander. 1998. Dictionary of recurrent domains in protein structures. Proteins. 33:88-96.
10. Deeds, E. J., B. Shakhnovich, and E. I. Shakhnovich. 2004. Proteomic traces of speciation. J. Mol. Biol. 336:695-706.
11. Shakhnovich, B. E., J. M. Harvey, S. Comreau, D. Lorenz, C. Delisi, and E. I. Shakhnovich. 2003. ELISA: Structure-function inferences based on statistically significant and evolutionarily inspired observations. BMC Bioinformatics. 4:34.
12. Deeds, E. J., H. Hennessey, and E. I. Shakhnovich. 2005. Procaryotic phylogenies inferred from protein structural domains. Genome Res. 15:393-402.
13. Albert, R., and A.-L. Barabasi. 2002. Statistical mechanics of complex networks. Rev. Mod. Phys. 74:47-97.
14. Mirny, L. A., and E. I. Shakhnovich. 1999. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics, and function. J. Mol. Biol. 291:177-196.
15. Dokholyan, N. V., and E. I. Shakhnovich. 2001. Understanding hierarchical protein evolution from first principles. J. Mol. Biol. 312:289-307.
16. Chothia, C., and A. M. Lesk. 1986. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:823-826.
17. Wilson, C. A., J. Kreychman, and M. Gerstein. 2000. Assessing annotation transfer for genomics: quantifying the relationships between protein sequence, structure and function through traditional and proabilistic scores. J. Mol. Biol. 297:233-249.
18. Rost, B. 1999. Twighlight zone of protein sequence alignments. Protein Eng. 12:85-94.
19. Kim, J., P. L. Krapivsky, B. Kahng, and S. Redner. 2002. Infinite-order percolation and giant fluctuations in a protein interaction network. Phys. Rev. E. 66:055101 (R).
20. Krapivsky, P. L., and S. Redner. 2001. Organization of growing random networks. Phys. Rev. E. 63:066123.
21. Deeds, E. J., N. V. Dokholyan, and E. I. Shakhnovich. 2003. Protein evolution within a structural space. Biophys. J. 85:2962-2972.