Towards Unifying Protein Evolution Theory

作者: Nikolay V. Dokholyan , Eugene I. Shakhnovich

DOI: 10.1007/978-3-540-35306-5_5

关键词: Protein evolutionDivergent evolutionGene ontologyProtein domainMain contentionEvolutionary biologyConvergent evolutionConvergent and divergent production

摘要: There are many proposed models for protein domain evolution. The main contention [1], however, is between divergent [2] and convergent [3] of Divergent evolution proposes that there was an ancestor to all domains we see today consequently historically related each other. Convergent claims chance largely responsible the appearance new kinds domains. explains prevalence certain types structures by stating those more favorable often recycled different functions. distinction neither abstract nor purely academic. If primary model domains, then it possible reconstruct lineages follow structural change, predict contextual functional ranges occur due well-defined evolutionary pressures. However, if driving force behind functions, in principle should be no discernable structure–function relationship. An important step understanding quantification dominant scenario(s) as theoretical background derivation correlation. Here, describe recent advances this direction.

参考文章(75)
Janet M Thornton, Christine A Orengo, Annabel E Todd, Frances M.G Pearl, Protein folds, functions and evolution. Journal of Molecular Biology. ,vol. 293, pp. 333- 342 ,(1999) , 10.1006/JMBI.1999.3054
Alexey G. Murzin, Steven E. Brenner, Tim Hubbard, Cyrus Chothia, SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology. ,vol. 247, pp. 536- 540 ,(1995) , 10.1016/S0022-2836(05)80134-2
J. A. Lake, Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 91, pp. 1455- 1459 ,(1994) , 10.1073/PNAS.91.4.1455
W. F. Doolittle, Phylogenetic Classification and the Universal Tree Science. ,vol. 284, pp. 2124- 2128 ,(1999) , 10.1126/SCIENCE.284.5423.2124
Eugene I. Shakhnovich, Nikolay V. Dokholyan, Eric J. Deeds, Protein evolution within a structural space. Biophysical Journal. ,vol. 85, pp. 2962- 2972 ,(2003) , 10.1016/S0006-3495(03)74716-X
Nick V. Grishin, Roman L. Tatusov, Michael Y. Galperin, L. Aravind, L. Aravind, Yuri I. Wolf, Eugene V. Koonin, Kira S. Makarova, Comparative Genomics of the Archaea (Euryarchaeota): Evolution of Conserved Protein Families, the Stable Core, and the Variable Shell Genome Research. ,vol. 9, pp. 608- 628 ,(1999) , 10.1101/GR.9.7.608
Shlomo Havlin, Daniel Ben-Avraham, Diffusion in disordered media Advances in Physics. ,vol. 51, pp. 187- 292 ,(2002) , 10.1080/00018730110116353
Boris E. Shakhnovich, Nikolay V. Dokholyan, Charles DeLisi, Eugene I. Shakhnovich, Functional Fingerprints of Folds: Evidence for Correlated Structure–Function Evolution Journal of Molecular Biology. ,vol. 326, pp. 1- 9 ,(2003) , 10.1016/S0022-2836(02)01362-1
A. S. Siddiqui, U. Dengler, G. J. Barton, 3Dee: a database of protein structural domains Bioinformatics. ,vol. 17, pp. 200- 201 ,(2001) , 10.1093/BIOINFORMATICS/17.2.200