Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences

Molecular Biology and Evolution

Volumn 22, Issue 3, 2005, Pages 630-638

  Porto, Markus ^a   Roman, H Eduardo ^b,e   Vendruscolo, Michele ^c   Bastolla, Ugo ^d  

^a DARMSTADT UNIVERSITY OF TECHNOLOGY   (Germany)

^b UNIVERSITY OF MILAN   (Italy)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d CENTRO DE ASTROBIOLOGÍA CSIC INTA   (Spain)

^e UNIVERSITY OF MILANO BICOCCA   (Italy)

Author keywords

Amino acid distributions; Boltzmann parameters; Divergent evolutionary changes; Principal eigenvector of the contact matrix; Structurally constrained neutral evolution

Indexed keywords

AMINO ACID;

AMINO ACID SEQUENCE; ARTICLE; EVOLUTION; GENETIC CONSERVATION; GENETIC VARIABILITY; HUMAN; MATHEMATICAL MODEL; NONHUMAN; PROTEIN CONFORMATION; PROTEIN DATA BANK; PROTEIN FOLDING; PROTEIN LOCALIZATION; PROTEIN STABILITY; SIMULATION; TEMPERATURE DEPENDENCE; THERMODYNAMICS;

AMINO ACIDS; ANIMALS; EVOLUTION, MOLECULAR; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEINS;

EID: 14544272929     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi048     Document Type: Article

References (50)

1. Abkevich, V. I., A. M. Gutin, and E. I. Shakhnovich. 1994. Free energy landscapes for protein folding kinetics-intermediates, traps and multiple pathways in theory and lattice model simulations. J. Chem. Phys. 101:6052-6062.
2. Bastolla, U., H. Frauenkron, E. Gerstner, P. Grassberger, and W. Nadler. 1998. Testing a new Monte Carlo algorithm for protein folding. Proteins 32:52-66.
3. Bastolla, U., M. Vendruscolo, and H. E. Roman. 1999. Neutral evolution of model proteins: diffusion in sequence space and overdispersion. J. Theor. Biol. 200:49-64.
4. -. 2000a. Structurally constrained protein evolution: results from a lattice simulation. Eur. Phys. J. B 15:385-397.
5. Bastolla, U., M. Vendruscolo, and E. W. Knapp. 2000b. A statistical mechanical method to optimize energy parameters for protein folding. Proc. Natl. Acad. Sci. USA 97:3977-3981.
6. Bastolla, U., E. W. Knapp, and M. Vendruscolo. 2001. How to guarantee optimal stability for most protein native structures in the Protein Data Bank. Proteins 44:79-96.
7. Bastolla, U., M. Porto, H. E. Roman, and M. Vendruscolo. 2002. Lack of self-averaging in neutral evolution of proteins. Phys. Rev. Lett. 89:208101/1-208101/4.
8. -. 2003a. Connectivity of neutral networks, overdispersion and structural conservation in protein evolution. J. Mol. Evol. 56:243-254.
9. -. 2003b. Statistical properties of neutral evolution. J. Mol. Evol. 57:S103-S119.
10. -. 2005. The principal eigenvector of contact matrices and hydrophobicity profiles in proteins. Proteins 58:22-30.
11. Bateman, A., E. Birney, R. Durbin, S. R. Eddy, K. L. Howe and E. L. L. Sonnhammer. 2000. The Pfam contribution to the annual NAR database issue. Nucleic Acids Res. 28:263-266.
12. Bernardi, G., and G. Bernardi. 1986. Compositional constraints and genome evolution. J. Mol. Evol. 24:1-11.
13. Bryngelson, J. D., and P. G. Wolynes. 1987. Spin-glasses and the statistical-mechanics of protein folding. Proc. Natl. Acad. Sci. USA 84:7524-7528.
14. Casari G., and M. J. Sippl. 1992. Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds. J. Mol. Biol. 224:725-732.
15. Casari, G., C. Sander, and A. Valencia. 1995. A method to predict functional residues in proteins. Nat. Struct. Biol. 2:171-178.
16. Dokholyan, N. V., and E. I. Shakhnovich. 2001. Understanding hierachical protein evolution from first principles. J. Mol. Biol. 312:289-307.
17. Dokholyan, N. V., L. A. Mirny, and E. I. Shakhnovich. 2002. Understanding conserved amino acids in proteins. Physica A 314:600-606.
18. England, J. L., and E. I. Shakhnovich. 2003. Structural determinant of protein designability. Phys. Rev. Lett. 90:218101/1-218101/4.
19. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
20. Finkelstein, A. V., A. Ya. Badretdinov, and A. M. Gutin. 1995. Why do protein architectures have Boltzmarm-like statistics? Proteins 23:142-150.
21. Fornasari, M. S., G. Parisi, and J. Echave. 2002. Site-specific amino acid replacement matrices from structurally constrained protein evolution simulations. Mol. Biol. Evol. 19:352-356.
22. Goldstein, R. A., Z. A. Luthey-Schulten, and P. G. Wolynes. 1992. Optimal protein-folding codes from spin-glass theory. Proc. Natl. Acad. Sci. USA 89:4918-4922.
23. Gutin, A. M., V. I. Abkevich, and E. I. Shakhnovich. 1995. Evolution-like selection of fast-folding model proteins. Proc. Natl. Acad. Sci. USA 92:1282-1286.
24. Halpern, A. L., and W. J. Bruno. 1998. Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. Mol. Biol. Evol. 15:910-917.
25. Helling, R., H. Li, R. Melin, J. Miller, N. Wingreen, C. Zeng and C. Tang. 2001. The designability of protein structures. J. Mol. Graphics Modelling 19:157-167.
26. Henikoff, S., and J. G. Henikoff. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89:10915-10919.
27. Henikoff, S., and J. G. Henikoff. 1993. Performance evaluation of amino acid substitution matrices. Proteins 17:49-61.
28. Hobohm, U., and C. Sander. 1994. Enlarged representative set of protein structure. Protein Sci. 3:522-524.
29. Holm, L., and C. Sander. 1996. Mapping the protein universe. Science 273:595-602.
30. Jones, D. T., W. R. Taylor, and J. M. Thomton. 1992. The rapid generation of mutation data matrices from protein sequences. Comp. Appl. Biosci. 8:275-282.
31. Kinjo, A. R., and K. Nishikawa. 2004. Eigenvalue analysis of amino acid substitution matrices reveal a sharp transition of the mode of sequence conservation in proteins. Bioinformatics 20:2504-2508.
32. Klimov, D. K., and D. Thirumalai. 1996. Factors governing the foldability of proteins. Proteins 26:411-441.
33. Koehl, P., and M. Levitt. 2002 Protein topology and stability define the space of allowed sequences Proc. Natl. Acad. Sci. USA 99:1280-1285.
34. Koshi, J. M., and R. A. Goldstein. 1998. Models of natural mutation including site heterogeneity. Proteins 32:289-295.
35. Koshi, J. M., D. P. Mindell, and R. A. Goldstein. 1999. Using physical-chemistry based substitution models in phylogenetic analysis of HIV-1 subtypes. Mol. Biol. Evol. 16:173-179.
36. Li, H., C. Tang, and N. S. Wingreen. 1997. Nature of driving force for protein folding: a result from analyzing the statistical potential. Phys. Rev. Lett. 79:765-768.
37. Li, H., C. Tang, and N. S. Wingreen. 1998. Are protein folds atypical? Proc. Natl. Acad. Sci. USA 95:4987-4990.
38. Lio, P. and N. Goldman. 1998. Models of molecular evolution and phylogeny. Genome Res. 8:1233-1244.
39. Meyer, T. E., M. A. Cusanovich, and M. D. Kamen. 1986. Evidence against use of bacterial amino acid sequence data for construction of all-inclusive phylogenetic trees Proc. Natl. Acad. Sci. USA 83:217-220.
40. Miyazawa, S., and R. L. Jemigan. 1985. Estimation of effective inter-residue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 18:534-552.
41. Ota, M., K. Kinoshita, and K. Nishikawa. 2003. Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation. J. Mol. Biol. 327:1053-1064.
42. Overington, J., M. S. Johnson, A. Sali, and T. L. Blundell. 1990. Tertiary structural constraints on protein evolutionary diversity-templates, key residues and structure prediction. Proc. R. Soc. Lond. Ser. B 241:132-145.
43. Parisi, G., and J. Echave. 2001. Structural constraints and emergence of sequence patterns in protein evolution. Mol. Biol. Evol. 18:750-756.
44. Porto, M., U. Bastolla, H. E. Roman, and M. Vendruscolo. 2004. Reconstruction of protein structures from a vectorial representation. Phys. Rev. Lett. 92:218101/1-218101/4.
45. Ptitsyn, O. B. 1998. Protein folding and protein evolution: common folding nucleus in different subfamilies of c-type cytochrome? J. Mol. Biol. 278:655-666.
46. Ptitsyn, O. B., and K. H. Ting. 1999. Non-functional conserved residues in globins and their possible role as a folding nucleus. J. Mol. Biol. 291:671-682.
47. Shakhnovich, E. I., and A. M. Gutin. 1993. Engineering of stable and fast-folding sequences of model proteins. Proc. Natl. Acad. Sci. USA 90:7195-7199.
48. Sueoka, N. 1961. Correlation between base composition of the deoxyribonucleic acid and amino acid composition of proteins. Proc. Natl. Acad. Sci. USA 47:469-478.
49. Thome, J. L. 2000. Models of protein sequence evolution and their applications. Curr. Opin. Genet. Dev. 10:602-605.
50. White, S. H. 1992. Amino acid preferences of small proteins. Implications for protein stability and evolution. J. Mol. Biol. 227:991-995.