Structurally constrained protein evolution: Results from a lattice simulation

European Physical Journal B

Volumn 15, Issue 2, 2000, Pages 385-397

  Bastolla, U ^a   Vendruscolo, M ^b   Roman, H E ^c  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^c UNIVERSITY OF MILAN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000105754     PISSN: 14346028     EISSN: None     Source Type: Journal    
DOI: 10.1007/s100510051140     Document Type: Article

References (43)

1. B. Rost, Prot. Eng. 12, 85 (1999).
2. L. Holm, C. Sander, Science 273, 595 (1996).
3. P.K. Qasba, S. Kumar, Crit. Rev. Biochem. Mol. Biol. 32, 255 (1997).
4. B. Rost, Fol. Des. 2, S19 (1997).
5. The number of amino acid matches obtained by pairing two random sequences of the same length is given by the binomial distribution with p = 1/20 if one assumes that the 20 amino acids have the same probability to occur. For sequences of length N there will be on average pN identical amino acids, with a variance Np(1 - p). For random sequences, 95% of pairwise comparisons yield a sequence identity between 1% and 9%.
6. M. Kimura, The neutral theory of molecular evolution (Cambridge University Press, 1983).
7. J.L. King, T.H. Jukes, Science 164, 788 (1969).
8. J.H. Gillespie, The causes of molecular evolution (Oxford University Press, 1991).
9. F.J. Ayala, Proc. Natl. Acad. Sci. USA 94, 7776 (1997).
10. This problem is much simpler than protein folding and can be studied through efficient and reliable algorithms. See, e.g., P. Schuster, W. Fontana, P.P. Stadler, I.L. Hofacker, Proc. R. Soc. London B 255, 279 (1994); M.A. Huynen, P.F. Stadler, W. Fontana, Proc. Natl. Acad. Sci. USA 93, 397 (1996).
11. This problem is much simpler than protein folding and can be studied through efficient and reliable algorithms. See, e.g., P. Schuster, W. Fontana, P.P. Stadler, I.L. Hofacker, Proc. R. Soc. London B 255, 279 (1994); M.A. Huynen, P.F. Stadler, W. Fontana, Proc. Natl. Acad. Sci. USA 93, 397 (1996).
12. E.I. Shakhnovich, A.M. Gutin, J. Theor. Biol. 149, 537 (1991).
13. G. Tiana, R.A. Broglia, H.E. Roman, E. Vigezzi, E.I. Shakhnovich, J. Chem. Phys. 108, 757 (1998).
14. V.I. Abkevich, A.M. Gutin, E.I. Shakhnovich, J. Chem. Phys. 101, 6052 (1994).
15. E. Bornberg-Bauer, Biophys. J. 73, 2393 (1997).
16. U. Bastolla, H.E. Roman, M. Vendruscolo, J. Theor. Biol. 200, 49 (1999).
17. A. Babajide, I.L. Hofacker, M.J. Sippl, P.F. Stadler, Fol. Des. 2, 261 (1997).
18. J.U. Bowie, R. Lüthy, D. Eisenberg, Science 253, 164 (1991).
19. S. Govindarajan, R.A. Goldstein, Proteins 29, 461 (1997).
20. S. Govindarajan, R.A. Goldstein, Biopolymers 42, 427 (1997).
21. G. Tiana, R.A. Broglia, E.I. Shakhnovich, Proteins (in press).
22. S. Miyazawa, R.L. Jernigan, Macromolecules 18, 534 (1985).
23. D.M. Epstein, S.J. Benkovic, P.E. Wright, Biochemistry 34, 11037 (1995).
24. E.I. Shakhnovich, A.M. Gutin, Proc. Natl. Acad. Sci. USA 90, 7195 (1993); E.I. Shakhnovich, Phys. Rev. Lett. 72, 3907 (1994).
25. E.I. Shakhnovich, A.M. Gutin, Proc. Natl. Acad. Sci. USA 90, 7195 (1993); E.I. Shakhnovich, Phys. Rev. Lett. 72, 3907 (1994).
26. J.D. Bryngelson, P.G. Wolynes, Proc. Natl. Acad. Sci. USA 84, 7524 (1987).
27. U. Bastolla (unpublished result).
28. A similar substitution scheme, but with different selection mechanism, was used in V.I. Abkevich, A.M. Gutin, E.I. Shakhnovich Proc. Natl. Acad. Sci. USA 93, 839 (1996).
29. P. Grassberger, Phys. Rev. E 56, 3682 (1997).
30. H. Frauenkron, U. Bastolla, E. Gerstner, P. Grassberger, W. Nadler, Phys. Rev. Lett. 80, 3149 (1998); H. Frauenkron, U. Bastolla, E. Gerstner, P. Grassberger, W. Nadler, Proteins 32, 52 (1998).
31. H. Frauenkron, U. Bastolla, E. Gerstner, P. Grassberger, W. Nadler, Phys. Rev. Lett. 80, 3149 (1998); H. Frauenkron, U. Bastolla, E. Gerstner, P. Grassberger, W. Nadler, Proteins 32, 52 (1998).
32. R.A. Broglia, G. Tiana, H.E. Roman, E. Vigezzi, E.I. Shakhnovich, Phys. Rev. Lett. 82, 4727 (1999).
33. L.A. Mirny, E.I. Shakhnovich, J. Mol. Biol. 291, 177 (1999).
34. E. Zuckerkandl, L. Pauling, in Horizons in Biochemistry, edited by M. Kasha, B. Pullman (Academic Press, New York, 1962).
35. L. Mirny, E.I. Shakhnovich, J. Mol. Biol. 264, 1164 (1996).
36. D.K. Klimov, D. Thirumalai, J. Chem. Phys. 109, 4119 (1998).
37. A. Sali, E.I. Shakhnovich, M. Karplus, J. Mol. Biol. 235, 1614 (1994); A.R. Dinner, V. Abkevich, E.I. Shakhnovich, M. Karplus, Proteins 35, 34 (1999).
38. A. Sali, E.I. Shakhnovich, M. Karplus, J. Mol. Biol. 235, 1614 (1994); A.R. Dinner, V. Abkevich, E.I. Shakhnovich, M. Karplus, Proteins 35, 34 (1999).
39. M. Vendruscolo, R. Najmanovich, E. Domany, Proteins 38, 134 (2000).
40. M. Vendruscolo, A. Maritan, J.R. Banavar, Phys. Rev. Lett. 78, 3967 (1997).
41. B. Honig, F. Cohen, Fold. Des. 1, R17 (1996).
42. E.I. Shakhnovich, Fold. Des. 1, R50 (1996).
43. A.V. Finkelstein, A.M. Gutin, A.Y. Badretdinov, FEBS Lett. 325, 23 (1993).