Model for calculation of electrostatic interactions in unfolded proteins

Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics

Volumn 65, Issue 1, 2002, Pages

  Kundrotas, P J ^a   Karshikoff, A ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

BACILLUS AMYLOLIQUEFACIENS RIBONUCLEASE; MICROCOCCAL NUCLEASE; PROTEIN; RIBONUCLEASE;

BINDING SITE; CHEMICAL MODEL; CHEMISTRY; PH; PROTEIN FOLDING; STATISTICAL MODEL; THEORETICAL MODEL;

BINDING SITES; HYDROGEN-ION CONCENTRATION; MICROCOCCAL NUCLEASE; MODELS, CHEMICAL; MODELS, STATISTICAL; MODELS, THEORETICAL; PROTEIN FOLDING; PROTEINS; RIBONUCLEASES;

APPROXIMATION THEORY; CHEMICAL BONDS; COMPUTER SIMULATION; ELECTROSTATICS; POLYPEPTIDES; STRUCTURE (COMPOSITION); TITRATION;

ELECTROSTATIC INTERACTIONS; NULL APPROXIMATION (NA); PROTEIN STABILITY; UNFOLDED PROTEINS;

PROTEINS;

EID: 41349115238     PISSN: 1063651X     EISSN: None     Source Type: Journal    
DOI: 10.1103/PhysRevE.65.011901     Document Type: Article

References (47)

1. A. Karshikoff and R. Ladenstein, Trends Biochem. Sci. 26, 550 (2001).
2. G.M. Ullmann and E.W. Knapp, Eur. Biophys. J. 28, 533 (1999).
3. C.N. Pace, R.W. Alston, and K.L. Shaw, Protein Sci. 9, 1395 (2000).
4. M. Oliveberg, S. Vuilleumier, and A.R. Fersht, Biochemistry 33, 8826 (1994).
5. M. Oliveberg, V.L. Arcus, and A.R. Fersht, Biochemistry 34, 9424 (1995).
6. Y.-J. Tan, M. Olivegerg, B. Davis, and A.R. Fersht, J. Mol. Biol. 254, 980 (1995).
7. M. Schaefer, M. Sommer, and M. Karplus, J. Chem. Phys. 101, 1663 (1997).
8. J. Warwicker, Protein Sci. 8, 418 (1999).
9. J. Warwicker (private communication).
10. A.-S. Yang and B. Honig, J. Mol. Biol. 237, 602 (1994).
11. A.H. Elcock, J. Mol. Biol. 294, 1051 (1999).
12. A. Warshel and S.T. Russell, Q. Rev. Biophys. 17, 283 (1984).
13. A. Warshel, S.T. Russell, and A.K. Churg, Proc. Natl. Acad. Sci. U.S.A. 81, 4785 (1984).
14. J. Warwicker and N.C. Watson, J. Mol. Biol. 175, 527 (1984).
15. I. Klapper et al., Proteins: Struct. Funct., Genet. 1, 47 (1986).
16. A. Nicholls and B. Honig, J. Comput. Chem. 12, 435 (1991).
17. B. Honig, K. Sharp, and A.-S. Yang, J. Phys. Chem. 97, 1101 (1993).
18. C. Tanford, Physical Chemistry of Macromolecules (Wiley, New York, 1961).
19. C. Branden and J. Tooze, Introduction to Proteine Structure (Garland Publishing, New York, 1998), Chap. 1, p. 8.
20. T.E. Creighton, Proteins: Structure and Molecular Properties, 2nd ed. (Freeman, New York, 1993).
21. S.L. Kazmirski and V. Daggett, J. Mol. Biol. 277, 487 (1998).
22. C.K. Smith et al., Protein Sci. 5, 2009 (1996).
23. Y.O. Kamatari, T. Konno, M. Kataoka, and K. Akasaka, J. Mol. Biol. 259, 512 (1996).
24. M. Kataoka, K. Kuwajima, F. Tokunaga, and Y. Goto, Protein Sci. 6, 422 (1997).
25. D.J. Segel et al., J. Mol. Biol. 288, 489 (1999).
26. L. Chen et al., J. Mol. Biol. 225, 225 (1998).
27. Y.O. Kamatari, T. Konno, M. Kataoka, and K. Akasaka, Protein Sci. 7, 681 (1998).
28. B. Ibarra-Molero and J.M. Sanchez-Ruiz, Biochemistry 36, 9616 (1997).
29. G.V. Semisotnov et al., J. Mol. Biol. 262, 559 (1996).
30. T. Konno, Y. Kamatari, M. Kataoka, and K. Akasaka, Protein Sci. 6, 2242 (1997).
31. L. Shi, M. Kataoka, and A.L. Fink, Biochemistry 35, 3297 (1996).
32. V. Receveur et al., FEBS Lett. 426, 57 (1998).
33. H.H. Gan, A. Tropsha, and T. Schlick, J. Chem. Phys. 113, 5511 (2000).
34. C. Tanford and J.G. Kirkwood, J. Am. Chem. Soc. 79, 5333 (1957).
35. J.G. Kirkwood, J. Chem. Phys. 2, 351 (1934).
36. K. Binder, in Monte Carlo Methods in Statistical Physics, edited by K. Binder (Springer-Verlag, Berlin, 1979).
37. J.B. Matthew, Annu. Rev. Biophys. Biophys. Chem. 14, 387 (1985), review.
38. D. Bashford and M. Karplus, Biochemistry 29, 10 219 (1990).
39. K.-B. Wong et al., J. Mol. Biol. 296, 1257 (2000).
40. J.L. Neira and A.R. Fersht, J. Mol. Biol. 285, 1309 (1999).
41. D. Sali, M. Bycroft, and A.R. Fersht, Nature (London) 335, 740 (1988).
42. D. Stigter, D.O.V. Alonso, and K.A. Dill, Proc. Natl. Acad. Sci. U.S.A. 88, 4176 (1991).
43. R. Roxby and C. Tanford, Biochemistry 10, 3348 (1971).
44. S.T. Whitten and B. Garcia-Moreno, Biochemistry 39, 14 292 (2000).
45. P.H. McPherson, M.Y. Okamura, and G. Feher, Biochim. Biophys. Acta 934, 348 (1988).
46. D. Bashford and M. Karplus, J. Phys. Chem. 95, 9556 (1991).
47. P. Beroza, D.R. Fredkin, M.Y. Okamura, and G. Feher, Biophys. J. 68, 2233 (1995).