Langevin dynamics of proteins at constant pH

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 66, Issue 5, 2002, Pages

  Walczak, Aleksandra M ^a   Antosiewicz, Jan M ^a  

^a UNIVERSITY OF WARSAW   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COMPUTER SIMULATION; MOLECULAR BIOLOGY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PH EFFECTS; PROTEINS;

BOLTZMANN DISTRIBUTION; LANGEVIN DYNAMICS; MULTISITE POLYMERS; PROTONATION;

MOLECULAR DYNAMICS;

EID: 37649030225     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.66.051911     Document Type: Article

References (50)

1. L. Stryer, Biochemistry, 4th ed. (Freeman, New York, 1995).
2. P.W. Atkins, Physical Chemistry (Freeman, New York, 1994).
3. D. Poland, Cooperative Equilibria in Physical Biochemistry (Clarendon Press, Oxford, 1978).
4. K. Bartik, C. Redfield, and C.M. Dobson, Biophys. J. 66, 1180 (1994).
5. A. Warshel, Biochemistry 20, 3167 (1981).
6. J. Antosiewicz, J.A. McCammon, and M.K. Gilson, Biochemistry 35, 7819 (1996).
7. R.A. Dimitrov and R.R. Crichton, Proteins: Struct., Funct., Genet. 27, 576 (1997).
8. Y.Y. Sham, Z.T. Chu, and A. Warshel, J. Phys. Chem. B 101, 4458 (1997).
9. H.W.T. van Vlijmen, M. Schaefer, and M. Karplus, Proteins: Struct, Funct., Genet. 33, 145 (1998).
10. A.A. Gorfe, P. Ferrara, A. Caflisch, D.N. Marti, H.R. Bosshard, and I. Jelesarov, Proteins: Struct., Funct, Genet. 46, 41 (2002).
11. J. Warwicker and H.C. Watson, J. Mol. Biol. 157, 671 (1982).
12. D. Bashford and M. Karplus, Biochemistry 29, 10219 (1990).
13. D. Bashford and K. Gerwert, J. Mol. Biol. 224, 473 (1992).
14. H. Zhou and M. Vijayakumar, J. Mol. Biol. 267, 1002 (1997).
15. L. Sandberg and O. Edholm, Biophys. Chem. 65, 189 (1997).
16. V. Dillet, H. Dyson, and D. Bashford, Biochemistry 37, 10298 (1998).
17. C.H. Pletcher, E.F. Bouhoutsos-Brown, R.G. Bryant, and G.L. Nelsestuen, Biochemistry 20, 6149 (1981).
18. D.R. Ripoll, Y.N. Vorobjev, A. Liwo, J.A. Vila, and H.A. Scheraga, J. Mol. Biol. 264, 770 (1996).
19. S.T. Wlodek, J. Antosiewicz, and J.A. McCammon, Protein Sci. 6, 373 (1997).
20. J.E. Mertz and B.M. Pettitt, Int. J. Supercomput. Appl. 8, 47 (1994).
21. A.M. Baptista, P.J. Martel, and S.B. Petersen, Proteins: Struct., Funct., Genet. 27, 523 (1997).
22. U. Börjesson and PH. Hünenberger, J. Chem. Phys. 114, 9706 (2001).
23. A.M. Baptista, J. Chem. Phys. 116, 7766 (2001).
24. R. Bürgi, P.A. Kollman, and W.F. van Gunsteren, Proteins: Struct., Funct., Genet. 47, 469 (2002).
25. J. Antosiewicz, Biophys. J. 69, 1344 (1995).
26. F.C. Bernstein, T.F. Koettzle, G.J.B. Williams, E.F. Meyer, M.D. Brice, J.R. Rodgers, O. Kennard, T. Shimanouchi, and M.J. Tasumi, J. Mol. Biol. 123, 557 (1977).
27. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).
28. A.D. MacKerell, Jr. et al., J. Phys. Chem. B 102, 3586 (1998).
29. W. Bode, O. Epp, R. Huber, M. Laskowski, Jr., and W. Ardelt, Eur. J. Biochem. 147, 387 (1985).
30. J. Antosiewicz, J.M. Briggs, A.E. Elcock, M.K. Gilson, and J.A. McCammon, J. Comput. Chem. 17, 1633 (1996).
31. M.E. Davis, J.D. Madura, B.A. Luty, and J.A. McCammon, Comput. Phys. Commun. 62, 187 (1991).
32. J.D. Madura et al., Comput. Phys. Commun. 91, 57 (1995).
33. M.K. Gilson, Proteins: Struct., Funct, Genet. 15, 266 (1993).
34. G. Widmalm and R.W. Pastor, J. Chem. Soc., Faraday Trans. 88, 1747 (1992).
35. W. Ardelt and J.M. Laskowski, J. Mol. Biol. 220, 1041 (1993).
36. L. Swint-Kruse and A.D. Robertson, Biochemistry 34, 4724 (1995).
37. C.B. Arlington and A.D. Robertson, Biochemistry 36, 8686 (1997).
38. W.R. Forsyth, M.K. Gilson, J. Antosiewicz, O.R. Jaren, and A.D. Robertson, Biochemistry 37, 8643 (1998).
39. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton, J. Appl. Crystallogr. 26, 283 (1993).
40. A. Bundi and K. Wüthrich, Biopolymers 18, 285 (1979).
41. W.R. Forsyth and A.D. Robertson, Biochemistry 39, 8067 (2000).
42. C.N. Schutz and A. Warshel, Proteins: Struct., Funct., Genet. 44, 400 (2001).
43. T. Grycuk, J. Phys. Chem. B 106, 1434 (2002).
44. M. Wojciechowski, T. Grycuk, J.M. Antosiewicz, and B. Lesyng, Biophys. J. (to be published).
45. K.A. Sharp, J. Comput. Chem. 12, 454 (1990).
46. B.N. Dominy and C.L. Brooks, Jr., J. Phys. Chem. B 103, 3765 (1999).
47. T. Lazardis and M. Karplus, Proteins: Struct., Funct., Genet. 35, 133 (1999).
48. M. Schaefer, C. Bartels, and M. Karplus, J. Mol. Biol. 284, 835 (1998).
49. J. Warwicker, Protein Eng. 10, 809 (1997).
50. R.A. Abagyan, M.M. Totrov, and D.N. Kuznetsov, J. Comput. Chem. 15, 488 (1994).