pH-dependent stability of a decalysine α-helix studied by explicit-solvent molecular dynamics simulations at constant pH

Journal of Physical Chemistry B

Volumn 108, Issue 35, 2004, Pages 13551-13559

  Börjesson, Ulf ^a   Hünenberger, Philippe H ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ACIDOSTAT METHOD; DECALYSINE PEPTIDES; POLYLYSINE PEPTIDES; PROTONATION;

COMPUTER SIMULATION; DATA ACQUISITION; FREE ENERGY; HYDROGEN BONDS; MOLECULAR DYNAMICS; MONTE CARLO METHODS; PH EFFECTS;

POLYPEPTIDES;

EID: 4444267747     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp037841n     Document Type: Article

References (54)

1. Poland, D. Cooperative Equilibria in Physical Biochemistry; Clarendon Press: Oxford, UK, 1978.
2. Yang, A. S.; Honig, B. J. Mol. Biol. 1993, 231, 459.
3. Bashford, D.; Karplus, M. J. Phys. Chem. 1991, 95, 9556.
4. Yang, A. S.; Gunner, M. R.; Sampogna, R.; Sharp, K.; Honig, B. Proteins: Struct. Funct. Genet. 1993, 15, 252.
5. Gilson, M. K. Proteins: Struct. Funct. Genet. 1993, 15, 266.
6. Antosiewicz, J.; McCammon, J. A.; Gilson, M. K. J. Mol. Biol. 1994, 238, 415.
7. Bashford, D.; Karplus, M. Biochemistry 1990, 29, 10219.
8. Beroza, P.; Fredkin, D. R.; Okamura, M. Y.; Feher, G. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 5804.
9. Beroza, P.; Fredkin, D. R. J. Comput. Chem. 1996, 17, 1229.
10. Bashford, D.; Gerwert, K. J. J. Mol. Biol. 1992, 224, 473.
11. Bashford, D.; Case, D. A.; Dalvit, C.; Tennant, L.; Wright, P. E. Biochemistry 1993, 32, 8045.
12. You, T. J.; Bahsford, D. Biophys. J. 1995, 69, 1721.
13. Wlodek, S. T.; Antosiewicz, J.; McCammon, J. A. Protein Sci. 1997, 6, 373.
14. Gorfe, A. A.; Ferrara, P.; Caflisch, A.; Marti, D. N.; Bosshard, H. R.; Jelesarov, I. Proteins: Struct. Funct. Genet. 2002, 46, 41.
15. Walczak, A. M.; Antosiewicz, J. Phys. Rev. E 2002, 66, 051911.
16. Vorobjev, Y. N.; Scheraga, H. A.; Hitz, B.; Honig, B. J. Phys. Chem. 1994, 98, 10940.
17. Vorobjev, Y. N.; Scheraga, H. A.; Honig, B. J. Phys. Chem. 1995, 99, 7180.
18. Mehler, E. L. J. Phys. Chem. 1996, 100, 16006.
19. Jayaram, B.; Liu, Y.; Beveridge, D. L. J. Chem. Phys. 1998, 109, 1465.
20. Bashford, D.; Case, D. A. Annu. Rev. Phys. Chem. 2000, 51, 129.
21. Lim, C.; Bashford, D.; Karplus, M. J. Phys. Chem. 1991, 95, 5610.
22. Sham, Y. Y.; Chu, Z. T.; Warshel, A. J. Phys. Chem. B 1997, 101, 4458.
23. Russell, S. T.; Warshel, A. J. Mol. Biol. 1985, 185, 389.
24. Zhou, R. H.; Berne, B. J. Proc. Nat:. Acad. Sci. U.S.A. 2002, 99, 12777.
25. Tuckerman, M. E.; Laasonen, K.; Sprik, M.; Parrinello, M. J. Chem. Phys. 1995, 103, 150.
26. Bala, P.; Grochowski, P.; Lesyng, B.; McCammon, J. A. J. Phys. Chem. 1996, 100, 2535.
27. Billeter, S. R.; van Gunsteren, W. F. J. Phys. Chem. A 1999, 102, 4669.
28. Billeter, S. R.; van Gunsteren, W. F. J. Phys. Chem. A 2000, 104, 3276.
29. Duh, D. M.; Perera, D. N.; Haymet, A. D. J. J. Chem. Phys. 1995, 102, 3736.
30. Lill, M. A.; Helms, V. J. Chem. Phys. 2001, 114, 1125.
31. Lill, M. A.; Hutter, M. C.; Helms, V. J. Phys. Chem. A 2000, 104, 8283.
32. Mertz, J. E.; Pettitt, B. M. Supercompt. Appl. High Perf. Comput. 1994, 8, 47.
33. Baptista, A. M.; Martel, P. J.; Petersen, S. B. Proleins: Struct. Funct. Genet. 1997, 27, 523.
34. Baptista, A. M.; Teixeira, V. H.; Soares, C. M. J. Chem. Phys. 2002, 117, 4184.
35. Bürgi, R.; Kollman, P. A.; van Gunsteren, W. F. Proteins: Struct. Funct. Genet. 2002, 47, 469.
36. Börjesson, U.; Hünenberger, P. H. J. Chem. Phys. 2001, 114, 9706.
37. Kong, X. J.; Brooks, C. L. J. Chem. Phys. 1996, 105, 2414.
38. Baptista, A. M. J. Chem. Phys. 2002, 116, 7766.
39. Chou, P. Y.; Scheraga, H. A. Biopolymers 1971, 10, 657.
40. Daura, X.; Mark, A. E.; van Gunsteren, W. F. J. Comput. Chem. 1998, 19, 535.
41. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. In Intermolecular Forces: Pullman, B., Ed.; Reidel: Dordrecht, The Netherlands, 1981.
42. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular simulation: The GROMOS96 manual and user guide: Verlag der Fachvereine: Zürich, Switzerland, 1996.
43. Scott, W. R. P.; Hünenberger, P. H.; Tironi, I. G.; Mark, A. E.; Billeter, S. R.; Fennen, J.; Torda, A. E.; Huber, T.; Krüger, P.; van Gunsteren, W. F. J. Phys. Chem. A 1999, 103, 3596.
44. Oostenbrink, C.; Villa, A.; Mark, A. E.; van Gunsteren, W. F. Manuscript in preparation.
45. Barker, J. A. Watts, R. O. Mol. Phys. 1973, 26, 789.
46. Tironi, I. G.; Sperb, R.; Smith, P. E.; van Gunsteren, W. F. J. Chem. Phys. 1995, 102, 5451.
47. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327.
48. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684.
49. Smith, R. M.; Martell, A. E. Critical Stability Constants; Plenum Press: New York, 1975; Vol. 2.
50. Smith, R. M.; Martell, A. E. Critical Stability Constants: Plenum Press: New York, 1982; Vol. 5.
51. Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577.
52. Peter, C.; van Gunsteren, W. F.; Hünenberger, P. H. J. Chem. Phys. 2003, 119, 12205.
53. Bergdorf, M.; Peter, C.; Hünenberger, P. H. J. Chem. Phys. 2003, 119, 9129.
54. Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187.