Evaluation of models of electrostatic interactions in proteins

Journal of Physical Chemistry B

Volumn 107, Issue 9, 2003, Pages 2075-2090

  Morozov, Alexandre V ^a   Kortemme, Tanja ^b   Baker, David ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; ELECTROSTATICS; ENERGY GAP; FREE ENERGY; HYDROGEN BONDS; MOLECULAR STRUCTURE; NUMERICAL METHODS;

COULOMB INTERACTIONS; ELECTROSTATIC INTERACTIONS; POISSON-BOLTZMANN EQUATION; SOLVATION ENERGY;

PROTEINS;

EID: 0037422359     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0267555     Document Type: Article

References (68)

1. Warshel, A.; Russell, S. T. Q. Rev. Biophys. 1984, 17, 283-422.
2. Sharp, K. A.; Honig, B. Annu. Rev. Biophys. Biophys. Chem. 1990, 19, 301-332.
3. Warshel, A.; Åqvist, J. Annu. Rev. Biophys. Biophys. Chem. 1991, 20, 267-298.
4. Nakamura, H. Q. Rev. Biophys. 1996, 29, 1-90.
5. Sheinerman, F. B.; Norel, R.; Honig, B. Cur. Opin. Str. Biol. 2000, 10, 153-159.
6. Jackson, J. D. Classical electrodynamics; John Wiley & Sons: New York, 1975.
7. Huang, K. Statistical mechanics; John Wiley & Sons: New York, 1987.
8. Landau, L. D.; Lifshitz, E. M. Electrodynamics of continuous media; Pergamon: Oxford, 1984.
9. Schutz, C. N.; Warshel, A. Proteins: Struct., Funct., Genet. 2001, 44, 400-417.
10. King, G.; Lee, F. S.; Warshel, A. J. Chem. Phys. 1991, 95, 4366-4377.
11. Nakamura, H.; Sakamoto, T.; Wada, A. Prot. Eng. 1988, 2, 177-183.
12. Dwyer, J. J.; Gittis, A. G.; Karp, D. A.; Lattman, E. E.; Spencer, D. S.; Stites, W. E.; Garcia-Moreno, B. Biophys. J. 2000, 79, 1610-1620.
13. Honig, B.; Nichols, A. Science 1995, 268, 1144-1194.
14. Warwicker, J.; Watson, H. C. J. Mol. Biol. 1982, 157, 671-679.
15. Gilson, M. K.; Sharp, K. A.; Honig, B. J. Comput. Chem. 1987, 9, 327-335.
16. Rocchia, W.; Alexov, E.; Honig, B. J. Phys. Chem. B 2001, 105, 6507-6514.
17. Yang, A.; Honig, B. J. Mol. Biol. 1995, 252, 351-365.
18. Lee, L. P.; Tidor, B. Nat. Struct. Biol. 2001, 8, 73-76.
19. Lee, L. P.; Tidor, B. Prot. Sci. 2001, 10, 362-377.
20. Marshall, S. A.; Morgan, C. S.; Mayo, S. L. J. Mol. Biol. 2002, 316, 189-199.
21. Vorobjev, Y. N.; Almagro, J. C.; Hermans, J. Proteins: Struct., Funct., Genet. 1998, 32, 399-413.
22. Vorobjev, Y. N.; Hermans, J. Biophys. Chem. 1999, 78, 195-205.
23. Vorobjev, Y. N.; Hermans, J. Protein Sci. 2001, 10, 2498-2506, addendum in Protein Sci. 2002, 11, 994.
24. Lee, M. R.; Tsai, J.; Baker, D.; Kollman, P. J. Mol. Biol. 2001, 313, 417-430.
25. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127-6129.
26. Schaefer, M.; Karplus, M. J. Phys. Chem. 1996, 100, 1578-1599.
27. Ghosh, A.; Rapp, C. S.; Friesner, R. A. J. Phys. Chem. B 1998, 102, 10983-10990.
28. Qiu, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. J. Phys. Chem. A 1997, 101, 3005-3014.
29. Dominy, B. N.; Brooks, C. L., III. J. Phys. Chem. B 1999, 103, 3765-3773.
30. Jayaram, B.; Sprous, D.; Beveridge, D. L. J. Phys. Chem. B 1998, 102, 9571-9576.
31. Jayaram, B.; Liu, Y.; Beveridge, D. L. J. Chem. Phys. 1998, 109, 1465-1471.
32. Bashford, D.; Case, D. A. Annu. Rev. Phys. Chem. 2000, 51, 129-152.
33. Cramer, C. J.; Truhlar, D. G. Chem. Rev. 1999, 99, 2161-2200.
34. Zou, X.; Sun, Y.; Kuntz, I. D. J. Am. Chem. Soc. 1999, 121, 8033-8043.
35. Zhang, L. Y.; Gallicchio, E.; Friesner, R. A.; Levy, R. M. J. Comput. Chem. 2001, 22, 591-607.
36. Srinivasan, J.; Cheatham, T. E., III; Cieplak, P.; Kollman, P. A.; Case, D. A. J. Am. Chem. Soc. 1998, 120, 9401-9409.
37. Tsui, V.; Case, D. A. J. Am. Chem. Soc. 2000, 122, 2489-2498.
38. Wallqvist, A.; Gallicchio, E.; Felts, A. K.; Levy, R. M. Adv. Chem. Phys. 2002, 120, 459-486.
39. Felts, A. K.; Gallicchio, E.; Wallqvist, A.; Levy, R. M. Proteins: Struct., Funct., Genet. 2002, 48, 404-422.
40. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
41. Gabb, H. A.; Jackson, R. M.; Sternberg, M. J. E. J. Mol. Biol. 1997, 272, 106-120.
42. Israelachvili, J. Intermolecular and surface forces; Academic Press: London, 1997.
43. Hassan, S. A.; Guarnieri, F.; Mehler, E. L. J. Phys. Chem. B 2000, 104, 6490-6498.
44. Baker, E. N.; Hubbard, R. E. Prog. Biophys. Mol. Biol. 1984, 44, 97-179.
45. Anfinsen, C. B. Science 1973, 181, 223-230.
46. Bryngelson, J. D.; Wolynes, P. G. Proc. Natl. Acad. Sci. 1987, 84, 7524-7528.
47. Petrey, D.; Honig, B. Prot. Sci. 2000, 9, 2181-2191.
48. Gatchell,D. W.; Dennis, S.; Vajda, S. Proteins: Struct., Funct., Genet. 2000, 41, 518-534.
49. Lazaridis, T.; Karplus, M. J. Mol. Biol. 1998, 288, 477-487.
50. Hassan, S. A.; Mehler, E. L. Proteins: Struct., Funct., Genet. 2002, 47, 45-61.
51. Norel, R.; Sheinerman, F.; Petrey, D.; Honig, B. Protein Sci. 2001, 10, 2147-2161.
52. Kortemme, T.; Morozov, A. V.; Baker, D. J. Mol. Biol. In press.
53. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
54. Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. Chem. Phys. Lett. 1995, 246, 122-129.
55. Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. 1996, 100, 19824-19839.
56. Kortemme, T.; Baker, D. Proc. Natl. Acad. Sci. 2002, 99, 14116-14121.
57. Kuhlman, B.; Baker, D. Proc. Natl. Acad. Sci. 2000, 97, 10383-10388.
58. Neria, E.; Fischer, S.; Karplus, M. J. Chem. Phys. 1996, 105, 1902-1921.
59. Simons, K. T.; Kooperberg, C.; Huang, E.; Baker, D. J. Mol. Biol. 1997, 268, 209-225.
60. Simons, K. T.; Ruczinski, I.; Kooperberg, C.; Fox, B. A.; Bystroff, C.; Baker, D. Proteins: Struct., Funct., Genet. 1999, 34, 82-95.
61. Tsai, J.; Bonneau, R.; Morozov, A. V.; Kuhlman, B.; Rohl, C.; Baker, D. Proteins: Struct., Funct., Genet. In press.
62. Conte, L. L.; Chothia, C.; Janin, J. J. Mol. Biol. 1999, 285, 2177-2198.
63. Gray, J. J.; Moughon, S.; Kortemme, T.; Schueler-Furman, O.; Misura, K. M. S.; Morozov, A. V.; Baker, D. Proteins: Struct., Funct., Genet. In press.
64. Hao, M. H.; Scheraga, H. A. Curr. Opin. Struct. Biol. 1999, 9, 184-188.
65. Srinivasan, J.; Trevathan, M. W.; Beroza, P.; Case, D. A. Theor. Chem. Acc. 1999, 101, 426-434.
66. Sitkoff, D.; Sharp, K. A.; Honig, B. J. Phys. Chem. 1994, 98, 1978-1988.
67. Lawrence, M. C.; Colman, P. M. J. Mol. Biol. 1993, 234, 946-950.
68. Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110, 1657-1666.