The role of bonded terms in free energy simulations: 1. Theoretical analysis

Journal of Physical Chemistry A

Volumn 103, Issue 1, 1999, Pages 103-118

  Boresch, Stefan ^a,b,c   Karplus, Martin ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b UNIVERSITÉ DE STRASBOURG   (France)

^c UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0042787283     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp981628n     Document Type: Article

References (77)

1. Brooks, C. L., III; Karplus, M.; Pettitt Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics; Advances in Chemical Physics LXXI; John Wiley & Sons: New York, 1988.
2. Beveridge, D. L.; DiCapua, F. M. Annu. Rev. Biophys. Chem. 1989, 18, 431-492.
3. McCammon, J. A.; Straatsma, T. P. Annu. Rev. Phys. Chem. 1992, 43, 407.
4. Kollman, P. A. Chem. Rev. 1993, 93, 2395-2417.
5. Dang, L. X.; Merz, K. M.; Kollman, P. A. J. Am. Chem. Soc. 1989, 111, 8505-8508.
6. Prevost, M.; Wodak, S. J.; Tidor, B.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 10880-10884.
7. Tidor, B.; Karplus, M. Biochemistry 1991, 30, 3217-3228.
8. Lau, F. T. K.; Karplus, M. J. Mol. Biol. 1994, 1049-1067.
9. Miyamoto, S.; Kollman, P. A. Proteins 1993, 16, 226-245.
10. Gao, J.; Kuczera, K.; Tidor, B.; Karplus, M. Science 1989, 244, 1069-1072.
11. Jorgensen, W. L.; Ravimohan, C. J. Chem. Phys. 1985, 83, 3050-3054.
12. Tobias, D. J.; Brooks, C. L., III J. Phys. Chem. 1992, 96, 3864-3870.
13. Bash, P. A.; Singh, U. C.; Langridge, R.; Kollman, P. A. Science 1987, 236, 564-568.
14. Elcock, A. H.; Richards, W. G. J. Am. Chem. Soc. 1993, 115, 7930-7931.
15. Elofsson, A.; Kulinski, T.; Rigler, R.; Nilsson, L. Proteins 1993, 17, 161-175.
16. Sun, Y.; Spellmeyer, D.; Pearlman, D. A.; Kollman, P. A. J. Am. Chem. Soc. 1992, 114, 6798-6801.
17. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. J. Am. Chem. Soc. 1995, 117, 5179-5197.
18. Tembe, B. L.; McCammon, J. A. Comput. Chem. 1984, 8, 281-283.
19. Boresch, S.; Archontis, G.; Karplus, M. Proteins 1994, 20, 25-33.
20. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
21. Jorgensen, W. L.; Swenson, C. J. Am. Chem. Soc. 1985, 106, 765-784.
22. Pearlman, D. A.; Kollman, P. A. J. Chem. Phys. 1991, 94, 4532-4546.
23. Rao, S. N.; Singh, U. C.; Bash, P. A.; Kollman, P. Nature 1987, 328, 551.
24. Van Gunsteren, W. F. In Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications; Van Gunsteren, W. F., Weiner, P. K., Eds.; Escom Science: Netherlands, 1989; pp 27-59.
25. Elofsson, A.; Nilsson, L. Mol. Simul. 1993, 10, 255-276.
26. Eriksson, M. A. L.; Nilsson, L. J. Mol. Biol. 1995, 253, 453-472.
27. Harris, D.; Loew, G. J. Comput. Chem. 1996, 17, 273-288.
28. Rao, B. G.; Kim, E. E.; Murcko, M. A. J. Comput. Aid. Mol. Des. 1996, 10, 23-30.
29. Sun, Y.-C.; Veenstra, D. L.; Kollman, P. A. Protein Eng. 1996, 9, 273-281.
30. Mark, A. E.; van Gunsteren, W. F. J. Mol. Biol. 1994, 240, 167-176.
31. Smith, P. E.; van Gunsteren, W. F. J. Chem. Phys. 1994, 100, 577-585.
32. Boresch, S.; Karplus, M., J. Mol. Biol. 1995, 254, 801-807.
33. Archontis, G.; Karplus, M. J. Chem. Phys. 1996, 105, 11246-11260.
34. Shi, Y.; Mark, A. E.; Wang, C.; Huang, F.; Berendsen, H. J. C.; van Gunsteren, W. F. Protein Eng. 1993, 6, 289-295.
35. Dill, K. A. J. Biol. Chem. 1997, 272, 701-704.
36. Simonson, T. Mol. Phys. 1993, 80, 441-447.
37. Beutler, T. C.; Mark, A. E.; van Schaik, R. C.; Gerber, P. R.; van Gunsteren, W. F. Chem. Phys. Lett. 1994, 222, 529-539.
38. Zacharias, M.; Straatsma, T. P.; McCammon, J. A. J. Chem. Phys. 1994, 100, 9025.
39. Simonson, T.; Archontis, G.; Karplus, M. J. Phys. Chem. 1997, 41, 8347-8360.
40. Hummer, G.; Pratt, L. R.; Garcia, A. E. J. Phys. Chem. 1996, 100, 1206-1215.
41. Archontis, G.; Simonson, T.; Moras, D.; Karplus, M. J. Mol. Biol. 1998, 275, 823-846.
42. Boresch, S.; Karplus, M. J. Phys. Chem. A 1988, 103, 119.
43. Kirkwood, J. G. J. Chem. Phys. 1935, 3, 300-313.
44. Hansen, J.-P.; McDonald, I. R. Theory of Simple Liquids; Academic Press: London, 1986.
45. Zwanzig, R. W.; J. Chem. Phys. 1954, 22, 1420-1426.
46. McQuarrie, D. A. Statistical Mechanics; Harper & Row: New York, 1976.
47. Straatsma, T. P.; Zacharias, M.; McCammon, J. A. In Computer Simulations in Biological Systems; van Gunsteren, W. F., Weiner, P. K., Wilkinson, A. J., Eds.; Escom Science: Netherlands, 1994.
48. Van Gunsteren, W. F.; Beutler, T. C.; Fraternali, F.; King, P. M.; Mark, A. E.; Smith, P. E. In Computer Simulations in Biological Systems; van Gunsteren, W. F., Weiner, P. K., Wilkinson, A. J., Eds.; Escom Science: Netherlands, 1994.
49. Simonson, T.; Brünger, A. T. Biochemistry 1992, 31, 8661-8674.
50. Hodel, A.; Simonson, T.; Fox, R. O.; Brünger, A. T. J. Phys. Chem. 1993, 97, 3409-3417.
51. Brady, G. P.; Sharp, K. A. J. Mol. Biol. 1995, 254, 77-85.
52. Pearlman, D. A. J. Phys. Chem. 1994, 98, 1487-1493.
53. Cross, A. J. Chem. Phys. Lett. 1986, 128, 198-202.
54. Hermans, J.; Yun, R. H.; Anderson, A. G. J. Comput. Chem. 1992, 13, 429-442.
55. Resat, H.; Mezei, M. J. Chem. Phys. 1993, 99, 6052-6061.
56. Jorgensen, W. L. BOSS, version 3.2, Department of Chemistry: Yale University, New Haven, 1992.
57. Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E., III; Ferguson, D. M.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. AMBER 4.1; University of California: San Francisco, 1995.
58. Van Gunsteren, W. F.; Berendsen, H. J. C. GROningen MOlecular Simulation (GROMOS) Library Manual; Laboratory of Physical Chemistry, University of Groningen: Groningen, 1987.
59. Straatsma, T. P.; Zacharias, M.; McCammon, J. A. Chem. Phys. Lett. 1992, 196, 297-302.
60. Wang, L.; Hermans, J. J. Chem. Phys. 1994, 100, 9129-9139.
61. Boresch, S.; Karplus, M. J. Chem. Phys. 1996, 105, 5145-5154.
62. Miranker, A.; Karplus, M Proteins 1995, 23, 472-490.
63. Verkhivker, G.; Elber, R.; Nowak, W. J. Chem. Phys. 1992, 97, 7838-7841.
64. Bash, P. A.; Field, M. J.; Karplus M. J. Am. Chem. Soc. 1987, 109, 8092-8094.
65. Gao, J. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; Verlag Chemie Publishers: New York, 1996; Vol. 7, Chapters, pp 119-185.
66. Herschbach, D. R.; Johnston, H. S.; Rapp, D. J. Chem. Phys. 1959, 31, 1652.
67. Severance. D. L.; Essex, J. W.; Jorgensen, W. L. J. Comput. Chem. 1995, 16, 311-327.
68. Ryckaert, J. P.; Cicotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341.
69. Karplus, M.; Kushick J. N. Macromolecules 1981, 14, 325-332.
70. Pearlman, D. A. J. Chem. Phys. 1993, 98, 8946-8957.
71. Guo, H.; Karplus, M. J. Phys. Chem. 1992, 96, 7273.
72. de Souza, L. E. S.; Guerin, C. B. E.; Ben-Amotz, D.; Szleifer, I. J. Chem. Phys. 1993, 99, 9954-9961.
73. Pettitt, B. M.; Karplus, M. J. Am. Chem. Soc. 1985, 107, 1166-1173.
74. MacKerell, A. D. Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L. Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E. III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Workiewicz-Kuczera, J.; Yinb, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586-3616.
75. Van Gunsteren, W. F. Mol. Phys. 1980, 40, 1015.
76. Ben-Naim, A.; Marcus, Y. J. Chem. Phys. 1984, 81, 2016-2027.
77. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. Biophys. J. 1997, 72, 1047-1069.