Balancing solvation and intramolecular interactions: Toward a consistent generalized born force field

Journal of the American Chemical Society

Volumn 128, Issue 11, 2006, Pages 3728-3736

  Chen, Jianhan ^a   Im, Wonpil ^a,b   Brooks III, Charles L ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; COMPUTER SIMULATION; ELECTROSTATICS; MOLECULAR DYNAMICS; OPTIMIZATION; TORSIONAL STRESS;

BALANCING SOLVATION; BIOLOGICAL PROBLEMS; INTRAMOLECULAR INTERACTIONS; POTENTIALS OF MEAN FORCE (PMF); STRUCTURAL DYNAMICS; TORSIONAL ENERGETICS;

CONTINUUM MECHANICS;

ARTICLE; CONFORMATIONAL TRANSITION; ELECTRIC POTENTIAL; ELECTROMAGNETIC FIELD; ENERGY; FORCE; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PROTEIN STRUCTURE; SOLVATION; STRUCTURE ANALYSIS; THEORETICAL MODEL;

AMINO ACID SEQUENCE; KINETICS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; SOLUTIONS; THERMODYNAMICS;

EID: 33645408056     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja057216r     Document Type: Article

References (102)

1. Brooks, C. L., III; Karplus, M.; Pettitt, B. M. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics; John Wiley and Sons: New York, 1988.
2. Feig, M.; Brooks, C. L., III. Curr. Opin. Struct. Biol. 2004, 14, 217-224.
3. Roux, B.; Simonson, T. Biophys. Chem. 1999, 78, 1-20.
4. Bashford, D.; Case, D. A. Annu. Rev. Phys. Chem. 2000, 51, 129-152.
5. Cramer, C. J.; Truhlar, D. G. Chem. Rev. 1999, 99, 2161-2200.
6. Lazaridis, T.; Karplus, M. Curr. Opin. Struct. Biol. 2000, 10, 139-145.
7. Simonson, T. Curr. Opin. Struct. Biol. 2001, 11, 243-252.
8. Im, W. Chen, J.; Brooks, C. L., III. Adv. Prot. Chem. 2006, 72, 171-195.
9. Warwicker, J.; Watson, H. C. J. Mol. Biol. 1982, 157, 671-679.
10. Klapper, I. Hagstrom, R.; Fine, R.; Sharp, K.; Honig, B. Proteins 1986, 1, 47-59.
11. Nicholls, A.; Honig, B. J. Comput. Chem. 1991, 12, 435-445.
12. Im, W. Beglov, D.; Roux, B. Comput. Phys. Comm. 1998, 111, 59-75.
13. Honig, B.; Nicholls, A. Science 1995, 268, 1144-1149.
14. Roux, B. Bernèche, S.; Im, W. Biochemistry 2000, 39, 13295-13306.
15. Luo, R.; David, L.; Gilson, M. K. J. Comput. Chem. 2002, 23, 1244-1253.
16. Prabhu, N. V.; Zhu, P.; Sharp, K. A. J. Comput. Chem. 2004, 25, 2049-2064.
17. Still, W. C.; Tempezyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127-6129.
18. Constanciel, R.; Contreras, R. Theo. Chim. Acta 1984, 65, 1-11.
19. Born, M. Z. Phys. 1920, 1, 45-48.
20. Onufriev, A. Case, D. A.; Bashford, D. J. Comput. Chem. 2002, 23, 1297-1304.
21. Feig, M.; Onufriev, A.; Lee, M. S.; Im, W.; Case, D. A.; Brooks, C. L., III. J. Comput. Chem. 2004, 25, 265-284.
22. Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. 1996, 100, 19824-19839.
23. Schaefer, M.; Karplus, M. J. Phys. Chem. 1996, 100, 1578-1599.
24. Qiu, D. Shenkin, P. S.; Hollinger, F. P.; Still, W. C. J. Phys. Chem. A 1997, 101, 3005-3014.
25. Scarsi, M.; Apostolakis, J.; Caflisch, A. J. Phys. Chem. A 1997, 101, 8098-8106.
26. Ghosh, A.; Rapp, C. S.; Friesner, R. A. J. Phys. Chem. B 1998, 102, 10983-10990.
27. Dominy, B. N.; Brooks, C. L., III J. Phys. Chem. B 1999, 103, 3765-3773.
28. Srinivasan, J.; Trevathan, M. W.; Berozu, P.; Case, D. A. Theor. Chem. Acc. 1999, 101, 426-434.
29. Tsui, V.; Case, D, A. J. Am. Chem. Soc. 2000, 11, 2489-2498.
30. Onufriev, A. Bashford, D.; Case, D. A. J. Phys. Chem. B 2000, 104, 3712-3720.
31. Lee, M. S.; Salsbury, F. R., Jr.; Brooks, C. L., III J. Chem. Phys. 2002, 116, 10606-10614.
32. Spassov, V. Z.; Yan, L.; Szalma, S. J. Phys. Chem. B 2002, 106, 8726-8738.
33. Im, W.; Lee, M. S.; Brooks, C. L., III J. Comput. Chem. 2003, 24, 1691-1702.
34. Im, W.; Feig, M.; Brooks, C. L., III Biophys. J. 2003, 85, 2900-2918.
35. Gallicchio, E.; Levy, R. M. J. Comput. Chem. 2004, 25, 479-499.
36. Feig, M. Im, W.; Brooks, C. L., III J. Chem. Phys. 2004, 120, 903-910.
37. Zhu, J.; Alexov, E.; Honig, B. J. Phys. Chem. B 2005, 109, 3008-3022.
38. Luo, R.; David, L.; Hung, H.; Devaney, J.; Gilson, M. K. J. Phys. Chem. B 1999, 103, 727-736.
39. Gallicchio, E.; Zhang, L. Y.; Levy, R. M. J. Comput. Chem. 2002, 5, 517-529.
40. R. Zhou Proteins 2003, 53, 148-161.
41. Masunov, A.; Lazaridis, T. J. Am. Chem. Soc. 2003, 125, 1722-1730.
42. Khandogin, J.; Brooks, C. L., III Biophys. J. 2005, 89, 141-157.
43. Zhou, R.; Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12777-12782.
44. Nymeyer, H.; Garcia, A. E. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13934-13939.
45. Jaramillo, A.; Wodak, S. J. Biophys. J. 2005, 88, 156-171.
46. Joregensen, W. L. Chandrasekhar, J.; Madura, D. J.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
47. MacKerell, A. D., Jr. J. Comput. Chem. 2004, 25, 1584-1604.
48. MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III J. Comput. Chem. 2004, 25, 1400-1415.
49. Okur, A.; Strockbine, B.; Hornak, V.; Simmerling, C. J. Comput. Chem. 2003, 24, 21-31.
50. Nina, M.; Beglov, D.; Roux, B. J. Phys. Chem. B 1997, 101, 5239-5248.
51. Nina, M.; Im, W.; Roux, B. Biophys. Chem. 1999, 78, 89-96.
52. Banavali, N. K.; Roux, B. J. Phys. Chem. B 2002, 106, 11026-11035.
53. Im, W.; Brooks, C. L. J. Mol. Biol. 2004, 337, 513-519.
54. Chen, J. Im, W.; Brooks, C. L., III J. Am. Chem. Soc. 2004, 126, 16038-16047.
55. Chen, J.; Won, H.-S.; Im, W.; Dyson, H. J.; Brooks, C. L. J. Biomol. NMR 2004, 31, 59-64.
56. Ferrara, P.; Apostolakis, J.; Caflisch, A. J. Phys. Chem. B 2000, 104, 5000-5010.
57. Felts, A. K.; Harano, Y.; Gallicchio, E.; Levy, R. M. Proteins 2004, 56, 310-321.
58. Ulmsehneider, J. P.; Jorgensen, W. L. J. Am. Chem. Soc. 2004, 126, 1849-1857.
59. Liwo, A. Khalili, M.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 2362-2367.
60. Irbäck, A.; Mohanty, S. Biophys. J. 2005, 88, 1560-1569.
61. Sugita, Y.; Okamoto, Y. Chem. Phys. Lett. 1999, 314, 141-151.
62. Hansmann, U. H. E.; Okamoto, Y. Curr. Opin. Struct. Biol. 1999, 9, 177-183.
63. Feig, M. Karanicolas, J.; Brooks, C. L., III MMTSB Tool Set, MMTSB NIH Research Resource, The Scripps Research Institute. 2001.
64. Feig, M.; Karanicolas, J.; Brooks, C. L., III J. Mol. Graph. Model. 2004, 22, 377-395.
65. MacKerell, A. D., Jr.; Bashford, D.; Bellott, R. L.; 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.; Stole, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem B 1998, 102, 3586-3616.
66. Feig, M.; MacKerell, A. D., Jr.; Brooks, C. L. III J. Phys. Chem. 2003, 107, 2831-2836,
67. MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III J. Am. Chem. Soc. 2004, 126, 98-699.
68. Yoda, T.; Sugita, Y.; Okamoto, Y. Chem. Phys. 2004, 307, 269-283.
69. Fesinmeyer, R. M.; Hudson, F. M.; Andersen, N. H. J. Am. Chem. Soc. 2004, 126, 7238-7243.
70. Hassan, S. A.; Mehler, E. L. Int. J. Quantum Chem. 2001, 83, 193-202.
71. Liu, Y.; Beveridge, D. L. Proteins 2002, 46, 128-146.
72. Zagrovic, B. Sorin, E. J.; Pande, V. J. Mol. Biol. 2001, 313, 151-169.
73. Zhou, R. H.; Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12777-12782.
74. Jang, S. Shin, S.; Pak, Y. J. Am. Chem. Soc. 2002, 124, 4976-4977.
75. Yang, W. Y.; Pitera, J. W.; Swope, W. C.; Gruebele, M. J. Mol. Biol. 2004, 336, 241-251.
76. Simmerling, C.; Strockbine, B.; Roitberg, A. E. J. Am. Chem. Soc. 2002, 124, 11258-11259.
77. Pitera, J. W.; Swope, W. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 7587-7592.
78. Carnevali, P.; Toth, G.; Toubassi, G.; Meshkat, S. N. J. Am. Chem. Soc. 2003, 125, 14244-14245.
79. Chowdhury, S.; Lee, M. C.; Xiong, G.; Duan, Y. J. Mol. Biol. 2003, 327, 711-717.
80. Steinbaeh, P. J. Proteins 2004, 57, 665-677.
81. Schug, A.; Herges, T.; Wenzel, W. Phys. Rev. Lett. 2003, 91, 158102.
82. Shalongo, W.; Dugad, L.; Stellwagen, E. J. Am. Chem. Soc. 1994, 116, 8288-8293.
83. Blanco, O.; Rivas, F. J.; Serrano, L. Nat. Struct. Biol. 1994, 1, 584-590.
84. Munoz, V. Thompson, P. A.; Hofrichter, J.; Eaton, W. A. Nature 1997, 390, 196-199.
85. Cochran, A. G.; Skelton, N. J.; Starovasnik, M. A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 5578-5583.
86. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
87. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8593.
88. Brooks, C. L., III; Pettitt, B. M.; Karplus, M. J. Chem. Phys. 1985, 83, 5897-5908.
89. Steinbach, P. J.; Brooks, B. R. J. Comput. Chem. 1994, 15, 667-683.
90. Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187-199.
91. Kumar, S. Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021.
92. Roux, B. Comput. Phys. Comm. 1995, 91, 275-282.
93. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341.
94. Goldstein, R. A.; Luthey-Schulten, Z. A.; Wolynes, P. G. Proc. Natl. Acad. Sci., U.S.A. 1992, 89, 9029-9033.
95. Kortemme, T.; Morozov, A. V.; Baker, D. J. Mol. Biol. 2003, 326, 1239-1259.
96. Guvench, O.; Brooks, C. L., III J. Chem. Phys. 2006, submitted for publication.
97. Tjandra, N. Garrett, D. S.; Gronenborn, A. M.; Bax, A.; Clore, G. M. Nat. Struct. Biol. 1997, 4, 443-449.
98. Du, D.; Zhu, Y.; Huang, C. Y.; Gai, F. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 15915-15920.
99. de la Paz, M. L.; Lacroix, E.; Ramirez-Alvarado, M.; Serrano, L. J. Mol. Biol. 2001, 312, 229-246.
100. Dahiyat, B. I.; Mayo, S. L. Science 1997, 278, 82-87.
101. Neidigh, J. W. Fesinmeyer, R. M.; Andersen, N. H. Nat. Struct. Biol. 2002, 9, 425-430.
102. Chen, J.; Im, W.; Brooks, C. L., III J. Camput. Chem. 2005, 26, 1565-1578.