Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules

Journal of Chemical Physics

Volumn 123, Issue 1, 2005, Pages

  Schaefer, Patricia ^a   Riccardi, Demian ^a   Cui, Qiang ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULAR SYSTEM; CHARGE DENSITY; MOLECULAR MECHANICS (MM); POISSON-BOLTZMANN LEVEL;

BOUNDARY CONDITIONS; COMPUTER SIMULATION; CONFORMATIONS; ELECTROSTATICS; ENZYMES; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; QUANTUM THEORY;

MACROMOLECULES;

CARBONATE DEHYDRATASE; IMIDAZOLE; IMIDAZOLE DERIVATIVE; SOLVENT;

ARTICLE; CATALYSIS; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; ELECTRICITY; ERYTHROCYTE; HUMAN; MACROMOLECULE; METABOLISM; POISSON DISTRIBUTION; QUANTUM THEORY; STATISTICAL MODEL; STATISTICS; X RAY CRYSTALLOGRAPHY;

CARBONIC ANHYDRASES; CATALYSIS; CRYSTALLOGRAPHY, X-RAY; ELECTROSTATICS; ERYTHROCYTES; HUMANS; IMIDAZOLES; MACROMOLECULAR SUBSTANCES; MODELS, STATISTICAL; MOLECULAR CONFORMATION; POISSON DISTRIBUTION; QUANTUM THEORY; SOFTWARE; SOLVENTS; STOCHASTIC PROCESSES;

EID: 34548059996     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1940047     Document Type: Article

References (90)

1. A. Fersht, Enzyme Structure, Mechanism and Protein Foldings 3rd ed. (Freeman, San Francisco, 1998).
2. C. L. Brooks III, M. Karplus, and B. M. Pettitt, Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics, Advances in Chemical Physics Vol. LXXI (Wiley, New York, 1988).
3. B. Honig and A. Nicholls, Science 268, 1144 (1995).
4. A. Warshel and A. Papazyan, Curr. Opin. Struct. Biol. 8, 211 (1998).
5. A. Warshel and S. T. Russell, Q. Rev. Biophys. 17, 283 (1984).
6. A. Warshel, Annu. Rev. Biophys. Biomol. Struct. 32, 425 (2003).
7. M. E. Davis and J. A. McCammon, Chem. Rev. (Washington, D.C.) 90, 509 (1990).
8. C. Sagui and T. A. Darden, Annu. Rev. Biophys. Biomol. Struct. 28, 155 (1999).
9. V. Luzhkov and A. Warshel, J. Comput. Chem. 13, 199 (1992).
10. J. Florian and A. Warshel, J. Phys. Chem. B 101, 5583 (1997).
11. J. Gao and C. Alhambra, J. Chem. Phys. 107, 1212 (1997).
12. K. Nam, J. Gao, and D. M. York, J. Chem. Theory Comput. 1, 2 (2005).
13. B. A. Gregersen and D. M. York, J. Phys. Chem. B 109, 536 (2005).
14. G. Li, X. Zhang, and Q. Cui, J. Phys. Chem. B 107, 8643 (2003).
15. A. R. Dinner, X. Lopez, and M. Karplus, Theor. Chem. Acc. 109, 118 (2003).
16. J. Gao, Acc. Chem. Res. 29, 298 (1996).
17. Q. Cui and M. Karplus, Adv. Protein Chem. 66, 315 (2003).
18. J. Gao and D. G. Truhlar, Annu. Rev. Phys. Chem. 53, 467 (2002).
19. S. Bogusz, T. E. Cheatham III, and B. R. Brooks, J. Chem. Phys. 108, 7070 (1998).
20. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98, 10089 (1993).
21. S. Kuwajima and A. Warshel, J. Chem. Phys. 89, 3751 (1988).
22. P. H. Hünenberger and J. A. McCammon, Biophys. Chem. 78, 69 (1999).
23. P. H. Hünenberger and J. A. McCammon, J. Chem. Phys. 110, 1856 (1999).
24. W. Weber, P. H. Hunenberger, and J. A. McCammon, J. Phys. Chem. B 104, 3668 (2000).
25. C. Tanford and J. Kirkwood, J. Am. Chem. Soc. 79, 5333 (1957).
26. J. Warwicker and H. Watson, J. Mol. Biol. 157, 671 (1982).
27. J. Tomasi and M. Persico, Chem. Rev. (Washington, D.C.) 94, 2027 (1994).
28. C. J. Cramer and D. G. Truhular, Chem. Rev. (Washington, D.C.) 99, 2161 (1999).
29. T. Simonson, Rep. Prog. Phys. 66, 737 (2003).
30. M. Feig and C. L. Brooks, Curr. Opin. Struct. Biol. 14, 217 (2004).
31. A. Jean-Charles, A. Nicholls, K. Sharp, B. Honig, A. Tempczyk, T. Hendrickson, and W. C. Still, J. Am. Chem. Soc. 113, 1454 (1991).
32. C. N. Schutz and A. Warshel, Proteins: Struct., Funct., Genet. 44, 400 (2001).
33. G. A. Papoian, J. Ulander, M. P. Ewastwood, Z. Luthey-Schulten, and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 101, 3352 (2004).
34. G. A. Papoian, J. Ulander, and P. G. Wolynes, J. Am. Chem. Soc. 125, 9170 (2003).
35. C. K. Reddy, A. Das, and B. Jayaram, J. Mol. Biol. 314, 619 (2001).
36. S. Bergqvist, M. A. Williams, R. O'Brien, and J. E. Ladbury, J. Mol. Biol. 336, 829 (2004).
37. A. Baerga-Ortiz, S. Bergqvist, J. G. Mandell, and E. A. Komives, Protein Sci. 13, 166 (2004).
38. L. Onsager, J. Am. Chem. Soc. 58, 1486 (1936).
39. M. M. Karelson and M. C. Zerner, J. Phys. Chem. 96, 6949 (1992).
40. P. N. Day, J. H. Jensen, M. S. Gordon S. P. Webber, W. J. Stevens, M. Krauss, D. Garmer, H. Basch, D. Cohen, J. Chem. Phys. 105, 1968 (1996).
41. A. Warshel, Chem. Phys. Lett. 55, 454 (1978).
42. G. King and A. Warshel, J. Chem. Phys. 91, 3647 (1989).
43. S. A. Adelman, J. Chem. Phys. 73, 3145 (1980).
44. S. A. Adelman and C. L. Brooks III, J. Phys. Chem. 86, 1511 (1982).
45. A. Warshel, J. Phys. Chem. 86, 2218 (1982).
46. M. Berkowitz and J. A. McCammon, Chem. Phys. Lett. 90, 215 (1982).
47. C. L. Brooks III and M. Karplus, J. Chem. Phys. 79, 6312 (1983).
48. D. Borgis, N. Levy, and M. Marchi, J. Chem. Phys. 119, 3516 (2003).
49. D. Beglov and B. Roux, J. Chem. Phys. 100, 9050 (1994).
50. J. G. Kirkwood, J. Chem. Phys. 2, 351 (1934).
51. A. Masunov and T. Lazaridis, J. Am. Chem. Soc. 125, 1722 (2003).
52. W. Im, S. Berǹche, and B. Roux, J. Chem. Phys. 114, 2924 (2001).
53. M. Elstner, D. Porezag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B 58, 7260 (1998).
54. Q. Cui, M. Elstner, E. Kaxiras, T. Frauenheim, and M. Karplus, J. Phys. Chem. B 105, 569 (2001).
55. B. Brooks, R. Bruccoleri, B. Olafson, D. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).
56. D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973).
57. M. J. Field, P. A. Bash, and M. Karplus, J. Comput. Chem. 11, 700 (1990).
58. M. Gilson, K. Sharp, and B. Honig, J. Comput. Chem. 9, 327 (1988).
59. H. L. Friedman, Mol. Phys. 29, 1533 (1975).
60. J. A. C. Rullmann and P. T. van Duijnen, Mol. Phys. 61, 293 (1987).
61. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983).
62. D. Riccardi, P. S. Schaefer, and Q. Cui, J. Phys. Chem. B (in press).
63. L. Backman, Eur. J. Biochem. 120, 257 (1981).
64. D. W. Christianson and C. A. Fierke, Acc. Chem. Res. 29, 331 (1996).
65. C. Tu, D. N. Silverman, C. Forsman, B.-H. Jonsson, and S. Lindskog, Biochemistry 28, 7913 (1989).
66. A. E. Eriksson, T. A. Jones, and A. Liljas, Proteins: Struct., Funct., Genet. 4, 274 (1988).
67. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).
68. R. H. Stote, D. J. States, and M. Karplus, J. Chim. Phys. Phys.-Chim. Biol. 88, 2419 (1991).
69. S. Toba, G. Colombo, and K. M. J. Merz, J. Am. Chem. Soc. 121, 2290 (1999).
70. D. Lu and G. A. Voth, Proteins: Struct., Funct., Genet. 33, 119 (1998).
71. S. Braun-Sand, M. Strajbl, and A. Warshel, Biophys. J. 87, 2221 (2004).
72. C. N. Schutz and A. Warshel, J. Phys. Chem. B 108, 2066 (2004).
73. K. Håkansson, M. Carlsson, L. A. Svensson, and A. Liljas, J. Mol. Biol. 227, 1192 (1992).
74. M. Nina, D. Beglov, and B. Roux, J. Phys. Chem. B 101, 5239 (1997).
75. C. L. Brooks III and M. Karplus, J. Am. Chem. Soc. 79, 6312 (1983).
76. J. P. Ryckaert, G. Ciccotti, and H. J. Berendsen, J. Comput. Phys. 23, 327 (1977).
77. A. D. MacKerell Jr., D. Bashford, M. Bellott, J. Phys. Chem. B 102, 3586 (1998).
78. T. Simonson, G. Archontis, and M. Karplus, J. Phys. Chem. B 101, 8349 (1997).
79. C. Forsman, G. Behravan, B.-H. Jonsson, Z. Liang, S. Lindskog, X. Ren, J. Sandström, and K. Wallgren, FEBS Lett. 229, 360 (1988).
80. C. K. Tu and D. N. Silverman, Biochemistry 24, 5881 (1985).
81. D. N. Silverman, C. K. Tu, S. Lindskog, and G. C. Wynns, J. Am. Chem. Soc. 101, 6734 (1979).
82. J. Aqvist and A. Warshel, J. Mol. Biol. 224, 7 (1992).
83. D. N. Silverman, Methods Enzymol. 249, 479 (1995).
84. D. Riccardi, G. Li, and Q. Cui, J. Phys. Chem. B 108, 6467 (2004).
85. Y. Zhang, T. Lee, and W. Yang, J. Chem. Phys. 110, 46 (1999).
86. A. Altun and W. Thiel, J. Phys. Chem. B 109, 1268 (2005).
87. H. Y. Liu, M. Elstner, E. Kaxiras, T. Frauenheim, J. Hermans, and W. T. Yang, Proteins: Struct., Funct., Genet. 44, 484 (2001).
88. P. H. Konig, M. Hoffmann, T. Frauenheim, and Q. Cui, J. Phys. Chem. B 109, 9082 (2005).
89. G. Li and Q. Cui, J. Phys. Chem. B 107, 14521 (2003).
90. X. Y. Song, J. Chem. Phys. 116, 9359 (2002).