A comprehensive analytical treatment of continuum electrostatics

Journal of Physical Chemistry

Volumn 100, Issue 5, 1996, Pages 1578-1599

  Schaefer, Michael ^a   Karplus, Martin ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0012227656     PISSN: 00223654     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp9521621     Document Type: Article

References (123)

1. Klopman, G. Chem. Phys. Lett. 1967, 1, 200.
2. Constanciel, R.; Contreras, R. Theor. Chim. Acta 1984, 65, 1.
3. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127.
4. Kirkwood, J. G. J. Chem. Phys. 1934, 2, 351.
5. Harris, F. E.; Rice, S. A. J. Phys. Chem. 1954, 58, 725.
6. Tanford, C.; Kirkwood, J. G. J. Am. Chem. Soc. 1957, 79, 5333.
7. Perutz, M. F. Science 1978, 201, 1187.
8. Paul, C. H. J. Mol. Biol. 1982, 155, 53.
9. Warshel, A.; Russell, S. T. Q. Rev. Biophys. 1984, 17, 283.
10. Gilson, M. K.; Honig, B. H. Proteins 1988, 4, 7.
11. Cabani, S.; Gianni, P.; Mollica, V.; Lepori, L. J. Solution Chem. 1981, 10, 563.
12. Mohan, V.; Davis, M. E.; McCammon, J. A.; Pettitt, B. M. J. Phys. Chem. 1992, 96, 6428.
13. Gelin, B. R.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1975, 72, 2002.
14. Warshel, A.; Levitt, M. J. Mol. Biol. 1976, 103, 227.
15. McCammon, J. A.; Wolynes, P. G.; Karplus, M. Biochemistry 1979, 18, 927.
16. Gelin, B. R.; Karplus, M. Biochemistry 1979, 18, 1256.
17. Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. J. Comput. Chem. 1986, 7, 230.
18. Toulouse, M.; Fritsch, V.; Westhof, E. Mol. Simul. 1992, 9, 193.
19. Honig, B. H.; Hubbell, W. L. Proc. Natl. Acad. Sci. U.S.A. 1984, 81, 5412.
20. Schaefer, M.; Froemmel, C. J. Mol. Biol. 1990, 216, 1045.
21. Yu, H.-A.; Pettitt, B. M.; Karplus, M. J. Am. Chem. Soc. 1991, 113, 2425.
22. Stouten, P. F. W.; Frömmel, C.; Nakamura, H.; Sander, C. Mol. Simul. 1993, 10, 97.
23. Levitt, M.; Sharon, R. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 7557.
24. Sharp, K. J. Comput. Chem. 1991, 12, 454.
25. Wesson, L.; Eisenberg, D. Protein Sci. 1992, 1, 227.
26. Chothia, C. Nature 1974, 248, 338.
27. Eisenberg, D.; McLachlan, A. D. Nature 1986, 319, 199.
28. Ooi, T.; Oobatake, M.; Nemethy, G.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 3086.
29. Ooi, T.; Oobatake, M. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 2859.
30. Schiffer, C. A.; Caldwell, J. W.; Stroud, R. M.; Kollman, P. A. Protein Sci. 1992, 1, 396.
31. Gibson, K. D.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 1967, 55, 420.
32. Kang, Y. K.; Némethy, G.; Scheraga, H. A. J. Phys. Chem. 1987, 91, 4105.
33. Kang, Y. K.; Gibson, K. D.; Nemethy, G.; Scheraga, H. A. J. Phys. Chem. 1988, 92, 4739.
34. Colonna-Cesari, F.; Sander, C. Biophys. J. 1990, 57, 1103.
35. Hasel, W.; Hendrickson, T. F.; Still, W. C. Tetrahedron Comput. Methodol. 1988, 1, 103.
36. van Gunsteren, W. F.; Karplus, M. Nature 1981, 293, 677.
37. Rossky, P. J.; Karplus, M. J. Am. Chem. Soc. 1979, 101, 1913.
38. van Gunsteren, W. F.; Berendsen, H. J. C.; Hermans, J.; Hol, W. G. J.; Postma, J. P. M. Proc. Natl. Acad. Sci. U.S.A. 1983, 80, 4315.
39. Russell, S. T.; Warshel, A. J. Mol. Biol. 1985, 185, 389.
40. Jorgensen, W. L.; Ravimohan, C. J. Chem. Phys. 1985, 83, 3050.
41. Lybrand, T. P.; Gosh, I.; McCammon, J. A. J. Am. Chem. Soc. 1985, 107, 7793.
42. Jorgensen, W. L.; Gao, J. J. Am. Chem. Soc. 1988, 110, 4212.
43. Jorgensen, W. L.; Nguyen, T. B. J. Comput. Chem. 1993, 14, 195.
44. Warshel, A.; Sussman, F.; King, G. Biochemistry 1986, 25, 8368.
45. Bash, P. A.; Singh, U. C.; Langridge, R.; Kollman, P. A. Science 1987, 236, 564.
46. Cieplak, P.; Kollman, P. J. Comput. Chem. 1991, 12, 1232.
47. Essex, J. W.; Reynolds, C. A.; Richards, W. G. J. Am. Chem. Soc. 1992, 114, 3634.
48. Jean-Charles, A.; Nicholls, A.; Sharp, K.; Honig, B.; Tempczyk, A.; Hendrickson, T. F.; Still, W. C. J. Am. Chem. Soc. 1991, 113, 1454.
49. Greengard, L.; Rohklin, V. J. Comput. Phys. 1987, 73, 325.
50. Heller, H.; Grubmüller, H.; Schulten, K. Mol. Simul. 1990, 5, 133.
51. Bharadwaj, R.; Windemuth, A.; Sridharan, S.; Honig, B.; Nicholls, A. J. Comput. Chem., in press.
52. Windemuth, A. Advanced algorithms for molecular dynamics simulation: The program PMD. In Parallel Computing in Computational Chemistry; Mattson, T. G., Ed.; ACS Books: Washington, DC, 1995.
53. Chandler, D.; Andersen, H. C. J. Chem. Phys. 1972, 57, 1930.
54. Hirata, F.; Pettitt, B. M.; Rossky, P. J. J. Chem. Phys. 1982, 77, 509.
55. Pettitt, B. M.; Rossky, P. J. J. Chem. Phys. 1982, 77, 1451.
56. Pettitt, B. M.; Karplus, M. J. Phys. Chem. 1988, 92, 3994.
57. Lee, P. H.; Maggiora, G. M. J. Phys. Chem. 1993, 97, 10175.
58. Kirkwood, J. G.; Westheimer, F. H. J. Chem. Phys. 1938, 6, 506.
59. Friedman, H. L. Mol. Phys. 1975, 29, 1533.
60. Abagyan, R.; Totrov, M. J. Mol. Biol. 1994, 235, 983.
61. Hill, T. L. J. Phys. Chem. 1956, 60, 253.
62. Tanford, C. J. Am. Chem. Soc. 1957, 79, 5340.
63. Shire, S. J.; Hanania, G. I. H.; Gurd, F. R. N. Biochemistry 1974, 13, 2967.
64. Ehrenson, S. J. Am. Chem. Soc. 1976, 98, 7510.
65. Imoto, T. Biophys. J. 1983, 44, 293.
66. Matthew, J. B.; Gurd, F. R. N. Methods Enzymol. 1986, 130, 413.
67. Beglov, D.; Roux, B. J. Chem. Phys. 1994, 100, 9050.
68. Orttung, W. H. Ann. N.Y. Acad. Sci. 1977, 303, 22.
69. Warwicker, J.; Watson, H. C. J. Mol. Biol. 1982, 157, 671.
70. States, D. J. Nuclear Magnetic Resonance and Theoretical Studies of the Refolding of Bovine Pancreatic Trypsin Inhibitor. Ph.D. Thesis, Harvard, 1983.
71. Zauhar, R. J.; Morgan, R. S. J. Comput. Chem. 1988, 9, 171.
72. Lim, C.; Bashford, D.; Karplus, M. J. Phys. Chem. 1991, 95, 5610.
73. Warshel, A. Chem. Phys. Lett. 1978, 55, 454.
74. Klapper, I.; Hagstrom, R.; Fine, R.; Sharp, K.; Honig, B. Proteins 1986, 1, 47.
75. Sharp, K. A.; Nicholls, A.; Friedman, R.; Honig, B. Biochemistry 1991, 30, 9686.
76. Bashford, D.; Karplus, M. Biochemistry 1990, 29, 10219.
77. Yang, A.-S.; Gunner, M. R.; Sampogna, R.; Sharp, K.; Honig, B. Proteins 1993, 15, 252.
78. Rodgers, K. K.; Sligar, S. G. J. Am. Chem. Soc. 1991, 113, 9419.
79. Niedermeier, C.; Schulten, K. Mol. Simul. 1992, 8, 361.
80. Gilson, M. K.; Davis, M. E.; Luty, B. A.; McCammon, A. J. Phys. Chem. 1993, 97, 3591.
81. Davis, M. E.; McCammon, J. A. J. Comput. Chem. 1991, 12, 909.
82. Bruccoleri, R. E. J. Comput. Chem. 1993, 14, 1417.
83. Nicholls, A.; Honig, B. J. Comput. Chem. 1991, 12, 435.
84. Luty, B. A.; Davis, M. E.; McCammon, A. J. Comput. Chem. 1992, 13, 768.
85. Zacharias, M.; Luty, B. A.; Davis, M. E.; McCammon, J. A. J. Mol. Biol. 1994, 238, 455.
86. Caflisch, A.; Karplus, M. Manuscript in preparation.
87. Sklenar, H.; Eisenhaber, F.; Poncin, M.; Lavery, R. Including solvent and counterion effects in the force fields of macromolecular mechanics: The field integrated electrostatic approach (FIESTA). In Theoretical Biochemistry & Molecular Biophysics; Beveridge, D. L., Lavery, R., Eds.; Adenine Press: New York, 1990; p 317.
88. Gilson, M. K.; Honig, B. J. Comput.-Aided Mol. Des. 1991, 5, 5.
89. Born, M. Z. Phys. 1920, 1, 45.
90. Schaefer, M. Unpublished results, 1995.
91. Davis, M. E.; Madura, J. D.; Luty, B. A.; McCammon, J. A. Comput. Phys. Commun. 1991, 62, 187.
92. Jayaram, B.; Fine, R.; Sharp, K.; Honig, B. J. Phys. Chem. 1989, 93, 4320.
93. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
94. Reiher, W. E. Theoretical Studies of Hydrogen Bonding. Ph.D. Thesis, Harvard, 1985.
95. Reiher, W. E.; Karplus, M. Unpublished results, 1985.
96. MacKerell, A. D., Jr.; et al. FASEB J. 1992, 6, A143.
97. MacKerell, A. D., Jr.; et al. Manuscript in preparation, 1995.
98. Jackson, J. D. Classical Electrodynamics; John Wiley & Sons: New York, 1975.
99. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S., Jr.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765.
100. Richards, F. M. Annu. Rev. Biochem. Bioeng. 1977, 6, 151.
101. Lee, B.; Richards, F. M. J. Mol Biol. 1971, 55, 379.
102. Gilson, M. K.; Sharp, K. A.; Honig, B. H. J. Comput. Chem. 1988, 9, 327.
103. Richards, F. M. J. Mol. Biol. 1974, 82, 1.
104. Chothia, C. Nature 1975, 254, 304.
105. Finney, J. L. J. Mol. Biol. 1975, 96, 721.
106. Schaefer, M. Unpublished results, 1995.
107. Shrake, A.; Rupley, J. A. J. Mol. Biol. 1973, 79, 351.
108. Prudnikov, A. P.; Brychkov, Y. A.; Marichev, O. I. Integrals and Series; Gordon and Breach Science Publishers: New York, 1988; Vol. 2.
109. Wolfram, S. Mathematica; A System for Doing Mathematics by Computer, Addison-Wesley: New York, 1988.
110. Schellman, J. A. J. Phys. Chem. 1953, 57, 472.
111. Tanford, C. J. Am. Chem. Soc. 1957, 79, 5348.
112. Rogers, N. K.; Sternberg, M. J. E. J. Mol. Biol. 1984, 174, 527.
113. Hagler, A. T.; Lifson, S. J. Am. Chem. Soc. 1974, 96, 5319.
114. Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110, 1657.
115. Davis, M. E.; McCammon, J. A. J. Comput. Chem. 1990, 11, 401.
116. Archontis, G. Z.; Karplus, M. Manuscript in preparation.
117. Protein Data Bank; Chemistry Department, Brookhaven National Laboratory: Upton, NY, 1985.
118. Schaefer, M.; Karplus, M. Manuscript in preparation.
119. Gilson, M. K.; Rashin, A.; Fine, R.; Honig, B. J. Mol. Biol. 1985, 183, 503.
120. Lounnas, V.; Pettitt, B. M.; Phillips, G. N., Jr. Biophys. J. 1994, 66, 601.
121. Cramer, C. J.; Truhlar, D. G. J. Am. Chem. Soc. 1991, 113, 8305.
122. Tuckerman, M. E.; Berne, B. J.; Martyna, G. J. J. Chem. Phys. 1992, 97, 1990.
123. Watanabe, M.; Karplus, M. J. Phys. Chem. 1995, 99, 5680.