Computer Simulations with Explicit Solvent: Recent Progress in the Thermodynamic Decomposition of Free Energies and in Modeling Electrostatic Effects

Annual Review of Physical Chemistry

Volumn 49, Issue 1, 1998, Pages 531-567

  Levy, Ronald M ^a   Gallicchio, Emilio ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

Entropy enthalpy compensation; Hydrophobic effect; Linear response; Protein electrostatics; Thermodynamic perturbation

Indexed keywords

SOLVENT;

CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; ELECTRICITY; REVIEW; SOLUTION AND SOLUBILITY; THERMODYNAMICS;

COMPUTER SIMULATION; ELECTROSTATICS; MODELS, CHEMICAL; SOLUTIONS; SOLVENTS; THERMODYNAMICS;

EID: 0032233055     PISSN: 0066426X     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.physchem.49.1.531     Document Type: Article

References (201)

1. Beveridge DL, Di Capua FM. 1989. Annu. Rev. Biophys. Chem. 18:431
2. Kollman PA. 1996. Acc. Chem. Res. 29: 461-69
3. Lamb ML, Jorgensen WL. 1997. Curr. Opin. Chem. Biol. 1:449-57
4. Gilson MK, Given JA, Bush BL, McCommon JA. 1997. Biophys. J. 72:1047-69
5. Brady GP, Szabo A, Sharp KA. 1996. J. Mol. Biol. 263:123-25
6. Dill KA. 1997. J. Biol. Chem. 272:701-4
7. Tembe BL, McCammon JA. 1984. Comput. Chem. 8(4):281
8. Jorgensen WL. 1989. Acc. Chem. Res. 22:184
9. Warshel A. Sussman F, King G. 1986. Biochemistry 25:8368
10. Kollman P. 1993. Chem. Rev. 93:2395
11. Jorgensen WL, Gao J, Ravimohan C. 1985. J. Phys. Chem. 89:3470
12. Durell SR, Wallqvist A. 1996. Biophys. J. 71:1695
13. Zeng J, Hush NS, Reimers JR. 1993. Chem. Phys. Lett. 206:318
14. Gallicchio E, Levy RM. Manuscript in preparation
15. Guillot B, Guissani Y, Bratos S. 1991. J. Chem. Phys. 95(5):3643
16. Guillot B, Guissani Y. 1993. J. Chem. Phys. 99(10):8075
17. Smith DE, Haymet ADJ. 1993. J. Chem. Phys. 98(8):6445
18. Chialvo AA. 1990. J. Chem. Phys. 92(1):673
19. Smith DE, Zhang L, Haymet ADJ. 1992. J. Am. Chem. Soc. 114:5876-78
20. Pearlman DA, Kollman PA. 1989. J. Chem. Phys. 90:2460
21. Ding Y. 1996. Computational studies of medium effects. PhD thesis. New Brunswick, NJ: Rutgers Univ.
22. Kubo MF, Gallicchio E, Levy RM. 1997. J. Phys. Chem. 101(49):10527-34
23. Privalov PL, Gill SJ. 1988. Adv. Protein Chem. 39:191
24. Brooks CL. 1986. J. Phys. Chem. 90: 6680-84
25. Fleischman SH, Brooks CL. 1987. J. Chem. Phys. 87:3029
26. Tobias DJ, Brooks CL. 1990. J. Chem. Phys. 92(4):2582
27. Qian H, Hopfield JJ. 1996. J. Chem. Phys. 105(20):9292
28. Ben-Naim A, Marcus Y. 1984. J. Chem. Phys. 81(4):2016
29. Matubayasi N, Reed LH, Levy RM. 1994. J. Phys. Chem. 98:10640
30. Cann NM, Patey GN. 1997. J. Chem. Phys. 106:8165
31. Franks F, ed. 1972-1982. Water, A Comprehensive Treatise. New York: Plenum. Vois. 1-7
32. Nemethy G, Sheraga HA. 1962. J. Chem. Phys. 36:3401
33. Lazaridis T. 1998. J. Phys. Chem. In press
34. Matubayasi N, Gallicchio E, Levy RM. Submitted
35. Matubayasi N, Levy RM. 1996. J. Phys. Chem. 100:2681
36. Straatsma TP, Berendsen JC, Postma JPN. 1986. J. Chem. Phys. 85:6720
37. Jorgensen WL, Blake JF, Buckner JK. 1989. Chem. Phys. 129:193
38. Kaminski G, Duffy EM, Matsui T, Jorgensen WL. 1994. J. Phys. Chem. 98: 13077-82
39. Mancera RL, Buckingham AD. 1995. J. Phys. Chem. 99:14632-40
40. Mountain RD, Thirumalai D. 1998. J. Chem. Phys. In press
41. Frank HS, Evans MW. 1945. J. Chem. Phys. 13(11):507-32
42. Madan B, Lee B. 1994. Biophys. Chem. 51:279-89
43. Widom B. 1963. J. Chem. Phys. 39:2808
44. Garde S, Hummer S, Pratt LR. 1996. Phys. Rev. Lett. 77:4966
45. Hummer G, Garde S, García AE, Pohorille A, Pratt LR. 1996. Proc. Natl. Acad. Sci. USA 93:8951-55
46. Berne BJ. 1996. Proc. Natl. Acad. Sci. USA 93:8800-3
47. Lazaridis T, Paulatis ME. 1992. J. Phys. Chem. 96:3847-55
48. Lazaridis T, Paulatis ME. 1994. J. Phys. Chem. 98:635-42
49. Green HS. 1952. The Molecular Theory of Fluids. Amsterdam: North-Holland
50. Wallace DC. 1987. J. Chem. Phys. 87: 2282
51. Wallace DC. 1989. Phys. Rev. A 39:4843
52. Ashbaugh HS, Paulatis ME. 1996. J. Phys. Chem. 100:1900-13
53. Lazaridis T, Karplus M. 1996. J. Chem. Phys. 105(10):4294
54. Jorgensen WL, Buckner JK, Boudon S, Tirado-Rives J. 1988. J. Chem. Phys. 89(6):3742
55. Watanabe K, Anderesen HC. 1986. J. Phys. Chem. 90:795-802
56. Wallqvist A, Berne BJ. 1988. Chem. Phys. Lett. 145:26
57. Van Belle D, Wodak SJ. 1993. J. Am. Chem. Soc. 115:647
58. New MH, Berne BJ. 1995. J. Am. Chem. Soc. 117:7172-79
59. Payne VA, Matubayasi N, Reed Murphy L, Levy RM. 1997. J. Phys. Chem. B 101:2054-60
60. Skipper NT. 1993. Chem. Phys. Lett. 207:424
61. Mancera RL, Buckingham AD. 1995. Chem. Phys. Lett. 234:296-303
62. Dang LX. 1994. J. Chem. Phys. 100: 9032
63. Lüdemann S, Schreiberg H, Abseher R, Steinhauser O. 1996. J. Chem. Phys. 104:286
64. Rick SW, Berne BJ. 1997. J. Phys. Chem. B 101:10488
65. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. 1983. J. Chem. Phys. 79(2):926
66. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, et al. 1995. J. Am. Chem. Soc. 117:5179
67. Breneman CM, Wiberg KB. 1990. J. Comput. Chem. 5:129
68. Gallicchio E, Kubo MM, Levy RM. Unpublished results
69. Ding Y, Bernardo DN, Krogh-Jespersen K, Levy RM. 1995. J. Phys. Chem. 99: 11575
70. Morgantini P-Y, Kollman PA. 1995. J. Am. Chem. Soc. 117:6057
71. Rao B, Singh U. 1989. J. Am. Chem. Soc. 111(9):3125
72. Orozco M, Jorgensen WL, Luque FJ. 1993. J. Comput. Chem. 14(12):1498
73. Marten B, Kim K, Cortis C, Friesner RA, Murphy RB, et al. 1996. J. Phys. Chem. 100:11775
74. Jorgensen WL, Maxwell DS, Tirado-Rives J. 1996. J. Am. Chem. Soc. 118: 11225
75. Lumry R, Rajender S. 1970. Biopolymers 9:1125-227
76. Ben-Naim A. 1975. Biopolymers 14: 1337-55
77. Kuroki R, Nitta K, Yutani K. 1992. J. Biol. Chem. 267(34):24297-301
78. Breslauer KJ, Remeta DP, Chou W-Y, Ferrante R, Curry J, et al. 1987. Proc. Natl. Acad. Sci. USA 84:8922-26
79. Cavani S, Gianni P, Mollica V, Lepori L. 1981. J. Solut. Chem. 10(8):563
80. Danil de Namor AF, Ritt M-C, Schwing-Weill M-J, Arnáud-Neu F, Lewis DVF. 1991. J. Chem. Soc. Faraday Trans. 87: 3231-39
81. Gilli P, Ferretti V, Gilli G, Borea PA. 1994. J. Phys. Chem. 98:1515-18
82. Peterson BR, Walliman P, Carcanague DR, Diederich F. 1995. Tetrahedron 51: 401-21
83. Dunitz JD. 1995. Chem. Biol. 2:709-12
84. Linert W, Jameson RF. 1989. Chem. Soc. Rev. 18:477
85. Krug RR, Hunter WG, Geiger RA. 1976. J. Phys. Chem. 80:2335
86. Yu H-A, Karplus M. 1988. J. Chem. Phys. 89(4):2366
87. Lee B. 1994. Biophys. Chem. 51:271
88. Gallicchio E, Kubo MF, Levy RM. 1998. J. Am. Chem. Soc. In press
89. Makhatadze GI, Privalov PL. 1993. J. Mol. Biol. 232:639-59
90. Privalov PL, Makhatadze GI. 1993. J. Mol. Biol. 232:660-79
91. Dill KA. 1985. Biochemistry 24:1501-9
92. Dill KA. 1990. Biochemistry 29:7133-55
93. Spolar RS, Livingstone JR, Record MT Jr. 1992. Biochemistry 31:3947-55
94. Yang A-S, Sharp KA, Honig B. 1992. J. Mol. Biol. 227:889-900
95. Makhatadze GI, Privalov PL. 1996. Protein Sci. 5:507-10
96. Sturtevant JM. 1977. Proc. Natl. Acad. Sci. USA 74:2236-40
97. Baldwin RL. 1986. Proc. Natl. Acad. Sci. USA 83:8069-72
98. Lee B. 1991. Proc. Natl. Acad. Sci. USA 88:5154-58
99. Privalov PL, Makhatadze GI. 1992. J. Mol. Biol. 224:715-23
100. Lazaridis T, Archontis G, Karplus M. 1995. Adv. Protein Chem. 47:231-306
101. Hermans J, Wang L. 1997. J. Am. Chem. Soc. 119:2707-14
102. Connelly PR, Aldape RA, Bruzzese FJ, Chambers SP, Fitzgibbon MJ, et al. 1994. Proc. Natl. Acad. Sci. USA 91:1964-68
103. Kato M, Makino R, Iizuka T. 1995. Biochim. Biophys. Acta 1246:178-84
104. Charifson PS, Shewchuk LM, Rocque W, Hummel CW, Jordan SR, et al. 1997. Biochemistry 36:6283-93
105. Searle MS, Williams DH, Gerhard U. 1992. J. Am. Chem. Soc. 114:10697-704
106. Gilli P, Ferretti V, Gilli G, Borea PA. 1994. J. Phys. Chem. 98:1515-18
107. Hawkins GD, Cramer CJ, Truhlar DG. 1996. J. Phys. Chem. 100:19824-34
108. Still A, Tempczyk WC, Hawley RC, Hendrikson R. 1990. J. Am. Chem. Soc. 112:6127-29
109. Gilson MK. 1995. Curr. Opin. Struct. Biol. 5:216-23
110. Sharp K, Nicholls A, Fine R, Honig B. 1991. Science 252:106-9
111. Warshel A, Aqvist J. 1991. Annu. Rev. Biophys. Biomol. Struct. 20:267-98
112. Resat H, McCammon JA. 1996. J. Chem. Phys. 104:7645-51
113. Simonson T, Archontis G, Karplus M. 1997. J. Phys. Chem. B 101:8349-62
114. Alper H, Levy RM. 1990. J. Phys. Chem. 94:8402
115. Papazyan A, Warshel A. 1997. J. Chem. Phys. 107:7975
116. Pratt LR, Hummer G, Garcia AE. 1994. Biophys. Chem. 51:147-60
117. Hirata F, Redfem P, Levy RM. 1988. J. Quantum Chem. 15:179-88
118. Figueirido F, Del Buono G, Levy RM. 1996. J. Phys. Chem. 100:6389-92
119. Levy RM, Belhadj M, Kitchen DB. 1991. J. Chem. Phys. 95:3627-33
120. Allen MP, Tildesley DJ. 1993. Computer Simulation of Liquids. New York: Oxford Univ. Press
121. Loncharich RJ, Brooks B. 1989 Proteins Struct. Funct. Genet. 6:32-35
122. Brooks CL, Pettitt BM, Karplus M. 1985. J. Chem. Phys. 83:5897-908
123. Linse P, Andersen HC. 1986. J. Chem. Phys. 85:3027-41
124. Madura JD, Pettitt BM. 1988. Chem. Phys. Lett. 150:105-8
125. York DM, Darden TA, Pedersen LG. 1993. J. Chem. Phys. 99:8345-51
126. Del Buono G, Figueirido F, Levy RM. 1996. Chem. Phys Lett. 263:521-29
127. Stillinger F, Rahman A. 1974. J. Chem. Phys. 60:1545-52
128. Pangali C, Rao M, Berne BJ. 1980. Mol. Phys. 40:661-70
129. Brooks CL. 1987. J. Chem. Phys. 86: 5156-62
130. Andrea T, Swope A, Andersen HC. 1983. J. Chem. Phys. 79:4576-84
131. Alper HE, Levy RM. 1989. J. Chem. Phys. 91:1242-51
132. Neumann M. 1985. J. Chem. Phys. 82: 5663-70
133. Bader JS, Chandler D. 1992. J. Phys. Chem. 96:6423-29
134. Houstin SE, Rossky PJ. 1989. J. Phys. Chem. 93:7888-93
135. Buckner JK, Jorgensen WL. 1989. J. Am. Chem. Soc. 111:2507-10
136. Dang LX, Pettitt BM. 1990. J. Phys. Chem. 94:4303-11
137. Guardia E, Rey R, Padro JA. 1991. J. Chem. Phys. 95:2823-28
138. Hummer G, Soumpasis DM, Neumann M. 1993. Mol. Phys. 81:1155-62
139. De Leeuw SW, Perram JW, Smith ER. 1980. Proc. R. Soc. London Ser. A 373: 27-26
140. Figueirido F, Del Buono G, Levy RM. 1995. J. Chem. Phys. 103:6133-42
141. Cichocki B, Felderhof B, Hinsen K. 1989. Phys. Rev. A 39:5350-56
142. Hummer G, Pratt LR, Garcia AE. 1996. J. Phys. Chem. 100:1206-15
143. Figueirido F, Del Buono G, Levy RM. 1997. J. Phys. Chem. B 101:5622-23
144. Hummer G, Pratt LR, Garcia AE. 1997. J. Chem. Phys. 107:9275-77
145. Bogusz S, Cheatham TE, Brooks BR. 1998. J. Chem. Phys. In press
146. Darden TA, York DM, Pedersen LG. 1993. J. Chem. Phys. 98:10089-92
147. Hockney RW, Eastwood JW. 1989. Computer Simulations Using Particles. Bristol, UK: Adam Hilger
148. Greengard L, Rokhlin V. 1989. Phys. A 29:139-52
149. Board JA, Causey JW, Leathrum JF, Windemuth A, Schulten K. 1992. Chem. Phys. Lett. 198:89-97
150. Schmidt KA, Lee MA. 1991. J. Stat. Phys. 63:1223-31
151. Ding HQ, Karasawa N, Goddard WA. 1992. J. Chem. Phys. 97:4309-18
152. Saito M. 1992. Mol. Simul. 8:321-30
153. Lee FS, Warshel A. 1992. J. Chem. Phys. 97:3100-9
154. Figueirido F, Levy RM, Zhou R, Berne BJ. 1997. J. Chem. Phys. 106:9835-49
155. Schlick T, Poarth E, Mandziuk M. 1996. Annu. Rev. Biophys. Biomol. Struct. 26: 181-22
156. Tuckerman AM, Berne BJ, Martyna GJ. 1992. J. Chem. Phys. 97:1990-98
157. Bishop TC, Skeel RD, Schulten K. 1997. J. Comp. Chem. 18:1785-91
158. Barker JA, Watts RO. 1973. Mol. Phys. 26:789-96
159. Alper H, Levy RM. 1993. J. Chem. Phys. 99:9847-52
160. Tanford C, Kirkwood JG. 1957. J. Am. Chem. Soc. 79:5333-37
161. Beglov D, Roux B. 1994. J. Chem. Phys. 100:9050-62
162. Wallqvist A. 1993. Mol. Simul. 10:13-15
163. Wang L, Hermans J. 1995. J. Phys. Chem. 99:12001-7
164. Friedman HL. 1975. Mol. Phys. 29: 1533-38
165. Jayram B, Fine R, Sharp K, Honig B. 1989. J. Phys. Chem. 93:4320-26
166. Figueirido F, Del Buono G, Levy RM. 1994. Biophys. Chem. 51:235-41
167. Smith PE, van Gunsteren WF. 1994. J. Chem. Phys. 100:577-85
168. 167a. Hyun JK, Babu C, Ichiye T. 1995. J. Phys. Chem. 99:5187-95
169. 167b. Hyun JK, Ichiye T. 1995. J. Phys. Chem. 101:3596-604
170. Liu H, Mark AE, van Gunsteren WF. 1996. J. Phys. Chem. 100:9485-94
171. Hummer G, Szabo A. 1996. J. Chem. Phys. 105:2004-10
172. Aqvist J, Medina C, Samuelsson JE. 1994. Protein Eng. 7:385-91
173. Jorgensen WL. 1995. J. Phys. Chem. 99: 10667-73
174. Chandler D. 1993. Phys. Rev. E 48: 2898-905
175. Hummer G, Garde S, Garcia AE, Pohorille A, Pratt LR. 1996. Proc. Natl. Acad. Sci. USA 93:8951-55
176. Simonsen T, Perahia D. 1995. J. Am. Chem. Soc. 117:7987-8000
177. Simonsen T, Brooks CL. 1996. J. Am. Chem. Soc. 118:8452-58
178. Yang L, Valdeavella C, Pettitt BM. 1996. Biophys. J. 71:3022-29
179. Merz KM, Banci L. 1996. J. Phys. Chem. 100:17414-20
180. Treutlein H, Schulten K, Brünger AT, Karplus M, Deisenhofer J, Michel H. 1992. Proc. Natl. Acad. Sci. USA 89:75-79
181. Gehlen JN, Marchi M, Chandler D. 1994. Science 263:499
182. Del Buono G, Figueirido F, Levy RM. 1994. Proteins Struct. Funct. Genet. 20: 85-87
183. Sham Y, Chu ZT, Warshel A. 1997. J. Phys. Chem. B 101:4458-72
184. Muegge I, Qi AJ, Wand P, Chu Z, Warshel A. 1997. J. Phys. Chem. 101: 825-36
185. Bashford D, Karplus M. 1990. Biochemistry 29:10219-25
186. Froloff N, Windemuth A, Honig B. 1997. Protein Sci. 6:1293-301
187. Deleted in proof
188. You TJ, Bashford D. 1995. Biophys. J. 69:1721-33
189. Yang AS, Gunner M, Sampogna R, Sharp K, Honig B. 1993. Proteins 15: 252-65
190. Bashford D, Gerwert K. 1992. J. Mol. Biol. 224:473-86
191. Antosiewicz J, McCammon JA, Gilson MK. 1996. Biochemistry 35:7819-33
192. Demchuk E, Wade R. 1996. J. Phys. Chem. 100:17373-87
193. King G, Warshel A. 1990. J. Chem. Phys. 93:8682-92
194. Carter EA, Hynes JT. 1989. J. Phys. Chem. 93:2184-87
195. Yelle RB, Ichiye T. 1997. J. Phys. Chem. B 101:4127-35
196. Marcus RA. 1960. Discuss. Faraday Soc. 29:21-56
197. Zhou HX, Szabo A. 1995. J. Chem. Phys. 103:3481-94
198. Bottcher CJF. 1973. Theory of Electric Polarization. Amsterdam: Elsevier
199. Smith PE, Brunne R, Mark AE, van Gunsteren WF. 1993. J. Phys. Chem. 97:2009-14
200. Loftier G, Schreiber H, Steinhauser O. 1997. J. Mol. Biol. 270:520-34
201. Sham Y, Muegge I, Warshel A. 1998. Biophys. J. In press