Charge equilibration force fields for molecular dynamics simulations of lipids, bilayers, and integral membrane protein systems

Biochimica et Biophysica Acta - Biomembranes

Volumn 1818, Issue 2, 2012, Pages 318-329

  Lucas, Timothy R ^a   Bauer, Brad A ^a   Patel, Sandeep ^a  

^a UNIVERSITY OF DELAWARE   (United States)

Author keywords

Bilayer; Charge equilibration; Lipid; Molecular dynamics simulation; Polarizable force field

Indexed keywords

LIPID; MEMBRANE PROTEIN; POTASSIUM ION;

ARTICLE; BINDING AFFINITY; CARBON NUCLEAR MAGNETIC RESONANCE; CONFORMATION; DIELECTRIC CONSTANT; ELECTROCHEMISTRY; ENERGY TRANSFER; HYDROPHOBICITY; ION TRANSPORT; LIPID BILAYER; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MEMBRANE PERMEABILITY; MEMBRANE POTENTIAL; METHODOLOGY; MOLECULAR DYNAMICS; NEUTRON SCATTERING; NITROGEN NUCLEAR MAGNETIC RESONANCE; POLARIZATION; PRIORITY JOURNAL; SOLVATION;

BACTERIA (MICROORGANISMS);

EID: 84855466022     PISSN: 00052736     EISSN: 18792642     Source Type: Journal    
DOI: 10.1016/j.bbamem.2011.09.016     Document Type: Review

References (131)

1. I. Leontyev, and A. Stuchebrukhov PCCP 13 2011 2613 2626
2. W.C. Swope, H.W. Horn, and J.E. Rice Chem. Phys. Lett. 114 2010 8621 8630
3. S.W. Rick, S.J. Stuart, and B.J. Berne J. Chem. Phys. 101 1994 6141 6156
4. L.R. Olano, and S.W. Rick J. Comput. Chem. 26 2005 699 707
5. S.W. Rick, S.J. Stuart, J.S. Bader, and B.J. Berne J. Mol. Liq. 65/66 1995 31
6. A.K. Rappe, and W.A. Goddard J. Phys. Chem. 95 1991 3358 3363
7. P. Ren, and J.W. Ponder J. Comput. Chem. 23 2002 1497 1506
8. P. Ren, and J.W. Ponder J. Phys. Chem. B 107 2003 5933 5947
9. P. Ren, and J.W. Ponder J. Comput. Chem. 23 2002 1497 1506
10. M.A. Brown, R. D'Auria, L.F.W. Kuo, M.J. Krisch, D.E. Starr, H. Bluhm, D.J. Tobias, and J.C. Hemminger Phys. Chem. Chem. Phys. 10 2008 4778 4784
11. P. Jungwirth, and D.J. Tobias J. Phys. Chem. B 105 2001 10468 10472
12. P. Jungwirth, and D.J. Tobias J. Phys. Chem. B 106 2002 6361 6373
13. P. Jungwirth, and D.J. Tobias Chem. Rev. 106 2006 1259 1281
14. D. Bucher, S. Raugei, L. Guidoni, M. DalPeraro, U. Rothlisberger, P. Carloni, and M.L. Klein Biophys. Chem. 124 2006 292 301
15. M. Sprik J. Chem. Phys. 95 1991 6762 6769
16. B. de Courcy, J. Piquemal, C. Garbay, and N. Gresh J. Am. Chem. Soc. 132 2010 3312 3320
17. J.-P. Piquemal, H. Chevreau, and N. Gresh J. Chem. Theory Comput. 3 2007 824 837
18. J. Applequist, J.R. Carl, and K. Fung J. Am. Chem. Soc. 94 1972 2952 2960
19. J.W. Caldwell, and P.A. Kollman J. Phys. Chem. 99 1995 6208 6219
20. A. Grossfield, P. Ren, and J.W. Ponder J. Am. Chem. Soc. 125 2003 15671 15682
21. A. Grossfield J. Chem. Phys. 122 2005 024506
22. D. Jiao, C. King, A. Grossfield, T.A. Darden, and P. Ren J. Phys. Chem. B 110 2006 18553 18559
23. J.W. Ponder, C. Wu, P. Ren, V.S. Pande, J.D. Chodera, M.J. Schnieders, I. Haque, D.L. Mobley, D.S. Lambrecht, R.A. DiStasio Jr., M. Head-Gordon, G.N.I. Clark, M.E. Johnson, and T. Head-Gordon J. Phys. Chem. B 114 2010 2549 2564
24. P. Ren, and J.W. Ponder J. Phys. Chem. B 108 2004 13427 13437
25. B.T. Thole Chem. Phys. 59 1981 341 350
26. V.M. Anisimov, G. Lamoureux, I.V. Vorobyov, N. Huang, B. Roux, and A.D. MacKerell Jr. J. Chem. Theory Comput. 1 2005 153 168
27. G. Lamoureux, and B. Roux J. Chem. Phys. 119 2003 3025
28. G. Lamoureux, A.D. MacKerell Jr., and B. Roux J. Chem. Phys. 119 2003 5185
29. G. Lamoureux, E. Harder, I.V. Vorobyov, B. Roux, and A.D. MacKerell Jr. Chem. Phys. Lett. 418 2006 245 249
30. P.E.M. Lopes, G. Lamoureux, B. Roux, and A.D. MacKerell Jr. J. Phys. Chem. B 111 2007 2873 2885
31. I.V. Vorobyov, V.M. Anisimov, and A.D. MacKerell Jr. J. Phys. Chem. B 109 2005 18988 18999
32. I.V. Vorobyov, V.M. Anisimov, S. Greene, R.M. Venable, A. Moser, R.W. Pastor, and A.D. MacKerell Jr. J. Chem. Theory Comput. 3 2007 1120 1133
33. C.M. Baker, P.E.M. Lopes, X. Zhu, B. Roux, and A.D. MacKerell Jr. J. Chem. Theory Comput. 6 2010 1181 1198
34. G. Lamoureux, and B. Roux J. Phys. Chem. B 110 2006 3308 3322
35. H. Yu, T.W. Whitfield, E. Harder, G. Lamoureux, I. Vorobyov, V.M. Anisimov, A.D. MacKerell Jr., and B. Roux J. Chem. Theory Comput. 6 2010 774 786
36. B. de Courcy, J.-P. Piquemal, C. Garbay, and N. Gresh J. Am. Chem. Soc. 132 2010 3312
37. M. Devereux, M.-C. van Severen, O. Parisel, J.-P. Piquemal, and N. Gresh J. Chem. Theory Comput. 7 2011 138 147
38. Chaudret, R.; Gresh, N.; Parisel, O.; Darden, T. A.; Cisneros, G. A.; Piquemal, J.-P. J. Chem. Phys. 2011, in revision.
39. J.-P. Piquemal, B. Williams-Hubbard, N. Fey, R.J. Deeth, N. Gresh, and C. giessner Prettre J. Comput. Chem. 2003 1963 24
40. N. Gresh, J.-P. Piquemal, and M. Krauss J. Comput. Chem. 26 2005 1113
41. J.-P. Piquemal, G.A. Cisneros, P. Reinhardt, N. Gresh, and T.A. Darden J. Chem. Phys. 124 2006 104101
42. R.T. Sanderson Science 114 1951 670 672
43. R.T. Sanderson Chemical Bonds and Bond Energy 1976 Academic Press New York
44. S.W. Rick, and B.J. Berne J. Am. Chem. Soc. 118 1996 672 679
45. S.W. Rick, and S.J. Stewart Reviews of Computational Chemistry 2002 John Wiley & Sons New York
46. S.W. Rick J. Chem. Phys. 114 2001 2276 2283
47. S. Patel, and C.L. Brooks III J. Comput. Chem. 25 2004 1 15
48. S. Patel, A.D. MacKerell Jr., and C.L. Brooks III J. Comput. Chem. 25 2004 1504 1514
49. S. Patel, and C.L. Brooks III J. Chem. Phys. 122 2005 024508
50. S. Patel, and C.L. Brooks III Mol. Simul. 32 2006 231 249
51. L.R. Olano, and S.W. Rick J. Comput. Chem. 26 2005 699 707
52. G.L. Warren, J.E. Davis, and S. Patel J. Chem. Phys. 128 2008 144110
53. Y. Zhong, G.L. Warren, and S. Patel J. Comput. Chem. 29 2007 1142 1152
54. J.E. Davis, G.L. Warren, and S. Patel J. Phys. Chem. B 112 2008 8298 8310
55. B.A. Bauer, and S. Patel J. Mol. Liq. 142 2008 32 40
56. C.J. Illingworth, and C. Domene Proc. R. Soc. A 465 2009 1701 1716
57. J.-P. Piquemal, L. Perera, G.A. Cisneros, P. Ren, L.G. Pedersen, and T.A. Darden J. Chem. Phys. 125 2006 054511
58. B.A. Bauer, G.L. Warren, and S. Patel J. Chem. Theory Comput. 5 2009 359 373
59. R.F. Nalewajski, J. Korchowiec, and Z. Zhou Int. J. Quant. Chem. 22 1988 349 366
60. A.J. Lee, and S.W. Rick J. Chem. Phys. 134 2011 184507
61. R. Chelli, P. Procacci, R. Righini, and S. Califano J. Chem. Phys. 111 1999 8569 8575
62. R. Car, and M. Parrinello Phys. Rev. Lett. 55 1985 2471 2474
63. H.A. Stern, and S.E. Feller J. Chem. Phys. 118 2003 3401 3412
64. L. Wang, P.S. Bose, and F.J. Sigworth PNAS 103 2006 18528 18533
65. J.L. MacCallum, W.F.D. Bennett, and D.P. Tieleman Biophys. J. 94 2008 3393 3404
66. N. Kučerka, Y. Liu, N. Chu, H.I. Petrache, S. Tristram-Nagle, and J.F. Nagle Biophys. J. 88 2005 2626 2637
67. N. Kučerka, J.F. Nagle, J.N. Sachs, S.E. Feller, J. Pencer, A. Jackson, and J. Katsaras Biophys. J. 95 2008 2356 2367
68. H.I. Petrache, S.W. Dodd, and M.F. Brown Biophys. J. 79 2000 3172 3192
69. D. Marsh Eur. Biophys. J. 31 2002 559 562
70. D.A. Erilov, R. Bartucci, R. Guzzi, A.A. Shubin, A.G. Maryasov, D. Marsh, S.A. Dzuba, and L. Sportelli J. Phys. Chem. B 109 2005 12003 12013
71. J.C. Mathai, S. Tristram-Nagle, J.F. Nagle, and M.L. Zeidel J. Gen. Physiol. 131 2008 69 76
72. B. Roux, T. Allen, S. Berneche, and W. Im Q. Rev. Biophys. 37 2004 15 103
73. T.W. Allen, T. Bastug, S. Kuyucak, and S.-H. Chung Biophys. J. 84 2003 2159 2168
74. S. Berneche, and B. Roux Biophys. J. 82 2002 772 780
75. T.W. Allen, O.S. Andersen, and B. Roux PNAS 101 2004 117 122
76. S. Dorairaj, and T.W. Allen PNAS 104 2007 4943 4948
77. M.P. Aliste, and D.P. Tieleman BMC Biochem. 6 2005 30
78. D.P. Tieleman, J.L. MacCallum, W.L. Ash, C. Kandt, Z. Xu, and L.M. Monticelli J. Phys. Condens. Matter 18 2006 S1221 S1234
79. Z. Xu, H.H. Luo, and D.P. Tieleman J. Comput. Chem. 28 2007 689 697
80. S.E. Feller Curr. Opin. Colloid Interface Sci. 5 2000 217 223
81. J.L. MacCallum, and D.P. Tieleman J. Am. Chem. Soc. 128 2006 125 130
82. S.A. Pandit, D. Bostick, and M.L. Berkowitz Biophys. J. 86 2004 1345 1356
83. M.L. Berkowitz, D.L. Bostick, and S.A. Pandit Chem. Rev. 106 2006 1527 1539
84. S.W.I. Siu, R. Vacha, P. Jungwirth, and R.A. Bockmann J. Chem. Phys. 128 2008 125103
85. J.B. Klauda, R.M. Venable, J.A. Freites, J.W. O'Connor, D.J. Tobias, C. Mondragon-Ramirez, I. Vorobyov, A.D. MacKerrel Jr., and R.W. Pastor J. Phys. Chem. B 114 2010 7830 7843
86. R.W. Pastor, and A.D. MacKerell Jr. J. Phys. Chem. Lett. 2 2011 1526 1532
87. J.E. Davis, O. Rahaman, and S. Patel Biophys. J. 96 2009 385 402
88. J.E. Davis, and S. Patel J. Phys. Chem. B 113 2009 9183 9196
89. S. Patel, and C.L. Brooks III J. Chem. Phys. 124 2006 204706
90. J.E. Davis, and S. Patel Chem. Phys. Lett. 484 2010 173 176
91. S. Kumar, D. Bouzida, R.H. Swendsen, P.A. Kollman, and J.M. Rosenberg J. Comput. Chem. 13 1992 1011 1021
92. B.A. Bauer, T.R. Lucas, D. Meninger, and S. Patel Chem. Phys. Lett. 508 2011 289 294
93. E.V. Schow, J.A. Freites, P. Cheng, A. Bernsel, G. von Heijne, S.H. White, and D.J. Tobias J. Membr. Biol. 239 2011 35 48
94. M. Orsi, W.E. Sanderson, and J.W. Essex J. Phys. Chem. B 2009 2009 12019 12029
95. T. Sugii, S. Takagi, and Y. Matsumoto J. Chem. Phys. 123 2005 184714
96. P. Jedlovszky, and M. Mezei J. Am. Chem. Soc. 122 2000 5125 5131
97. E. Harder, A.D. MacKerell Jr., and B. Roux J. Am. Chem. Soc. 131 2009 2760 2761
98. H. Brockman Chem. Phys. Lipids 73 1994 57 79
99. R.J. Clarke Adv. Colloid Interface Sci. 89 2001 263 281
100. K. Gawrisch, D. Ruston, J. Zimmerberg, V.A. Parsegian, R.P. Rand, and N. Fuller Biophys. J. 61 1992 1213 1223
101. Y. Yang, K.M. Mayer, N.S. Wickremasinghe, and J.H. Hafner Biophys. J. 95 2008 5193 5199
102. J. Schamberger, and R.J. Clarke Biophys. J. 82 2002 3081 3088
103. R. Schurhammer, E. Engler, and G. Wipff J. Phys. Chem. B 105 2001 10700 10708
104. D.L. Mobley, A.E. Barber, C.J. Fennell, and K. Dill J. Phys. Chem. B 112 2008 2405 2414
105. Y. Shao, A.A. Stewart, and H.H. Girault J. Chem. Soc., Faraday Trans. 87 1991 2593 2597
106. R. Schurhammer, and G. Wipff J. Phys. Chem. A 104 2000 11159 11168
107. V. Luzhkov, and A. Warshel J. Comput. Chem. 13 1992 199 213
108. B. Roux, H.-A. Yu, and M. Karplus J. Phys. Chem. 94 1990 4684 4688
109. G. Hummer, L.R. Pratt, and A.E. Garcia J. Phys. Chem. 100 1996 1206 1215
110. R.M. Lynden-Bell, and J.C. Rasaiah J. Chem. Phys. 107 1997 1981 1991
111. E. Harder, and B. Roux J. Chem. Phys. 129 2008 234706
112. J.M. Smaby, and H.L. Brockman Biophys. J. 58 1990 195 204
113. G. Mahan Phys. Rev. A 22 1980 1780 1785
114. F.M. Siu, N.L. Ma, and C.W. Tsang J. Chem. Phys. 114 2001 7045 7051
115. S. Patel, J.E. Davis, and B.A. Bauer J. Am. Chem. Soc. 131 2009 13890 13891
116. F. Tian, and T.A. Cross J. Mol. Biol. 285 1999 1993 2003
117. R. Smith, D.E. Thomas, A.R. Atkins, F. Separovic, and B.A. Cornell Biochim. Biophys. Acta (BBA): Biomembr. 1026 1990 161 166
118. Y. Deng, and B. Roux J. Phys. Chem. B 108 2004 16567 16576
119. T. Hessa, S.H. White, and G. von Heijne Science 307 2005 1427
120. J.A. Freites, D.J. Tobias, G. von Heijne, and S.H. White PNAS 102 2005 15050 15064
121. J.L. MacCallum, W.F.D. Bennett, and D.P. Tieleman J. Gen. Physiol. 129 2007 371 377
122. B.A. Bauer, J.E. Davis, M. Taufer, and S. Patel J. Comput. Chem. 32 2011 375 385
123. Ganesan, N.; Bauer, B. A.; Lucas, T. R.; Patel, S.; Taufer, M. J. Comput. Chem. 2011, Submitted for publication, in revision.
124. Y. Zhong, and S. Patel J. Phys. Chem. B 113 2009 767 778
125. Zhong, Y.; Bauer, B. A.; Patel, S. J. Comput. Chem. 2011, in revision.
126. Y. Zhong, and S. Patel J. Phys. Chem. B 114 2010 11076 11092
127. S. Patel, Y. Zhong, B.A. Bauer, and J.E. Davis J. Phys. Chem. B 113 2009 9241 9254
128. Lucas, T. R.; Bauer, B. A.; Patel, S. J. Comput. Chem. 2011, in revision.
129. Z. Zhao, D.M. Rogers, and T.L. Beck J. Chem. Phys. 132 2010 014502
130. I. Vorobyov, and T.W. Allen J. Chem. Phys. 132 2010 185101
131. W. Humphrey, A. Dalke, and K. Schulten J. Mol. Graph. 14 1996 33 38