CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model

Journal of Computational Chemistry

Volumn 25, Issue 12, 2004, Pages 1504-1514

  Patel, Sandeep ^a   Mackerell Jr , Alexander D ^a   Brooks III, Charles L ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Charge equilibration; Molecular dynamics; Molecular simulations; Polarizable protein force field

Indexed keywords

CHARGE EQUILIBRATION; DIPOLE MOMENTS; MOLECULAR SIMULATIONS; POLARIZABLE PROTEIN FORCE FIELD;

COMPUTER SIMULATION; CONDENSATION; ELECTROSTATICS; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; QUANTUM THEORY; SOLVENTS;

PROTEINS;

PROTEIN; SOLVENT; WATER;

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ELECTRICITY; METHODOLOGY; PROTEIN SECONDARY STRUCTURE;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; ELECTROSTATICS; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SOLVENTS; WATER;

EID: 4043057278     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.20077     Document Type: Article

References (83)

1. Karplus, M.; McCammon, J. A. Nat Struct Bol 2002, 9, 646.
2. McCammon, J. A.; Harvey, S. C. Dynamics of Proteins and Nucleic Acids; Cambridge University Press: Cambridge, 1987.
3. Brooks, C. L., III; Karplus, M.; Pettitt, B. M. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics; John Wiley & Sons: New York, 1988.
4. Becker, O. M.; MacKerell, J., A. D.; Roux, B.; Watanabe, M., Eds. Computational Biochemistry and Biophysics; Marcel-Dekker, Inc.: New York, 2001.
5. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J Phys Chem 1993, 97, 10269.
6. Breneman, C. M.; Wiberg, K. B. J Comp Chem 1990, 11, 361.
7. Chirlian, L. E.; Francl, M. M. J Comp Chem 1987, 8, 894.
8. Jorgensen, W. L.; Tirado-Rives, J. J Am Chem Soc 1988, 110, 1657.
9. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; 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.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J Phys Chem B 1998, 102, 3586.
10. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1995, 117, 5179.
11. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollman, P. A. J Am Chem Soc 1993, 115, 9620.
12. Foresman, J. B.; Brooks, C. L., III. J Chem Phys 1987, 87, 5892.
13. Dang, L. X. J Chem Phys 1992, 97, 2659.
14. Dang, L. X.; Chang, T.-M. J Chem Phys 2003, 119, 9851.
15. Jungwirth, P.; Tobias, D. J. J Phys Chem B 2002, 106, 6361.
16. Rick, S. W.; Stuart, S. J. Rev Comp Chem 2002, 18, 89.
17. Dang, L. X. J Phys Chem B 2001, 105, 804.
18. Caldwell, J. W.; Kollman, P. A. J Phys Chem 1995, 99, 6208.
19. Dang, L. X.; Chang, T.-M. J Chem Phys 1997, 106, 8149.
20. Chang, T.-M.; Dang, L. X.; Peterson, K. A. J Phys Chem 1997, 101, 3413.
21. Sprik, M. J Chem Phys 1991, 95, 6762.
22. Sprik, M.; Klein, M. L. J Chem Phys 1988, 89, 7556.
23. van Marren, P. J.; van der Spoel, D. J Phys Chem B 2001, 105, 2618.
24. Lamoureux, G.; Alexander D. MacKerell, J.; Roux, B. J Chem Phys 2003, 119, 5185.
25. Sprik, M.; Klein, M. L.; Watanabe, K. J Phys Chem 1990, 94, 6483.
26. Anisimov, V. M., Vorobyov, I. V., Lamoureux, G., Noskov, S., Roux, B., MacKerell, A. D., Jr. Biophys J 2004, 86, 415a.
27. Ando, K. J Chem Phys 2001, 115, 5228.
28. Krishnan, M.; Verma, A.; Balasubramanian, S. Proc Indian Acad Sci (Chem Sci) 2001, 113, 579.
29. Chen, B.; Xing, J.; Siepmann, J. I. J Phys Chem 2000, 104, 2391.
30. Rick, S. W.; Stuart, S. J.; Berne, B. J. J Chem Phys 1994, 101, 6141.
31. Rick, S. W.; Berne, B. J. J Am Chem Soc 1996, 118, 672.
32. Stuart, S. J.; Berne, B. J. J Phys Chem 1996, 100, 11934.
33. Rick, S. W.; Stuart, S. J.; Bader, J. S.; Berne, B. J. J Mol Liq 1995, 65/66, 31.
34. Ribeiro, M. C. C.; Almeida, L. C. J. J Chem Phys 1999, 110, 11445.
35. Llanta, E.; Ando, K.; Rey, R. J Phys Chem B 2001, 105, 7783.
36. Rick, S. W.; Berne, B. J. J Phys Chem B 1997, 101, 10488.
37. Yoshii, N.; Miura, S.; Okazaki, S. Chem Phys Lett 2001, 345, 195.
38. Yoshii, N.; Yoshie, H.; Miura, S.; Okazaki, S. J Chem Phys 1998, 109, 4873.
39. Rick, S. W. J Chem Phys 2001, 114, 2276.
40. Stuart, S. J.; Berne, B. J. J Phys Chem B 1999, 103, 10300.
41. Bryce, R. A.; Vincent, M. A.; Malcolm, N. O. J.; Hillier, I. H.; Burton, N. A. J Chem Phys 1998, 109, 3077.
42. Ren, P.; Ponder, J. W. J Phys Chem B 2003, 107, 5933.
43. Grossfield, A.; Ren, P.; Ponder, J. W. J Am Chem Soc 2003, 125, 15671.
44. Banks, J. L.; Kaminski, G. A.; Zhou, R.; Mainz, D. T.; Berne, B. J.; Friesner, R. A. J Chem Phys 1999, 110, 741.
45. Stern, H. A.; Rittner, F.; Berne, B. J.; Friesner, R. J Chem Phys 2001, 115, 2237.
46. Ren, P.; Ponder, J. W. J Comp Chem 2002, 23, 1497.
47. Wang, J.; Cieplak, P.; Kollman, P. A. J Comp Chem 2000, 21, 1049.
48. Gresh, N.; Garmer, D. R. J Comp Chem 1996, 17, 1481.
49. Gresh, N. J Comp Chem 1995, 16, 856.
50. Garmer, D. R.; Gresh, N.; Roques, B.-P. Proteins 1998, 31, 42.
51. Allen, T. W.; Bastug, T.; Kuyucak, S.; Chung, S.-H. Biophys J 2003, 84, 2159.
52. Soto, P.; Mark, A. E. J Phys Chem B 2002, 106, 12830.
53. Garcia-Viloca, M.; Truhlar, D. G.; Gao, J. J Mol Biol 2003, 327, 549.
54. Rossmeisl, J.; Hinnemann, B.; Jacobsen, K. W.; Norskov, J. K.; Olsen, O. H.; Pedersen, J. T. J Chem Phys 2003, 118, 9783.
55. Liu, H.; Elstner, M.; Kaxiras, E.; Frauenheim, T.; Hermans, J.; Yang, W.Proteins 2001, 44, 484.
56. Dahiyat, B. I.; Mayo, S. L. Science 1997, 278, 82.
57. Sheinerman, F. B.; Brooks, C. L., III. Proteins 1997, 29, 193.
58. Rappe, A. K.; Goddard, W. A., III. J Phys Chem 1991, 95, 3358.
59. Rick, S. W. Simulation and Theory of Electrostatic Interactions in Solution: Computational Chemistry, Biophysics, and Aqueous Solutions, Pratt, L. R. and Hummer G., eds. American Institute of Physics. Santa Fe, NM, 1999.
60. Parr, R. G.; Yang, W. Density-Functional Theory of Atoms and Molecules; Oxford University Press: Oxford, 1989.
61. Nalewajski, R. F.; Korchowiec, J.; Zhou, Z. Int J Quantum Chem: Quantim Chem Symp 1988, 22, 349.
62. Sanderson, R. T. Science 1951, 114, 670.
63. Sanderson, R. T. Chemical Bonds and Bond Energy; Academic: New York, 1976.
64. York, D. M.; Yang, W. J Chem Phys 1996, 104, 159.
65. Patel, S.; Brooks, C. L., III. J Comp Chem 2004, 25, 1.
66. Kaminski, G. A.; Stern, H. A.; Berne, B. J.; Friesner, R. A.; Cao, Y. X. ; Murphy, R. B.; Zhou, R.; Halgren, T. A. J Comp Chem 2002, 23, 1515.
67. Stern, H. A.; Kaminski, G. A.; Banks, J. L.; Zhou, R.; Berne, B. J.; Friesner, R. A. J Phys Chem B 1999, 103, 4730.
68. Morita, A. J Comp Chem 2002, 23, 1466.
69. Nose, S. Mol Phys 1984, 52, 255.
70. Andersen, H. C. J Chem Phys 1980, 72, 2384.
71. Parrinello, M.; Rahman, A. Phys Rev Lett 1980, 45, 1196.
72. Car, R.; Parrinello, M. Phys Rev Lett 1985, 55, 2471.
73. Pastore, G.; Smargiassi, E.; Buda, F. Phys Rev A 1991, 44, 6334.
74. Martyna, G. J.; Klein, M. L.; Tuckerman, M. J Chem Phys 1992, 97, 2635.
75. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Clarendon Press: Oxford, 1987.
76. MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III. J Am Chem Soc 2004, 126, 698.
77. MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III. J Comp Chem 2004, 25, 1400.
78. Feig, M.; MacKerell, A. D., Jr.; Brooks, C. L., III. J Phys Chem B 2003, 107, 2831.
79. Beachy, M. D.; Chasman, D.; Murphy, R. B.; Halgren, T. A.; Friesner, R. A. J Am Chem Soc 1997, 119, 5908.
80. Baker, E. N.; Hubbard, R. E. Prog Biophys Molec Biol 1984, 44, 97.
81. Im, W.; Lee, M. S.; Brooks, C. L., III. J Comp Chem 2003, 24, 1691.
82. Lee, M. S.; Salsbury, F. R., Jr.; Brooks, C. L., III. J Chem Phys 2002, 116, 10606.
83. Kraulis, P. J. J Appl Crystallogr 1991, 24, 946.