Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models?

Journal of Chemical Physics

Volumn 127, Issue 15, 2007, Pages

  Cerutti, David S ^a   Baker, Nathan A ^b   McCammon, J Andrew ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULES; MOLECULAR DYNAMICS; REACTION KINETICS; SOLVENTS;

SOLVENT MODELS; SOLVENT REACTION FIELD POTENTIAL;

PROTEINS;

PROTEIN; SOLVENT; WATER;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; ELECTRICITY; METHODOLOGY; PHYSICAL CHEMISTRY; POISSON DISTRIBUTION; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; STATISTICAL MODEL; THEORETICAL MODEL; TIME;

CHEMISTRY, PHYSICAL; COMPUTER SIMULATION; ELECTROSTATICS; MODELS, CHEMICAL; MODELS, STATISTICAL; MODELS, THEORETICAL; MOLECULAR CONFORMATION; POISSON DISTRIBUTION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SOLVENTS; TIME FACTORS; WATER;

EID: 38449120033     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2771171     Document Type: Article

References (92)

1. F. Dong, M. Vijaykumar, and H. X. Zhou, Biophys. J. BIOJAU 0006-3495 85, 49 (2003).
2. Y. Lu, C.-Y. Yang, and S. Wang, J. Am. Chem. Soc. JACSAT 0002-7863 128, 11830 (2006).
3. N. Yoshida, S. Phongphanphanee, Y. Maruyama, T. Imai, and F. Hirata, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja0633262 128, 12042 (2006).
4. S. A. Allison, J. D. Carbeck, C. Chen, and F. Burkes, J. Phys. Chem. B JPCBFK 1089-5647 108, 4516 (2004).
5. G. U. Bublitz and S. G. Boxer, Annu. Rev. Phys. Chem. ARPLAP 0066-426X 10.1146/annurev.physchem.48.1.213 48, 213 (1997).
6. A. Chenal, P. Savarin, P. Nizard, F. Guillain, D. Gillet, and V. Forge, J. Biol. Chem. JBCHA3 0021-9258 277, 43425 (2002).
7. S. H. Northrup, T. G. Wensel, C. F. Meares, J. J. Wendoloski, and J. B. Matthew, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 87, 9503 (1990).
8. A. Grossfield, P. Ren, and J. W. Ponder, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja037005r 125, 15671 (2003).
9. J. Antosiewicz, J. M. Briggs, A. H. Elcock, M. K. Gilson, and J. A. McCammon, J. Comput. Chem. JCCHDD 0192-8651 10.1002/(SICI)1096-987X(19961115)17: 14<1633::AID-JCC5>3.0.CO;2-M 17, 1633 (1996).
10. J. Antosiewicz, J. A. McCammon, and M. K. Gilson, Biochemistry BICHAW 0006-2960 10.1021/bi9601565 35, 7819 (1996).
11. D. Bashford and M. Karplus, Biochemistry BICHAW 0006-2960 10.1021/bi00496a010 29, 10219 (1990).
12. R. E. Georgescu, E. G. Alexov, and M. R. Gunner, Biophys. J. BIOJAU 0006-3495 83, 1731 (2002).
13. J. H. Jensen, H. Li, A. D. Robertson, and P. A. Molina, J. Phys. Chem. A JPCAFH 1089-5639 10.1021/jp051922x 109, 6634 (2005).
14. J. Mongan, D. A. Case, and J. A. McCammon, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.20139 25, 2038 (2004).
15. J. E. Nielsen and J. A. McCammon, Protein Sci. PRCIEI 0961-8368 10.1110/ps.0229903 12, 313 (2003).
16. B. M. Tynan-Connolly and J. E. Nielsen, Protein Sci. PRCIEI 0961-8368 16, 239 (2007).
17. J. Warwicker, Protein Sci. PRCIEI 0961-8368 10.1110/ps.04785604 13, 2793 (2004).
18. A. S. Yang and B. Honig, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1993.1294 231, 459 (1993).
19. P. G. Kusalik and I. M. Svishchev, Science SCIEAS 0036-8075 10.1126/science.265.5176.1219 265, 1219 (1994).
20. M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.481505 112, 8910 (2000).
21. S. W. Rick, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1652434 120, 6085 (2004).
22. G. Lamoureux, A. D. MacKerell, Jr., and B. Roux, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1598191 119, 5185 (2003).
23. P. Ren and J. W. Ponder, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp0484332 108, 13427 (2004).
24. C. J. Cramer and D. G. Truhlar, Chem. Rev. (Washington, D.C.) CHREAY 0009-2665 10.1021/cr960149m 99, 2161 (1999).
25. R. H. Henchman and J. A. McCammon, Protein Sci. PRCIEI 0961-8368 10.1110/ps.0214002 11, 2080 (2002).
26. V. P. Denisov, B.-H. Jonsson, and B. Halle, Nat. Struct. Biol. NSBIEW 1072-8368 10.1038/6692 6, 253 (1999).
27. T. Ikura, Y. Urakubo, and N. Ito, Chem. Phys. CMPHC2 0301-0104 307, 111 (2004).
28. C. J. Morton and J. E. Ladbury, Protein Sci. PRCIEI 0961-8368 5, 2115 (1996).
29. B. Chen, I. Ivanov, M. L. Klein, and M. Parrinello, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.91.215503 91, 215503 (2003).
30. P. L. Geissler, C. Dellago, D. Chandler, J. Hutter, and M. Parrinello, Science SCIEAS 0036-8075 10.1126/science.1056991 291, 2121 (2001).
31. A. V. Gubskaya and P. G. Kusalik, Mol. Phys. MOPHAM 0026-8976 10.1080/00268970110041218 99, 1107 (2001).
32. I.-F. W. Kuo and C. J. Mundy, Science SCIEAS 0036-8075 10.1126/science.1092787 303, 658 (5658).
33. I.-F. W. Kuo, C. J. Mundy, M. J. McGrath, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp047788i 108, 12990 (2004).
34. M. Allesch, E. Schwegler, F. Gygi, and G. Galli, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1647529 120, 5192 (2004).
35. P. L. Silvestrelli and M. Parrinello, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.82.3308 82, 3308 (1999).
36. Y. S. Badyal, M.-L. Saboungi, D. L. Price, S. D. Shastri, D. R. Haeffner, and A. K. Soper, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.481541 112, 9206 (2000).
37. N. A. Baker, D. Sept, S. Joseph, M. J. Holst, and J. A. McCammon, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.181342398 98, 10037 (2001).
38. B. Roux and T. Simonson, Biophys. Chem. BICIAZ 0301-4622 10.1016/S0301-4622(98)00226-9 78, 1 (1999).
39. I. T. Suydam, C. D. Snow, V. S. Pande, and S. G. Boxer, Science SCIEAS 0036-8075 313, 200 (2006).
40. A. H. Elcock, R. R. Gabdoulline, R. C. Wade, and J. A. McCammon, J. Mol. Biol. JMOBAK 0022-2836 291, 149 (1999).
41. R. Konecny, J. Trylska, F. Tama, D. Zhang, N. A. Baker, C. L. Brooks, III, and J. A. McCammon, Biopolymers BIPMAA 0006-3525 10.1002/bip.20409 82, 106 (2006).
42. J. Trylska, R. Konecny, F. Tama, III, C. L. Brooks, III, and J. A. McCammon, Biopolymers BIPMAA 0006-3525 74, 423 (2004).
43. S. R. McGuffee and A. H. Elcock, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja0614058 128, 12098 (2006).
44. J. J. Gray, S. Moughon, C. Wang, O. Schueler-Furman, B. Kuhlman, C. A. Rohl, and D. Baker, J. Mol. Biol. JMOBAK 0022-2836 331, 281 (2003).
45. G. M. Morris, D. S. Goodsell, R. S. Halliday, R. Huey, W. E. Hart, R. K. Belew, and A. J. Olson, J. Comput. Chem. JCCHDD 0192-8651 10.1002/(SICI)1096- 987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B 19, 1639 (1998).
46. M. L. Verdonk, J. C. Cole, M. J. Hartshorn, C. W. Murray, and R. D. Taylor, Proteins 18PLAF 0887-3585 52, 609 (2003).
47. G. A. Papoian, J. Ulander, M. P. Eastwood, Z. Luthey-Schulten, and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0307851100 101, 3352 (2004).
48. C. L. Vizcarra and S. L. Mayo, Curr. Opin. Chem. Biol. COCBF4 1367-5931 9, 622 (2005).
49. E. S. Zollars, S. A. Marshall, and S. L. Mayo, Protein Sci. PRCIEI 0961-8368 15, 2014 (2006).
50. R. E. Amaro, R. S. Myers, V. J. Davisson, and Z. A. Luthey-Schulten, Biophys. J. BIOJAU 0006-3495 89, 475 (2005).
51. H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C. D. Snow, M. D. Shirts, E. J. Sorin, and V. S. Pande, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1999637 123, 084108 (2005).
52. H. J. Woo and B. Roux, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0409005102 102, 6825 (2005).
53. R. Susukita, T. Ebisuzaki, B. G. Elmegreen, H. Furusawa, K. Kato, A. Kawai, Y. Kobayashi, T. Koishi, G. D. McNiven, T. Narumi, and K. Yasuoka, Comput. Phys. Commun. CPHCBZ 0010-4655 10.1016/S0010-4655(03)00349-7 155, 115 (2003).
54. J. M. J. Swanson, S. A. Adcock, and J. A. McCammon, J. Chem. Theory Comput. JCTCCE 1549-9618 10.1021/ct049834o 1, 484 (2005).
55. J. Wagoner and N. A. Baker, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.20089 25, 1623 (2004).
56. M. Bostrom, F. W. Tavares, D. Bratko, and B. W. Ninham, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp0551869 109, 24489 (2005).
57. I. Chorny, K. A. Dill, and M. P. Jacobson, J. Phys. Chem. B JPCBFK 1089-5647 109, 24056 (2005).
58. J. Forsman, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp049571u 108, 9236 (2004).
59. M. Fixman, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.437340 70, 4995 (1979).
60. D. Beglov and B. Roux, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.471557 104, 8678 (1996).
61. W. Im, S. Berneche, and B. Roux, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1336570 114, 2924 (2001).
62. H. S. Ashbaugh, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp0015067 104, 7235 (2000).
63. S. Rajamani, T. Ghosh, and S. Garde, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1644536 120, 4457 (2004).
64. H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma, J. Phys. Chem. JPCHAX 0022-3654 10.1021/j100308a038 91, 6269 (1987).
65. P. Kuhn, A. M. Deacon, S. Comoso, G. Rajaseger, R. M. Kini, I. Usón, and P. R. Kolatkar, Acta Crystallogr., Sect. D: Biol. Crystallogr. ABCRE6 0907-4449 56, 1401 (2000).
66. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, Nucleic Acids Res. NARHAD 0305-1048 10.1093/nar/28.1.235 28, 235 (2000).
67. D. A. Case, T. A. Darden, T. E. Cheatham, III, AMBER 9, University of California San Francisco, San Francisco, CA, 2006.
68. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja955032e 118, 2309 (1995).
69. J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, and D. A. Case, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.20035 25, 1157 (2004).
70. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.470117 103, 8577 (1995).
71. T. Darden, D. York, and L. G. Pedersen, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.464397 98, 10089 (1993).
72. P. Kumar, G. Franzese, S. V. Buldyrev, and H. Eugene Stanley, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.73.041505 73, 041505 (2006).
73. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1987).
74. M. Frigo and S. G. Johnson, Proc. IEEE IEEPAD 0018-9219 10.1109/JPROC.2004.840301 93, 216 (2005).
75. M. J. Holst and F. Saied, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540160308 16, 337 (1995).
76. M. Holst, R. E. Kozack, F. Saied, and S. Subramaniam, J. Biomol. Struct. Dyn. JBSDD6 0739-1102 11, 1437 (1994).
77. M. Holst, R. E. Kozack, F. Saied, and S. Subramaniam, Proteins 18PLAF 0887-3585 10.1002/prot.340180304 18, 231 (1994).
78. M. Holst and F. Saied, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540140114 14, 105 (1993).
79. M. L. Connolly, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja00291a006 107, 1118 (1985).
80. Y. Wu, H. L. Tepper, and G. A. Voth, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2136877 124, 024503 (2006).
81. D. S. Cerutti, T. Jain, and J. A. McCammon, Protein Sci. PRCIEI 0961-8368 15, 1579 (2006).
82. C. Peter, W. F. van Gunsteren, and P. H. Hünenberger, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1465396 116, 7434 (2002).
83. J. M. J. Swanson, J. A. Wagoner, N. A. Baker, and J. A. McCammon, J. Chem. Theory Comput. JCTCCE 1549-9618 3, 170 (2007).
84. L. R. Olano and S. W. Rick, J. Am. Chem. Soc. JACSAT 0002-7863 126, 7991 (2004).
85. H. Gohlke and D. A. Case, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.10379 25, 238 (2004).
86. P. Paricaud, M. Predota, A. A. Chialvo, and P. T. Cummings, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1940033 122, 244511 (2005).
87. D. J. Price and C. L. Brooks, III, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1808117 121, 10096 (2004).
88. F. J. Lovas, J. Phys. Chem. Ref. Data JPCRBU 0047-2689 7, 1445 (1978).
89. G. Lamoureux and B. Roux, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp056043p 110, 3308 (2006).
90. See EPAPS Document No. E-JCPSA6-127-023733 for depictions of the dipole moment, charge, hydrogen, and oxygen densities around the uncharged protein. This document can be reached via a direct link in the online article's HTML reference section or via the EPAPS homepage (http: //www.aip.org/pubservs/epaps. html).
91. http://www.fetk.org
92. http://apbs.sf.net