Solvation forces on biomolecular structures: A comparison of explicit solvent and poisson-boltzmann models

Journal of Computational Chemistry

Volumn 25, Issue 13, 2004, Pages 1623-1629

  Wagoner, Jason ^a   Baker, Nathan A ^a  

^a WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

Author keywords

Molecular dynamics; Poisson Boltzmann; Solvation energy; Solvation force

Indexed keywords

POISSON-BOLTZMANN EQUATION; SOLVATION ENERGY; SOLVATION FORCE; SURFACE AREA;

BIOMATERIALS; CONFORMATIONS; CONTINUUM MECHANICS; ENERGY ABSORPTION; FATTY ACIDS; MOLECULAR DYNAMICS; POISSON EQUATION; PROTEINS; SURFACE PHENOMENA;

SOLVENTS;

SOLVENT;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; ELECTRICITY; MATHEMATICAL COMPUTING; THERMODYNAMICS;

COMPUTER SIMULATION; ELECTROSTATICS; MATHEMATICAL COMPUTING; MODELS, CHEMICAL; SOLVENTS; THERMODYNAMICS;

EID: 4444323489     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.20089     Document Type: Article

References (63)

1. Honig, B.; Nicholls, A. Science 1995, 268, 1144.
2. Roux, B.; Simonson, T. Biophys Chem 1999, 78, 1.
3. Davis, M. E.; McCammon, J. A. Chem Rev 1990, 94, 7684.
4. Baker, N. A.; McCammon, J. A. In Structural Bioinformatics; Bourne, P.; Weissig, H., Eds.; John Wiley & Sons, Inc.: New York, 2003, p. 427.
5. Feig, M.; Onufriev, A.; Lee, M. S.; Im, W.; Case, D. A.; Brooks, C. L. I. J Comput Chem 2004, 25, 265.
6. Baker, N. A.; Sept, D.; Joseph, S.; Holst, M. J.; McCammon, J. A. Proc Natl Acad Sci USA 2001, 98, 10037.
7. Lamm, O. In Reviews in Computational Chemistry; Lipkowitz, K. B.; Larter, R.; Cundari, T. R., Eds.; John Wiley and Sons, Inc.: Hoboken, NJ, 2003, p. 147.
8. Luo, R.; Head, M. S.; Moult, J.; Gilson, M. K. J Am Chem Soc 1998, 120, 6138.
9. Onufriev, A.; Bashford, D.; Case, D. A. J Phys Chem B 2000, 104, 3712.
10. Im, W.; Lee, M. S.; Brooks, C. L. I. J Comput Chem 2003, 24, 1691.
11. Bashford, D.; Case, D. A. Annu Rev Phys Chem 2000, 51, 129.
12. Bordner, A. J.; Huber, G. A. J Comput Chem 2003, 24, 353.
13. Coalson, R. D.; Duncan, A. J Chem Phys 1992, 97, 5653.
14. Davis, M. E.; McCammon, J. A. J Comput Chem 1989, 10, 386.
15. Grant, J. A.; Pickup, B. T.; Nicholls, A. J Comput Chem 2001, 22, 608.
16. Luo, R.; David, L.; Gilson, M. K. J Comput Chem 2002, 23, 1244.
17. Zauhar, R. J.; Morgan, R. S. J Mol Biol 1985, 186, 815.
18. Zhou, H. X. Biophys J 1993, 65, 955.
19. Cortis, C. M.; Friesner, R. A. J Comput Chem 1997, 18, 1591.
20. Holst, M.; Baker, N.; Wang, F. J Comput Chem 2000, 21, 1319.
21. Warwicker, J.; Watson, H. C. J Mol Biol 1982, 157, 671.
22. Sharp, K. A.; Honig, B. J Phys Chem 1990, 94, 7684.
23. Gilson, M. K.; Davis, M. E.; Luty, B. A.; McCammon, J. A. J Phys Chem 1993, 97, 3591.
24. Im, W.; Beglov, D.; Roux, B. Comput Phys Commun 1998, 111, 59.
25. Nina, M.; Im, W.; Roux, B. Biophys Chem 1999, 78, 89.
26. Davis, M. E.; McCammon, J. A. J Comput Chem 1990, 11, 401.
27. Egwolf, B.; Tavan, P. J Chem Phys 2004, 120, 2056.
28. Friedrich, M.; Zhou, R. H.; Edinger, S. R.; Friesner, R. A. J Phys Chem B 1999, 103, 3057.
29. Lu, Q.; Luo, R. J Chem Phys 2003, 119, 11035.
30. Gilson, M. K. J Comput Chem 1995, 16, 1081.
31. Dominy, B. N.; Brooks, C. L. J Phys Chem B 1999, 103, 3765.
32. Onufriev, A.; Case, D. A.; Bashford, D. J Comput Chem 2002, 23, 1297.
33. Feig, M.; Im, W.; Brooks, C. L. I. J Chem Phys 2004, 120, 903.
34. Sitkoff, D.; Sharp, K. A.; Honig, B. J Phys Chem 1994, 98, 1978.
35. Hodson, M. E.; Cistola, D. P. Biochemistry 1997, 36, 2278.
36. Lindahl, E.; Hess, B.; van der Spoel, D. J Mol Model 2001, 7, 306.
37. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D. J Chem Phys 1983, 79, 926.
38. Pearlmann, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E., 3rd; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. Comput Phys Commun 1995, 91, 1.
39. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1996, 118, 2309.
40. Ryckaert, J.-P.; Ciccotti, G.; van Gunsteren, W. F. J Comput Phys 1977, 23, 327.
41. Ponder, J. W.; Washington University in St. Louis: St. Louis, MO, 2003.
42. Personal communication: Swanson, J. M. J.; McCammon, J. A. MM/ PBSA calculations with APBS using nonzero ionic strengths has been shown to lead to unrealistically large energies when incompatible spline-based characteristic functions are used to describe the dielectric coefficient and the ion accessibility. 2004.
43. Dong, F.; Vijaykumar, M.; Zhou, H. X. Biophys J 2003, 85, 49.
44. Mertz, E. L.; Krishtalik, L. I. Proc Natl Acad Sci USA 2000, 97(5), 2081-2086.
45. Sharp, K.; Jeancharles, A.; Honig, B. J Phys Chem 1992, 96, 3822.
46. Simonson, T. Int J Quantum Chem 1999, 75, 45.
47. Elcock, A. H.; Sept, D.; McCammon, J. A. J Phys Chem B 2001, 105, 1504.
48. Roux, B. In Computational Biochemistry and Biophysics; Becker, O. M.; MacKerell, A. D. J.; Roux, B.; Watanabe, M., Eds.; Marcel Dekker: New York, 2001, p. 133.
49. Nielsen, J. E.; Andersen, K. V.; Honig, B.; Hooft, R. W. W.; Klebe, G.; Vriend, G.; Wade, R. C. Protein Eng 1999, 12, 657.
50. Sham, Y. Y.; Muegge, I.; Warshel, A. Biophys J 1998, 74, 1744.
51. Herman, R. B. J Phys Chem 1972, 76, 2754.
52. Chothia, C. Nature 1974, 248, 338.
53. Sharp, K. A.; Nicholls, A.; Fine, R. F.; Honig, B. Science 1991, 252, 106.
54. Wesson, L.; Eisenberg, D. Protein Sci 1992, 1, 227.
55. Sitkoff, D.; Sharp, K. A.; Honig, B. Biophys Chem 1994, 51, 397; discussion 404.
56. Press, W. H.; Teukolsky, S. A.; Vetterling, W. T.; Flannery, B. P. Numerical Recipes in C; Cambridge University Press: New York, 1992.
57. Höchtl, P.; Boresch, S.; Bitomsky, W.; Steinhauser, O. J Chem Phys 1998, 109, 4927.
58. Bhattacharyya, S. M.; Wang, Z.-G.; Zewail, A. H. J Phys Chem B 2003, 107, 13218.
59. Lin, J.-H.; Baker, N. A.; McCammon, J. A. Biophys J 2002, 83, 1374.
60. Russo, D.; Hura, G.; Head-Gordon, T. Biophys J 2004, 86, 1852.
61. Ford, R. C.; Ruffle, S. V.; Ramirez-Cuesta, A. J.; Michalarias, I.; Beta, I.; Miller, A.; Li, J. J Am Chem Soc 2004, 126, 4682.
62. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Clarendon: Oxford, 1987.
63. Lee, B.; Richards, F. M. J Mol Biol 1971, 55, 379.