A Poisson-Boltzmann dynamics method with nonperiodic boundary condition

Journal of Chemical Physics

Volumn 119, Issue 21, 2003, Pages 11035-11047

  Lu, Qiang ^a   Luo, Ray ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BOUNDARY CONDITIONS; COMPUTER AIDED SOFTWARE ENGINEERING; COMPUTER SIMULATION; COULOMB BLOCKADE; DIELECTRIC MATERIALS; ELECTROSTATICS; FINITE DIFFERENCE METHOD; MONTE CARLO METHODS; POISSON EQUATION; SOLVENTS; VAN DER WAALS FORCES;

BIOMOLECULES; COULOMBIC INTERACTION; MEAN FORCE POTENTIAL SURFACE; MINING MINIMA METHOD; NONPERIODIC BOUNDARY CONDITION; POISSON-BOLTZMANN DYNAMICS METHOD; REACTION FIELD INTERACTION;

MOLECULAR DYNAMICS;

EID: 0347410858     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1622376     Document Type: Article

References (82)

1. B. Honig, K. Sharp, and A.-S. Yang, J. Phys. Chem. 97, 1101 (1993).
2. B. Honig and A. Nicholls, Science 268, 1144 (1995).
3. M. E. Davis and J. A. McCammon, Chem. Rev. 90, 509 (1990).
4. M. K. Gilson, A. A. Rashin, R. Fine, and B. Honig, J. Mol. Biol. 183, 503 (1985).
5. M. K. Gilson and B. Honig, Proteins 3, 32, (1988).
6. M. K. Gilson and B. Honig, Proteins 4, 7 (1988).
7. D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973).
8. J. Warwicker and H. C. Watson, J. Mol. Biol. 157, 671 (1982).
9. I. Klapper, R. Hagstrom, R. Fine, K. Sharp, and B. Honig, Proteins 1, 47 (1986).
10. K. Sharp, Curr. Opin. Struct. Biol. 4, 234 (1994).
11. M. K. Gilson, Curr. Opin. Struct. Biol. 5, 216 (1995).
12. K. Mardis et al., J. Biomol. Struct. Dyn. S1, 89 (2000).
13. P. A. Kollman et al., Acc. Chem. Res. 33, 889 (2000).
14. M. E. Davis and J. A. McCammon, J. Comput. Chem. 11, 401 (1990).
15. R. J. Zauhar, J. Comput. Chem. 12, 575 (1991).
16. K. Sharp, J. Comput. Chem. 12, 454 (1991).
17. B. A. Luty, M. E. Davis, and J. A. McCammon, J. Comput. Chem. 13, 768 (1992).
18. C. Niedermeier and K. Schulten, Mol. Simul. 8, 361 (1992).
19. M. K. Gilson, M. E. Davis, B. A. Luty, and J. A. McCammon, J. Phys. Chem. 97, 3591 (1993).
20. M. K. Gilson, J. A. McCammon, and J. D. Madura, J. Comput. Chem. 16, 1081 (1995).
21. J. Srinivasan, T. E. Cheatham, P. Cieplak, P. A. Kollman, and D. A. Case, J. Am. Chem. Soc. 120, 9401 (1998).
22. R. Luo, L. David, H. Hung, J. Devaney, and M. K. Gilson, J. Phys. Chem. 103, 727 (1999).
23. R. Luo, M. S. Head, J. A. Given, and M. K. Gilson, Biophys. Chem. 78, 183 (1999).
24. R. Luo and M. K. Gilson, J. Am. Chem. Soc. 122, 2934 (2000).
25. M. E. Davis and J. A. McCammon, J. Comput. Chem. 10, 386 (1989).
26. A. Nicholls and B. Honig, J. Comput. Chem. 12, 435 (1991).
27. M. E. Davis, J. D. Madura, B. A. Luty, and J. A. McCammon, Comput. Phys. Commun. 62, 187 (1991).
28. A. Nicholls, K. Sharp, and B. Honig, Proteins 11, 281 (1991).
29. W. Rocchia, E. Alexov, and B. Honig, J. Phys. Chem. B 105, 6507 (2001).
30. R. J. Zauhar and R. S. Morgan, J. Comput. Chem. 11, 603 (1990).
31. M. Holst and F. Saied, J. Comput. Chem. 14, 105 (1993).
32. H.-X. Zhou, J. Chem. Phys. 100, 3152 (1994).
33. Y. N. Vorobjev and H. A. Scheraga, J. Comput. Chem. 18, 569 (1997).
34. C. M. Cortis and R. A. Friesner, J. Comput. Chem. 18, 1591 (1997).
35. M. Holst, N. Baker, and F. Wang, J. Comput. Chem. 21, 1319 (2000).
36. N. Baker, M. Holst, and F. Wang, J. Comput. Chem. 21, 1343 (2000).
37. A. H. Boschitsch, M. O. Fenley, and H. X. Zhou, J. Phys. Chem. B 106, 2741 (2002).
38. D. Bashford, An Object-Oriented Programming Suite for Electrostatic Effects in Biological Molecules, ISCOPE97 (Springer, Berlin, 1997), pp. 233-240.
39. R. Luo, L. David, and M. K. Gilson, J. Comput. Chem. 23, 1244 (2002).
40. S. Z. Wan, C. X. Wang, Z. X. Xiang, and Y. Y. Shi, J. Comput. Chem. 18, 1440 (1997).
41. W. Im, D. Beglov, and B. Roux, Comput. Phys. Commun. 111, 59 (1998).
42. M. Friedrichs, R. H. Zhou, S. R. Edinger, and R. A. Friesner, J. Phys. Chem. B 103, 3057 (1999).
43. M. Marchi, D. Borgis, N. Levy, and P. Ballone, J. Chem. Phys. 114, 4377 (2001).
44. B. Z. Lu, W. Z. Chen, C. X. Wang, and X. J. Xu, Proteins 48, 497 (2002).
45. M. K. Gilson, K. A. Sharp, and B. H. Honig, J. Comput. Chem. 9, 327 (1988).
46. S. Sridharan, A. Nicholls, and K. A. Sharp, J. Comput. Chem. 16, 1038 (1995).
47. T. You and D. Bashford, J. Comput. Chem. 16, 743 (1995).
48. J. A. Grant, B. T. Pickup, and A. Nicholls, J. Comput. Chem. 22, 608 (2001).
49. W. Rocchia et al., J. Comput. Chem. 23, 128 (2002).
50. W. C. Still, A. Tempczyk, R. C. Hawley, and T. Hendrickson, J. Am. Chem. Soc. 112, 6127 (1990).
51. M. S. Lee, F. R. Salsbury, and C. L. Brooks, J. Chem. Phys. 116, 10606 (2002).
52. R. W. Hockney and J. W. Eastwood, Computer Simulation Using Particles (Adam Hilger, Bristol, 1988).
53. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98, 10089 (1993).
54. B. Roux and T. Simonson, Biophys. Chem. 78, 1 (1999).
55. D. Sitkoff, K. A. Sharp, and B. Honig, J. Phys. Chem. 98, 1978 (1994).
56. C. J. F. Bottcher, O. C. van Belle, P. Bordewijk, and A. Rip, Theory of Electric Polarization, 2nd ed. (Elsevier Scientific, Amsterdam, 1973), Vol. 1.
57. D. T. Edmonds, N. K. Rogers, and M. J. E. Sternberg, Mol. Phys. 52, 1487 (1984).
58. M. E. Davis and J. A. McCammon, J. Comput. Chem. 12, 909 (1991).
59. F. M. Richards, Annu. Rev. Biophys. Bioeng. 6, 151 (1977).
60. J. A. Grant and B. T. Pickup, J. Phys. Chem. 99, 3503 (1995).
61. I. Gustafsson, BIT 18, 142 (1978).
62. S. C. Eisenstat, SIAM J. Comput. 18, 142 (1978).
63. J. Antosiewicz, J. A. McCammon, and M. K. Gilson, Biochemistry 35, 7819 (1996).
64. M. K. Gilson, Modeling Protonation Equilibria in Biomolecules (Kluwer/Escom, Dordrecht, 1997), Vol. 3, pp. 199-222.
65. A.-S. Yang and B. Honig, J. Mol. Biol. 231, 459 (1993).
66. A.-S. Yang, M. R. Gunner, R. Sampogna, K. Sharp, and B. Honig, Proteins 15, 252 (1993).
67. T. J. You and D. Bashford, Biophys. J. 69, 1721 (1995).
68. E. G. Alexov and M. R. Gunner, Biophys. J. 74, 2075 (1997).
69. M. Schaefer and M. Karplus, J. Phys. Chem. 100, 1578 (1996).
70. There are two general categories of patterns. (1) Most patterns are inside the solute interior: ...li...ih...hi...il..., where ...l and l... means one or more low dielectric edges in a row; i...i (termed i substring below) means zero or more intermediate dielectric edges in a row; and h...h (termed h substring below) means zero or more high dielectric edges in a row. Note that if there are too many h edges in the h substring, the substring may well belong to the solvent region. Therefore, a maximum length, N (in grid unit), is set to be less than the solvent probe diameter for the h substring. The diameter of a water probe is about 6 grid units when the 0.5 Å grid spacing is used, so that N should be at most 5. Considering the possible space used by intermediate edges, N is set to 4. Note also that at least one of the three substrings (two i substrings and one h substring) has to be nonezero to be a possible pattern of external edges. With all these considerations, the regular expression is 1+i*h{1,4}i*1+|1+i+1 +, where + means that the preceding letter will be matched one or more times, * means that the preceding letter will be matched zero or more times, {1,4} means that the preceding letter is matched at least 1 times, but not more than 4 times, and | means logical "or" (see LINUX grep or egrep manual page). The regular expression is designed to consider the case where there are only i edges in the patterns [Fig. 2(a)]. (2) There are also patterns that are adjacent to the bulk solvent, i.e., a pattern may start as ...h, ...hi...ih...hi...il..., or may end as h..., ...li...ih...hi...ih..., where ...h and h... means N + 1 or more external dielectric edges in a row (see above). Apparently the length of the i substring between the two h substrings has to be at least 1. Therefore, the regular expression for these two cases is h{5,}i+h{1,4}i*1+|1+i*h{1,4}i+h{5}, where {5,} means that the preceding letter is matched 5 or more times. Finally, the combined regular expression is 1+i*h{1,4}i*1+|1+i+1+|h{5,}i+h{1, 4}i*1+|1+i*h{1,4}i+h{5,}.
71. OpenEye Scientific Software, Santa Fe, NM, 1999.
72. W. F. van Gunsteren and H. J. C. Berendsen, Mol. Phys. 34, 1311 (1977).
73. J.-P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23, 327 (1977).
74. W. Wang and P. A. Kollman, J. Mol. Biol. 303, 567 (2000).
75. J. Q. Lu and R. Luo (in preparation).
76. E. Z. Wen, J. Q. Lu, W. Wang, and R. Luo (in preparation).
77. B. N. Dominy and C. L. Brooks, J. Phys. Chem. B 103, 3765 (1999).
78. V. Tsui and D. A. Case, J. Am. Chem. Soc. 122, 2489 (2000).
79. D. Bashford and D. A. Case, Annu. Rev. Phys. Chem. 51, 129 (2000).
80. K. A. Sharp and B. Honig, J. Phys. Chem. 94, 7684 (1994).
81. M. Holst, R. E. Kozack, F. Saied, and S. Subramaniam, Proteins 18, 231 (1994).
82. W. F. van Gunsteren and H. J. C. Berendsen, Mol. Simul. 1, 173 (1988).