Influence of Artificial Periodicity and Ionic Strength in Molecular Dynamics Simulations of Charged Biomolecules Employing Lattice-Sum Methods

Journal of Physical Chemistry B

Volumn 108, Issue 2, 2004, Pages 774-788

  Kastenholz, Mika A ^a   Hünenberger, Philippe H ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BOUNDARY CONDITIONS; COMPUTER SIMULATION; ELECTROSTATICS; FREE ENERGY; LATTICE CONSTANTS; MOLECULAR DYNAMICS; PERTURBATION TECHNIQUES;

BIOMOLECULES; ELECTROSTATIC FREE ENERGY; MOLECULAR DYNAMICS SIMULATIONS;

IONIC STRENGTH;

EID: 1642525904     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0350924     Document Type: Article

References (114)

1. Madelung, E. Phys. Z. 1918, 19, 524.
2. Ewald, P. P. Ann. Phys. (Leipzig) 1921, 64, 253.
3. Hockney, R. W.; Eastwood, J. W. Computer simulation using particles; McGraw-Hill: New York, 1981.
4. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089.
5. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577.
6. de Leeuw, S. W.; Perram, J. W.; Smith, E. R. Proc. R. Soc. London, Ser. A 1980, 373, 27.
7. de Leeuw, S. W.; Perram, J. W.; Smith, E. R. Proc. R. Soc, London, Ser. A 1980, 373, 57.
8. Hünenberger, P. H. Simulation and Theory of Electrostatic Interactions in Solution; AIP: Melville, NY, 1999.
9. Luty, B. A.; Davis, M. E.; Tironi, I. G.; van Gunsteren, W. F. Mol. Simul. 1994, 14, 11.
10. Luty, B. A.; Tironi, I. G.; van Gunsteren, W. F. J. Chem. Phys. 1995, 103, 3014.
11. Pollock, E. L.; Glosli, J. Comput. Phys. Commun. 1996, 95, 93.
12. Deserno, M.; Holm, C. J. Chem. Phys. 1998, 109, 7678.
13. Desemo, M.; Hohn, C. J. Chem. Phys. 1998, 109, 7694.
14. Smith, P. E.; Pettitt, B. M. J. Chem. Phys. 1991, 95, 8430.
15. Cheatham, T. E.; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 4193.
16. Fox, T.; Kollman, P. A. Proteins; Struct., Fund., Genet 1996, 25, 315.
17. Cheatham, T. E.; Young, M. A. Biopolymers 2000, 56, 232.
18. Cheatham, T. E.; Kollman, P. A. Annu. Rev. Phys. Chem. 2000, 57, 435.
19. Auffinger, P.; Westhof, E. Curr. Opin. Struct. Biol. 1998, 8, 227.
20. Allen, M. P.; Tildesley, D. J. Computer Simulations of Liquids; Clarendon Press: Oxford, 1987.
21. Brooks, C. L. Curr. Opin. Struct. Biol. 1995, 5, 211.
22. LouiseMay, S.; Auffinger, P.; Westhof, E. Curr. Opin. Struct. Biol. 1996, 6, 289.
23. Auffinger, P.; LouiseMay, S.; Westhof, E. J. Am. Chem. Soc. 1996, 118, 1181.
24. de Bakker, P. I. W.; Hünenberger, P. H.; McCammon, J. A. J. Mol. Biol. 1999, 285, 1811.
25. Hünenberger, P. H.; McCammon, J. A. Biophys. Chem. 1999, 78, 69.
26. Barker, J. A.; Watts, R. O. Mol. Phys. 1973, 26, 789.
27. Neumann, M. Mol. Phys. 1983, 50, 841.
28. Barker, J. A. Mol. Phys. 1994, 83, 1057.
29. Tironi, I. G.; Sperb, R.; Smith, P. E.; van Gunsteren, W. F. J. Chem. Phys. 1995, 012, 5451.
30. Hünenberger, P. H.; van Gunsteren, W. F. J. Chem. Phys. 1998, 108, 6117.
31. Stocker, U.; van Gunsteren, W. F. Proteins; Struct., Funct., Genet. 2000, 40, 145.
32. Daura, X.; Haaksma, E.; van Gunsteren, W. F. J. Comput.-Aided Mol. Des. 2000, 14, 507.
33. Nina, M.; Simonson, T. J. Phys. Chem. B 2002, 106, 3696.
34. Neumann, M.; Steinhauser, O. Mol. Phys. 1980, 39, 437.
35. Pollock, E. L.; Alder, B. J. Physica A 1980, 102, 1.
36. Alder, B. J.; Pollock, E. L. Annu. Rev. Phys. Chem. 1981, 32, 311.
37. Adams, D. J.; Adams, E. M. Mol. Phys. 1981, 42, 907.
38. Neumann, M.; Steinhauser, O. Chem. Phys. Lett. 1983, 102, 508.
39. Steinhauser, O. Chem. Phys. 1983, 79, 465.
40. Neumann, M.; Steinhauser, O. Chem. Phys. Lett. 1984, 106, 563.
41. Neumann, M.; Steinhauser, O.; Pawley, G. S. Mol. Phys. 1984, 52, 97.
42. de Leeuw, S. W.; Perram, J. W.; Smith, E. R. Annu. Rev. Phys. Chem. 1986, 37, 245.
43. Smith, E. R.; Wielopolski, P. A. Mol. Phys. 1987, 61, 1063.
44. Boresch, S.; Steinhauser, O. Ber. Bunsen-Ges. 1997, 101, 1019.
45. Boresch, S.; Steinhauser, O. J. Chem. Phys. 1999, 111, 8271.
46. Boresch, S.; Ringhofer, S.; Hochtl, P.; Steinhauser, O. Biophys. Chem. 1999, 78, 43.
47. Kirkwood, J. G. J. Chem. Phys. 1939, 7, 911.
48. Boresch, S.; Steinhauser, O. J. Chem. Phys. 2001, 115, 10780.
49. Boresch, S.; Steinhauser, O. J. Chem. Phys. 2001, 115, 10793.
50. Kusalik, P. G. J. Chem. Phys. 1990, 93, 3520.
51. Belhadj, M.; Alper, H. E.; Levy, R. M. Chem. Phys. Lett. 1991, 179, 13.
52. Roberts, J. E.; Schnitker, J. J. Phys. Chem. 1995, 99, 1322.
53. Vorobjev, Y. N.; Hermans, J. J. Phys. Chem. B 1999, 103, 10234.
54. Sloth, P.; Sorensen, T. S. Chem. Phys. Lett. 1990, 173, 51.
55. Hummer, G.; Pratt, L. R.; Garcia, A. E. J. Phys. Chem. 1996, 100, 1206.
56. Figueirido, F.; DelBueno, G. S.; Levy, R. M. J. Phys. Chem. B 1997, 101, 5622.
57. Hummer, G.; Pratt, L. R.; Garcia, A. E. J. Chem. Phys. 1997, 107, 9275.
58. Hummer, G.; Pratt, L. R.; Garcia, A. E. J. Phys. Chem. A 1998, 102, 7885.
59. Sakane, S.; Ashbaugh, H. S.; Wood, R. H. J. Phys. Chem. B 1998, 102, 5673.
60. Hünenberger, P. H.; McCammon, J. A. J. Chem. Phys. 1999, 110, 1856.
61. Bogusz, S.; Cheatham, T. E.; Brooks, B. R. J. Chem. Phys. 1998, 108, 7070.
62. Peter, C.; van Gunsteren, W. F.; Hünenberger, P. H. J. Chem. Phys. 2002, 116, 7434.
63. Nijboer, B. R. A.; Ruijgrok, T. W. J. Stat. Phys. 1988, 53, 361.
64. Cichocki, B.; Felderhof, B. U.; Hinsen, K. Phys. Rev. A 1989, 39, 5350.
65. Hummer, G.; Soumpasis, D. M. J. Chem. Phys. 1993, 98, 581.
66. Ashbaugh, H. S.; Wood, R. H. J. Chem. Phys. 1997, 106, 8135.
67. Hummer, G.; Pratt, L. R.; Garcia, A. E.; Berne, B. J.; Rick, S. W. J. Phys. Chem. B 1997, 101, 3017.
68. Aqvist, J.; Hansson, T. J. Phys. Chem. B 1998, 102, 3837.
69. Ashbaugh, H. S.; Sakane, S.; Wood, R. H. J. Phys. Chem. B 1998, 102, 3844.
70. Babu, C. S.; Yang, P. K.; Lim, C. J. Biol. Phys. 2002, 28, 95.
71. Valleau, J. P.; Whittington, S. G. A Guide to Monte Carlo for Statistical Mechanics: 1. Highways; Plenum: New York, 1977; Vols. 5 and 6.
72. Figueirido, F.; Delbuono, G. S.; Levy, R. M. J. Chem. Phys. 1995, 103, 6133.
73. Luty, B. A.; van Gunsteren, W. F. J. Phys. Chem. 1996, 100, 2581.
74. Guardia, E.; Rey, R.; Padro, J. A. J. Chem. Phys. 1991, 95, 2823.
75. Bader, J. S.; Chandler, D. J. Phys. Chem. 1992, 96, 6423.
76. Hummer, G.; Soumpasis, D. M.; Neumann, M. Mol. Phys. 1994, 81, 1155.
77. DelBuono, G. S.; Figueirido, F. E.; Levy, R. M. Chem. Phys. Lett. 1996, 203, 521.
78. Rozanska, X.; Chipot, C. J. Chem. Phys. 2000, 112, 9691.
79. York, D. M.; Darden, T. A.; Pedersen, L. G. J. Chem. Phys. 1993, 99, 8345.
80. Walser, R.; Hünenberger, P. H.; van Gunsteren, W. F. Proteins; Struct., Funct., Genet. 2001, 43, 509.
81. Walser, R.; Hünenberger, P. H.; van Gunsteren, W. F. Proteins: Struct., Funct., Genet. 2002, 48, 327.
82. Smith, P. E.; Pettitt, B. M. J. Chem. Phys. 1996, 105, 4289.
83. Smith, P. E.; Blatt, H. D.; Pettitt, B. M. J. Phys. Chem. B 1997, 101, 3886.
84. de Souza, O. N.; Ornstein, R. L. Biophys. J. 1997, 72, 2395.
85. Cheatham, T. E.; Kollman, P. A. Molecular Dynamics Simulation of Nucleic Acids in solution: How sensitive are the results to small perturbations in the force field and environment? Adenine Press: Schenectady, NY, 1998; Vol. 1.
86. Weber, W.; Hünenberger, P. H.; McCammon, J. A. J. Phys. Chem. B 2000, 104, 3668.
87. Takaoka, Y.; Pasenkiewicz-Gierula, M.; Miyagawa, H.; Kitamura, K.; Tamura, Y.; Kusumi, A. Biophys. J. 2000, 79, 3118.
88. Egberts, E.; Marrink, S. J.; Berendsen, H. J. C. Eur. Biophys. J. Biophys. Lett. 1994, 22, 423.
89. Tieleman, D. P.; Hess, B.; Sansom, M. S. P. Biophys. J. 2002, 83, 2393.
90. Ibragimova, G. T.; Wade, R. C. Biophys. J. 1998, 74, 2906.
91. Ibragimova, G. T.; Wade, R. C. Biophys. J. 1999, 77, 2191.
92. Pfeiffer, S.; Fushman, D.; Cowburn, D. Proteins: Struct, Funct., Genet. 1999, 35, 206.
93. Wood, R. H. J. Chem. Phys. 1995, 103, 6177.
94. Ippel, J. H.; Larsson, G.; Behravan, G.; Lundqvist, M.; Lycksell, P. O.; Schleucher, J.; Zdunek, J.; Wijmenga, S. S. J. Biomol. NMR 1998, 12, 357.
95. Ippel, H.; Larsson, G.; Behravan, G.; Zdunek, J.; Lundqvist, M.; Schleucher, J.; Lycksell, P. O.; Wijmenga, S. J. Mol Biol. 1999, 288, 689.
96. Berendsen, H. J. C. Interaction Models for Water in Relation to Protein Hydration, Intermolecular Forces ed.; Reidel: Dordrecht, The Netherlands, 1981.
97. Yoon, C.; Prive, G. G.; Goodsell, D. S.; Dickerson, R. E. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 6332.
98. Real, A. N.; Greenall, R. J. J. Mol. Model 2000, 6, 654.
99. 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. 1995, 117, 5179.
100. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684.
101. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327.
102. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Kruger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; Verlag der Fachvereine Hochschulverlag AG an der ETH Zürich: Zürich, Switzerland, 1996.
103. Daura, X.; Mark, A. E.; van Gunsteren, W. F. J. Comput. Chem. 1998, 19, 535.
104. Scott, W. R. P.; Hunenberger, P. H.; Tironi, I. G.; Mark, A. E.; Billeter, S. R.; Fennen, J.; Torda, A. E.; Huber, T.; Kruger, P.; van Gunsteren, W. F. J. Phys. Chem. A 1999, 103, 3596.
105. Hunenberger, P. H. J. Chem. Phys. 2000, 113, 10464.
106. Madura, J. D.; Davis, M. E.; Gilson, M. K.; Wade, R. C.; Luty, B. A.; McCammon, J. A. Biological Applications of Electrostatic Calculations and Brownian Dynamics Simulations; VCH: New York, 1994; Vol. 4.
107. Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577.
108. Laskowski, R. A.; Macarthur, M. W.; Moss, D. S.; Thornton, J. M. J. Appl. Crystallogr. 1993, 26, 283.
109. Hubbard, S. J.; Thornton, J. M. NACCESS, 2.0 ed.; University College London: London, 1993.
110. Fletcher, C. M.; Jones, D. N. M.; Diamond, R.; Neuhaus, D. J. Biomol. NMR 1996, 8, 292.
111. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; Verlag der Fachvereine Hochschulverlag AG an der ETH Zürich: Zürich, Switzerland, 1996.
112. Cheatham, T. E.; Kollman, P. A. J. Mol. Biol. 1996, 259, 434.
113. Atkins, P. W. Physical Chemistry, 6th ed.; Oxford University Press: Oxford, 1998.
114. Zwanzig, R. W. J. Chem. Phys. 1954, 22, 1420.