Molecular dynamics in physiological solutions: Force fields, alkali metal ions, and ionic strength

Journal of Chemical Theory and Computation

Volumn 6, Issue 7, 2010, Pages 2167-2175

  Zhang, Chao ^a   Raugei, Simone ^b   Eisenberg, Bob ^c   Carloni, Paolo ^a,d  

^a RWTH AACHEN UNIVERSITY   (Germany)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^c RUSH UNIVERSITY MEDICAL CENTER   (United States)

^d SEZIONE DI TRIESTE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77956931884     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct9006579     Document Type: Article

References (113)

1. 2O.
2. Costanzo, L. S. Physiology; Elsevier/Saunders: Philadelphia, PA, 2006; pp 2-4.
3. Gouaux, E.; MacKinnon, R. Science 2005, 310, 1461.
4. Doyle, D. A.; Cabral, J. M.; Pfuetzner, R. A.; Kuo, A.; Gulbis, J. M.; Cohen, S. L.; Chait, B. T.; MacKinnon, R. Science 1998, 280, 69.
5. Domene, C.; Vemparala, S.; Furini, S.; Sharp, K.; Klein, M. L. J. Am. Chem. Soc. 2008, 130, 11.
6. Jayaram, B.; Jain, T. Annu. Rev. Biophys. Biomol. Struct. 2004, 33, 343.
7. Auffinger, P.; Hashem, Y. Curr. Opin. Struct. Biol. 2007, 17, 325.
8. Chu, V. B.; Bai, Y.; Lipfert, J.; Herschlag, D.; Doniach, S. Curr. Opin. Chem. Biol. 2008, 12, 619.
9. Lee, L. L. Molecular Thermodynamics of Electrolyte Solutions; World Scientific: New York, 2008; pp 11-38.
10. Beck, T. L.; Paulaitis, M. E.; Pratt, L. R. The Potential Distribution Theorem and Models of Molecular Solutions; Cambridge University Press: Cambridge, U.K., 2006; pp 45- 68.
11. Butt, H. J.; Graf, K.; Kappl, M. Physics and Chemistry of Interfaces; Wiley-VCH: Weinheim, Germany, 2006; pp 77- 79.
12. Liquids, Solutions, and Interfaces: From Classical Macroscopic Descriptions to Modern Microscopic Details; Fawcett, W. R., Ed.; Oxford University Press: New York, 2004; pp 3-147.
13. Kastenholz, M. A.; Hnenberger, P. H. J. Chem. Phys. 2006, 124, 224501.
14. Lamoureux, G.; Roux, R. J. Phys. Chem. B 2006, 110, 3308.
15. van Gunsteren, W. F.; et al. Angew. Chem., Int. Ed. 2006, 45, 4064.
16. McDowell, S. E.; Spackova, N.; Sponer, J.; Walter, N. G. Biopolymer 2007, 82, 169.
17. Hummer, G.; Pratt, L. R.; García, A. E. J. Phys. Chem. 1996, 100, 1206.
18. Hummer, G.; Pratt, L. R.; Garcá, A. E. J. Chem. Phys. 1997, 107, 9275.
19. Hünenberger, P. H.; McCammon, J. A. J. Chem. Phys. 1999, 110, 1856.
20. Conway, B. E. J. Sol. Chem. 1978, 7, 720-770.
21. Marcus, Y. J. Chem. Soc. Faraday Trans. 1987, 83, 2985.
22. Tissandier, M. D.; Cowen, K. A.; Feng, W. Y.; Gundlach, E.; Cohen, M. H.; Earhart, A. D.; Coe, J. V. J. Phys. Chem. A 1998, 102, 7787.
23. Fawcett, W. R. Langmuir 2008, 24, 9868.
24. Wilczek-Vera, G.; Rodil, E.; Vera, J. H. AIChE J. 2004, 50, 445.
25. -.
26. Joung, I. S.; Cheatham, T. E., III J. Phys. Chem. B 2008, 112, 9020.
27. Beglov, D.; Roux, B. J. Chem. Phys. 1994, 100, 9050.
28. Roux, B. Biophys. J. 1996, 71, 3177.
29. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225.
30. Dang, L. X. J. Am. Chem. Soc. 1995, 117, 6954.
31. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J. Phys. Chem. 1987, 91, 6269.
32. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
33. Patra, M.; Karttunen, M. J. Comput. Chem. 2004, 25, 678.
34. Hamer, W. J.; Wu, Y.-C. J. Phys. Chem. Ref. Data 1972, 1, 1047.
35. Fawcett, W. R. Liquids, Solutions, and Interfaces: From Classical Macroscopic Descriptions to Modern Microscopic Details; Oxford University Press: New York, 2004; pp 395-422.
36. Paluch, M. Adv. Colloid Interface Sci. 2000, 84, 27.
37. Petersen, P. B.; Saykally, R. J. Annu. Rev. Phys. Chem. 2006, 57, 333.
38. Continuum models encounter difficulties in describing the Galvani potential because the latter depends on the polarization of the system.
39. Kirkwood, J. G. J. Chem. Phys. 1935, 3, 300.
40. Ferrrario, M.; Ciccoti, G.; Spohr, E.; Cartailler, T.; Turq, P. J. Chem. Phys. 2002, 117, 4947.
41. Free Energy Calculations; Chipot, C., Pohorille, A., Eds.; Springer-Verlag: Berlin, Germany, 2007; pp 33-72.
42. Fukunishi, H.; Watanabe, O.; Takada, S. J. Chem. Phys. 2002, 116, 9058.
43. Woods, C. J.; Essex, J. W.; King, M. A. J. Phys. Chem B 2003, 107, 13711.
44. Jiang, W.; Hodoscek, M.; Roux, B. J. Chem. Theory Comput. 2009, 5, 2583.
45. Uchida, H.; Matsuoka, M. Fluid Phase Equilib. 2004, 219, 49.
46. Chowdhuri, S.; Chandra, A. J. Chem. Phys. 2001, 115, 3732.
47. Instead, the diffusion of ions has no impact on the convergence of TI calculation at infinite dilution.
48. Wick, C. D.; Dang, L. X.; Jungwirth, P. J. Chem. Phys. 2006, 125, 024706.
49. Bauer, B. A.; Patel, S. J. Chem. Phys. 2010, 132, 024713.
50. Kastenholz, M. A.; Hünenberger, P. H. J. Chem. Phys. 2006, 124, 124106.
51. Sagul, C.; Darden, T. A. Annu. Rev. Biophys. Biomol. Struct. 1999, 28, 155.
52. Feller, S. E.; Pastor, R. W.; Rojnuckarin, A.; Bogusz, S.; Brooks, B. R. J. Phys. Chem. 1996, 100, 17011.
53. Sokhan, V. P.; Tildesley, D. J. Mol. Phys. 1997, 92, 625.
54. Lamoureux, G.; Mackerell, A. D., Jr.; Roux, B. J. Chem. Phys. 2003, 119, 5185.
55. Cheng, J.; Sulpizi, M.; Sprik, M. J. Chem. Phys. 2009, 131, 154504.
56. The calculated static dielectric constants ε (0) of KCl and NaCl solutions comparing with experimental data as a function of the molal ionic strength can be seen in Supporting Information, Figure S2.
57. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J. Comput. Chem. 2005, 26, 1701.
58. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435.
59. MacKerell, A. D., Jr.; et al. J. Phys. Chem. B 1998, 102, 3586.
60. Modified TIP3P water in CHARMM59.
61. Lin, Y.; Baumketner, A.; Deng, S.; Xu, Z.; Jacobs, D.; Cai, W. J. Chem. Phys. 2009, 131, 154103.
62. Nośe, S. J. Chem. Phys. 1984, 81, 511.
63. Hoover, W. G. Phys. Rev. A: At., Mol., Opt. Phys. 1985, 31, 1695.
64. Parrinello, M.; Rahman, A. Phys. Rev. Lett. 1980, 45, 1196.
65. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577.
66. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids: Oxford Science Publications: Oxford, U.K., 1987; pp 64-68.
67. Miyamoto, S.; Kollman, P. A. J. Comput. Chem. 1992, 13, 952.
68. Exact number depends on the water model and the salt type.
69. Kollman, P. Chem. Rev. 1993, 93, 2395.
70. Beutler, T. C.; Mark, A. E.; Van Schaik, R. C.; Gerber, P. R.; Van Gunsteren, W. F. Chem. Phys. Lett. 1994, 222, 529.
71. Hess, B. J. Chem. Phys. 2002, 116, 209.
72. Note that it is also possible to obtain the Galvani potential by creating a virtual air-solution interface with those snapshots from simulations of bulk solutions under PBC and then integrating the charge density.
73. Joung, I. S.; Cheatham, T. E. J. Phys. Chem. B 2009, 113, 13279.
74. Notice that the time-scale of our simulation is shorter than that of these authors.73 They use straightforward TI instead of replica-exchange TI. The latter converges faster, See Figure S1 in Supporting Information..
75. Luo, Y.; Roux, B. J. Phys. Chem. Lett. 2010, 1, 183.
76. -.
77. I, ex but may be relevant as a reference.
78. We only observed a slight preference of the anions at the interface than cations in the simulations (See Figure S3 in Supporting Information).
79. Randles, J. E. Phys. Chem. Liq. 1977, 7, 107.
80. Jungwirth, P.; Tobias, D. J. Chem. Rev. 2006, 106, 1259.
81. Jarvis, N. J.; Scheiman, M. A. J. Phys. Chem. 1968, 72, 74.
82. Wright, M. R. An Introduction to Aqueous Electrolyte Solutions; Wiley: Chichester, U.K., 2007.
83. We expect similar results for all the other force fields as they have the same trend in Figure 5. However, free energy decomposition is force field and path dependent.
84. Harder, E.; Roux, B. J. Chem. Phys. 2008, 129, 234706.
85. Hille, B. Ionic Channels of Excitable Membranes, 3rd ed.; Sinauer Associates Inc.: Sunderland, MA, 2001; pp 1-19.
86. Zuhlke, R. D.; Pitt, G. S.; Deisseroth, K.; Tsien, R. W.; Reuter, H. Nature 1999, 399, 159.
87. Hodgkin, A.; Huxley, A.; Katz, B. Arch. Sci. Physiol. 1949, 3, 129.
88. Hodgkin, A. J. Physiol. 1976, 263, 1.
89. Conley, E. C. The Ion Channel Facts Book. I. Extracellular Ligand-gated Channels; Academic Press: New York, 1996; pp 3-11.
90. Conley, E. C. The Ion Channel Facts Book. II. Intracellular Ligand-gated Channels; Academic Press: New York, 1996; pp 3-20.
91. Conley, E. C.; Brammar, W. The Ion Channel Facts Book III: Inward Rectifier and Intercellular Channels; Academic Press: New York 2000; pp 3-21.
92. Conley, E. C.; Brammar, W. The Ion Channel Facts Book IV: Voltage Gated Channels; Academic Press: New York, 1999; pp 3-21.
93. Barry, P. H. Am. J. Physiol. 1990, 259, S15.
94. Barry, P. H. Ann. Biomed. Eng. 1994, 22, 218.
95. Barry, P. H. J. Neurosci. Methods 1994, 51, 107.
96. Barry, P. H. Cell Biochem. Biophys. 2006, 46, 143.
97. Ng, B.; Barry, P. H. J. Neurosci. Methods 1995, 56, 37.
98. Miedema, H.; Meter-Arkema, A.; Wieregna, J.; Tang, J.; Eisenberg, B.; Nonner, W.; Hektor, H.; Gillespie, D.; Meijberg, W. Biophys. J. 2004, 87, 3137.
99. Miedema, H.; Vrouenraets, M.; Wieregna, J.; Eisenberg, B.; Gillespie, D.; Meijberg, W.; Nonner, W. Biophys. J. 2006, 91, 4392.
100. Vrouenraets, M.; Wieregna, J.; Meijberg, W.; Miedema, H. Biophys. J. 2006, 90, 1202.
101. Berg, J. M. Annu. Rev. Biophys. Biophys. Chem. 1990, 19, 405.
102. Berg, J. M. J. Biol. Chem. 1990, 265, 6513.
103. Cantwell, M. A.; Di Cera, E. J. Biol. Chem. 2000, 275, 39827.
104. Berg, J. M.; Godwin, H. A. Annu. Rev. Biophys. Biomol. Struct. 1997, 26, 357.
105. Carnell, C. J.; Bush, L. A.; Mathews, F. S.; Di Cera, E. Biophys. Chem. 2006, 121, 177.
106. De Gristofaro, R.; Fenton II, J. W.; Di Cera, E. J. Mol. Biol. 1992, 226, 263.
107. Di Cera, E. Biopolymer 1994, 34, 1001.
108. Doroshenko, P. A.; Kostyuk, P. G.; Lukyanetz, E. A. Neurosci. 1998, 27, 1073.
109. Eisenberg, R. S. J. Membr. Biol. 1990, 115, 1.
110. Lambers, T. T.; Mahieu, F.; Oancea, E.; Hoofd, L.; de Lange, F.; Mensenkamp, A. R.; Voets, T.; Nilinus, B.; Clapham, D. E.; Hoenderop, J. G.; Bindels, R. J. EMBO J. 2006, 25, 2978.
111. Tripathy, A.; Xu, L.; Mann, G.; Meissner, G. Biophys. J. 1995, 69, 106.
112. Vescovi, E. G.; Ayala, Y. M.; Di Cera, E.; Groisman, E. A. J. Biol. Chem. 1997, 272, 1440.
113. Suzuki, M.; Morita, T.; Iwamoto, T. Cell. Mol. Life Sci. 2006, 63, 12.