Continuum electrostatics of proteins: Experimental test with model solvents and the method of the proteins pK calculations

Chemical Physics

Volumn 319, Issue 1-3, 2005, Pages 316-329

  Krishtalik, Lev I ^a  

^a FRUMKIN INSTITUTE OF PHYSICAL CHEMISTRY AND ELECTROCHEMISTRY   (Russian Federation)

Author keywords

Continuum electrostatics; Dielectric response; Ion solvation; Ion transfer energy; Optical dielectric permittivity; pK in proteins; pK in solvents; Pre existing field; Protein's dielectric constant; Static dielectric permittivity

Indexed keywords

EID: 28644438898     PISSN: 03010104     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chemphys.2005.04.013     Document Type: Article

References (90)

1. A.M. Kuznetsov Charge transfer in physics, chemistry and biology 1995 Gordon & Breach Amsterdam
2. L.I. Krishtalik Molek. Biol. (Moscow) 8 1974 91
3. L.I. Krishtalik J. Theor. Biol. 86 1980 757
4. G. Johannin, and N. Kellersohn Biochem. Biophys. Res. Commun. 49 1972 321
5. J. Warwicker, and H. Watson J. Mol. Biol. 157 1982 671
6. L.I. Krishtalik, and V.V. Topolev Molek. Biol. (Moscow) 17 1983 1034
7. L.I. Krishtalik, and V.V. Topolev Molek. Biol. (Moscow) 18 1984 712, 892
8. L.I. Krishtalik J. Theor. Biol. 112 1985 251
9. L.I. Krishtalik, and V.V. Topolev Biochem. Biophys. Acta 1459 2000 88
10. S.C. Harvey Proteins 5 1989 78
11. K.A. Sharp, and B.H. Honig Annu. Rev. Biophys. Biophys. Chem. 19 1990 301
12. M.E. Davis, and J.A. McCammon Chem. Rev. 90 1990 509
13. D. Bashford Curr. Opin. Struct. Biol. 1 1991 175
14. K.A. Sharp Curr. Opin. Struct. Biol. 4 1994 234
15. M.K. Gilson Curr. Opin. Struct. Biol. 5 1995 216
16. B.H. Honig, and A. Nicholls Science 268 1995 1144
17. M. Schaefer, H. van Vlijmen, and M. Karplus Adv. Protein Chem. 51 1998 1
18. T. Simonson Curr. Opin. Struct. Biol. 11 2001 243
19. T. Simonson Rep. Prog. Phys. 66 2003 737
20. D. Bashford Front. Biosci. 9 2004 1082
21. A. Papazyan, and A. Warshel J. Phys. Chem. B 101 1997 11254
22. L.I. Krishtalik, N.M. Alpatova, and E.V. Ovsyannikova Electrochim. Acta 36 1991 435
23. L.V. Bunakova, V.V. Topolev, L.A. Khanova, and L.I. Krishtalik Elektrokhimiya (Russian) 40 2004 913
24. L.A. Khanova, and L.F. Lafi J. Electroanal. Chem. 345 1993 393
25. K. Slowinski, K.U. Slowinska, and M. Majda J. Phys. Chem. 103 1999 8544
26. L.V. Bunakova, L.A. Khanova, and L.I. Krishtalik Elektrokhimiya (Russian) 41 2005 329
27. A. Nicholls, and B. Honig J. Comput. Chem. 12 1991 435
28. M. Fujinaga, A.R. Sielecki, R.J. Read, W. Ardelt, M. Laskowski Jr., and M.N.G. James J. Mol. Biol. 195 1987 397
29. W. Bode, and R. Huber Eur. J. Biochem. 204 1992 433
30. A. Bondi J. Phys. Chem. 68 1964 441
31. L.I. Krishtalik, A.M. Kuznetsov, and E.L. Mertz Proteins 28 1997 174
32. E.L. Mertz, and L.I. Krishtalik Proc. Natl. Acad. Sci. USA 97 2000 2081
33. E.L. Mertz, and L.I. Krishtalik Bioelectrochem. Bioener. 48 1999 397
34. S.J. Weiner, P.A. Kollman, D.A. Case, U.C. Singh, C. Ghio, G. Alagona, S. Profeta Jr., and P. Weiner J. Am. Chem. Soc. 106 1984 765
35. W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz Jr., D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, and P.A. Kollman J. Am. Chem. Soc. 117 1995 5179
36. I.V. Leontyev, M.V. Vener, I.V. Rostov, M.V. Basilevsky, and M.D. Newton J. Chem. Phys. 119 2003 8024
37. M.V. Vener, I.V. Leontyev, and M.V. Basilevsky J. Chem. Phys. 119 2003 8038
38. I.V. Leontyev, M.V. Basilevsky, and M.D. Newton Theor. Chem. Acc. 111 2004 110
39. E.L. Mertz, in preparation.
40. J. Tomasi, and M. Persico Chem. Rev. 94 1994 2027
41. C.J. Cramer, and D.G. Truhlar Chem. Rev. 99 1999 2161
42. C.-P. Hsu, Yu. Georgievskii, and R.A. Marcus J. Phys. Chem. A 102 1998 2658
43. D.V. Matyushov, and M.D. Newton J. Phys. Chem. A 105 2001 8516
44. L.I. Krishtalik Elektrokhimiya (Russian) 33 1997 1260
45. Yu.I. Kharkats, and L.I. Krishtalik J. Theor. Biol. 112 1985 221
46. L.I. Krishtalik, G.-S. Tae, D.A. Cherepanov, and W.A. Cramer Biophys. J. 65 1993 184
47. G.M. Soriano, W.A. Cramer, and L.I. Krishtalik Biophys. J. 73 1997 3265
48. H.X. Zhou J. Am. Chem. Soc. 116 1994 10362
49. Yu.I. Kharkats, and J. Ulstrup Chem. Phys. 141 1990 117
50. Y.-P. Liu, and M.D. Newton J. Phys. Chem. 98 1994 7162
51. J. Antosiewicz, J.A. McCammon, and M.K. Gilson J. Mol. Biol. 238 1994 415
52. B. Garsia-Moreno, J. Dwyer, A. Gittis, E. Lattman, D. Spencer, and W. Stites Biophys. Chem. 64 1997 211
53. G. Gritzner Electrochim. Acta 44 1998 73
54. Y. Marcus Electrochim. Acta 44 1998 91
55. V.A. Pleskov Zh. Fiz. Khim. 14 1940 1477
56. V.A. Pleskov Usp. Khim. 16 1947 254
57. H.M. Koepp, H. Wendt, and H. Strehlow Z. Electrochem. 64 1960 483
58. G. Gritzner Inorg. Chim. Acta 24 1977 5
59. E. Grunwald, J. Baughman, and G. Kohnstam J. Am. Chem. Soc. 82 1960 5801
60. E.M. Arnett, and D.R. McKelvey J. Am. Chem. Soc. 88 1966 2598
61. A.J. Parker, and R. Alexander J. Am. Chem. Soc. 90 1968 3313
62. J.F. Coetzee, and W.P. Sharpe J. Phys. Chem. 75 1971 3141
63. L.I. Krishtalik, N.M. Alpatova, and E.V. Ovsyannikova Elektrokhimiya (Russian) 26 1990 436
64. M. Senda, and R. Takahashi Rev. Polarogr. (Japan) 20 1974 56
65. T. Kakutani, M. Joshikazu, M. Senda, R. Takahashi, and K. Matsumoto Bull. Chem. Soc. Jpn. 51 1978 2847
66. C. Madec, and J. Courtot-Coupez J. Electroanal. Chem. 84 1977 177
67. N.M. Alpatova, E.V. Ovsyannikova, and L.I. Krishtalik Elektrokhimiya (Russian) 27 1991 931
68. G. Gritzner J. Phys. Chem. 90 1986 5478
69. L.I. Krishtalik, N.M. Alpatova, and E.V. Ovsyannikova Elektrokhimiya (Russian) 31 1995 871
70. D. Sitkoff, K.A. Sharp, and B. Honig J. Phys. Chem. 98 1994 1978
71. D. Sitkoff, N. Ben-Tal, and B. Honig J. Phys. Chem. 100 1996 2744
72. G.E. Chudinov, D.V. Napolov, and M.V. Basilevsky Chem. Phys. 160 1992 41
73. B.P. Nikol'skii Spravochnik khimika (Chemistry Handbook) Khimiya vol. III 1965 Leningrad Moscow
74. B.W. Clare, D. Cook, E.C.F. Ko, Y.C. Mac, and A.J. Parker J. Am. Chem. Soc. 88 1966 1911
75. J. Zielinska, M. Makowski, K. Maj, A. Liwo, and L. Chmurzynski Anal. Chim. Acta 401 1999 317
76. V.V. Topolev, and L.I. Krishtalik Molek. Biol. (Moscow) 17 1983 1177
77. G.E. Titova, and L.I. Krishtalik Biofizika (Russian) 30 1985 363
78. V.P. Bulychev, and N.D. Sokolov N.D. Sokolov Vodorodnaya svyaz' (Hydrogen bond) 1981 Nauka Moscow 10
79. A.R. Fersht, and J. Sperling J. Mol. Biol. 74 1973 137
80. F.J. Kézdy, G.E. Clement, and M.L. Bender J. Am. Chem. Soc. 86 1964 3690
81. P.E. Wilcox G.E. Perlmann L. Lorand Methods in enzymology Proteolytic enzymes vol. XIX 1970 Academic Press New York 64
82. B.M. Baker, and K.P. Murphy J. Mol. Biol. 268 1997 557
83. M.K. Gilson, and B.H. Honig Biopolymers 25 1986 2097
84. H. Nakamura, T. Sakamoto, and A. Wada Protein Eng. 2 1988 177
85. T. Simonson, D. Perahia, and G. Bricogne J. Mol. Biol. 218 1991 1859
86. T. Simonson, D. Perahia, and A.T. Brünger Biophys. J. 59 1991 670
87. G. King, F.S. Lee, and A. Warshel J. Chem. Phys. 95 1991 4366
88. P.E. Smith, R.M. Brunne, A.E. Mark, and van W.F. Gunsteren J. Phys. Chem. 97 1993 2009
89. T. Simonson, and D. Perahia J. Am. Chem. Soc. 117 1995 7987
90. J.L. Markley, and I.B. Ibańez Biochemistry 17 1978 4627