On the use of different dielectric constants for computing individual and pairwise terms in poisson-boltzmann studies of protein ionization equilibrium

Journal of Physical Chemistry B

Volumn 109, Issue 30, 2005, Pages 14691-14706

  Teixeira, Vitor H ^a   Cunha, Carlos A ^a   Machuqueiro, Miguel ^a   Oliveira, A Sofia F ^a   Victor, Bruno L ^a   Soares, Cláudio M ^a   Baptista, Antonio M ^a  

^a INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTROSTATICS; IONIZATION; PERMITTIVITY; PH EFFECTS; PHASE EQUILIBRIA; POISSON EQUATION;

CONFORMATION EFFECTS; ELECTROSTATIC PROCESS; IONIZATION EQUILIBRIUM; REDOX PROTEINS;

PROTEINS;

ION; PROTEIN; WATER;

ANIMAL; ARTICLE; CHEMISTRY; ELECTRON; OXIDATION REDUCTION REACTION; TITRIMETRY;

ANIMALS; ELECTRONS; IONS; OXIDATION-REDUCTION; PROTEINS; TITRIMETRY; WATER;

EID: 23844500381     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp052259f     Document Type: Article

References (109)

1. Linderstrøm-Lang, K. C. R. Trav. Lab. Carlsberg 1924, 15, 1-29.
2. Tanford, C.; Kirkwood, J. G. J. Am. Chem. Soc. 1957, 79, 5333-5339.
3. Kollman, P. Chem. Rev. 1993, 93, 2395-2417.
4. Simonson, T. Rep. Prog. Phys. 2003, 66, 737-787.
5. Warshel, A.; Parson, W. W. Q. Rev. Biophys. 2001, 34, 563-679.
6. Field, M. J. J. Comput. Chem. 2002, 23, 48-58.
7. Noodleman, L.; Lovell, T.; Han, W.-G.; Li, J.; Himo, F. Chem. Rev. 2004, 104, 459-508.
8. Lee, F. S.; Chu, Z. T.; Warshel, A. J. Comput. Chem. 1993, 14, 161-185.
9. Sham, Y. Y.; Chu, Z. T.; Warshel, A. J. Phys. Chem. B 1997, 101, 4458-4472.
10. Warwicker, J.; Watson, H. C. J. Mol. Biol. 1982, 157, 671-679.
11. Sharp, K. A.; Honig, B. Annu. Rev. Biophys. Biophys. Chem. 1990, 19, 301-332.
12. Bashford, D.; Karplus, M. Biochemistry 1990, 29, 10219-10225.
13. Yang, A.-S.; Gunner, M. R.; Sampogna, R.; Sharp, K.; Honig, B. Proteins: Struct., Funct., Genet. 1993, 15, 252-265.
14. Simonson, T. Curr. Opin. Struct. Biol. 2001, 11, 243-252.
15. Bashford, D. Front. Biosci. 2004, 9, 1082-1099.
16. Feig, M.; Brooks, C. L., III. Curr. Opin. Struct. Biol. 2004, 14, 217-224.
17. Antosiewicz, J.; Porschke, D. Biochemistry 1989, 28, 10072-10078.
18. Beroza, P.; Fredkin, D. R.; Okamura, M. Y.; Feher, G. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 5804-5808.
19. Baptista, A. M.; Martel, P. J.; Soares, C. M. Biophys. J. 1999, 76, 2978-2998.
20. Tanford, C.; Roxby, R. Biochemistry 1972, 11, 2192-2198.
21. Bashford, D.; Karplus, M. J. Phys. Chem. 1991, 95, 9956-9561.
22. Gilson, M. K. Proteins: Struct., Funct., Genet. 1993, 15, 266-282.
23. Spassov, V.; Bashford, D. J. Comput. Chem. 1999, 20, 1091-1111.
24. Warshel, A. Biochemistry 1981, 20, 3167-3177.
25. Antosiewicz, J.; McCammon, J. A.; Gilson, M. K. J. Mol. Biol. 1994, 238, 415-436.
26. Demchuk, E.; Wade, R. C. J. Phys. Chem. 1996, 100, 17373-17387.
27. Gibas, C. J.; Subramanian, S. Biophys. J. 1996, 71, 138-147.
28. Alexov, E. G.; Gunner, M. R. Biophys. J. 1997, 72, 2075-2093.
29. Baptista, A. M.; Soares, C. M. J. Phys. Chem. B 2001, 105, 293-309.
30. Schutz, C. N.; Warshel, A. Proteins: Struct, Funct., Genet. 2001, 44, 400-417.
31. Georgescu, R. E.; Alexov, E. G.; Gunner, M. R. Biophys. J. 2002, 83, 1731-1748.
32. Warwicker, J. Protein Sci. 2004, 13, 2793-2805.
33. Martel, P. J.; Soares, C. M.; Baptista, A. M.; Fuxreiter, M.; NáraySzabó, G.; Louro, R. O.; Carrondo, M. A. J. Biol. Inorg. Chem. 1999, 4, 73-86.
34. Gunner, M.; Alexov, E. Biochim. Biophys. Acta 2000, 1458, 63-87.
35. Ullmann, G. M. J. Phys. Chem. B 2000, 104, 6293-6301.
36. Louro, R. O.; Bento, I.; Matias, P. M.; Catarino, T.; Baptista, A. M.; Soares, C. M.; Carrondo, M. A.; Turner, D. L.; Xavier, A. V. J. Biol. Chem. 2001, 276, 44044-44051.
37. Teixeira, V. H.; Soares, C. M.; Baptista, A. M. J. Biol. Inorg. Chem. 2002, 7, 200-216.
38. Bento, I.; Matias, P. M.; Baptista, A. M.; da Costa, P. N.; van Dongen, W. M. A. M.; Saraiva, L. M.; Schneider, T. R.; Soares, C. M.; Carrondo, M. A. Proteins: Struct., Funct., Bioinf. 2004, 54, 135-152.
39. Lee, F. S.; Chu, Z.-T.; Bolger, M. B.; Warshel, A. Protein Eng. 1992, 5, 215-228.
40. Eberini, I.; Baptista, A. M.; Gianazza, E.; Fraternali, F.; Beringhelli, T. Proteins: Struct., Funct., Bioinf. 2004, 54, 744-758.
41. Baptista, A. M.; Martel, P. J.; Petersen, S. B. Proteins: Struct., Funct., Genet. 1997, 27, 523-544.
42. Baptista, A. M.; Teixeira, V. H.; Soares, C. M. J. Chem. Phys. 2002, 117, 4184-4200.
43. Böttcher, C. J. F.; van Belle, O. C.; Bordewijk, P.; Rip, A. Theory of Electric Polarization; Elsevier: Amsterdam, 1973; Vol. I.
44. Warshel, A.; Åqvist, J. Annu. Rev. Biophys. Biophys. Chem. 1991, 20, 267-298.
45. Schaefer, M.; Sommer, M.; Karplus, M. J. Phys. Chem. B 1997, 101, 1663-1683.
46. Sham, Y. Y.; Muegge, I.; Warshel, A. Biophys. J. 1998, 74, 1744-1753.
47. Warshel, A.; Russell, S. T. Q. Rev. Biophys. 1984, 17, 283-422.
48. Harvey, S. C. Proleins: Struct., Funct., Genet. 1989, 5, 78-92.
49. King, G.; Lee, F. S.; Warshel, A. J. Chem. Phys. 1991, 95, 4366-4377.
50. Simonson, T.; Perahia, D. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 1082-1086.
51. Simonson, T.; Brooks, C. L., III. J. Am. Chem. Soc. 1996, 118, 8452-8458.
52. Warshel, A.; Papazyan, A. Curr. Opin. Struct. Biol. 1998, 8, 211-217.
53. Simonson, T.; Archontis, G.; Karplus, M. J. Phys. Chem. B 1999, 103, 6142-6156.
54. Krishtalik, L. I.; Kuznetsov, A. M.; Mertz, E. L. Proteins: Struct., Funct., Genet. 1997, 28, 174-182.
55. Sharp, K. A.; Jean-Charles, A.; Honig, B. J. Phys. Chem. 1992, 96, 3822-3828.
56. Khare, D.; Alexander, P.; Antosiewicz, J.; Bryan, P.; Gilson, M.; Orban, J. Biochemistry 1997, 36, 3580-3589.
57. Oliveberg, M.; Arcus, V. L.; Fersht, A. R. Biochemistry 1995, 34, 9424-9433.
58. March, K. L.; Maskalick, D. G.; England, R. D.; Friend, S. H.; Gurd, F. R. N. Biochemistry 1982, 21, 5241-5251.
59. Kuramitsu, S.; Hamaguchi, K. J. Biochem. 1980, 87, 1215-1219.
60. Bartik, K.; Redfield, C.; Dobson, C. M. Biophys. J. 1994, 66, 1180-1184.
61. Schaller, W.; Robertson, A. D. Biochemistry 1995, 34, 4714-4723.
62. Forsyth, W. R.; Gilson, M. K.; Antosiewicz, J.; Jaren, O. R.; Robertson, A. D. Biochemistry 1998, 37, 8643-8652.
63. Oda, Y.; Yoshida, M.; Kanaya, S. J. Biol. Chem. 1993, 268, 88-92.
64. Oda, Y.; Yamazaki, T.; Nagayama, K.; Kanaya, S.; Kuroda, Y.; Nakamura, H. Biochemistry 1994, 33, 5275-5284.
65. Fujii, S.; Akasaka, K.; Hatano, H. J. Biochem. 1980, 88, 789-796.
66. Chivers, P. T.; Prehoda, K. E.; Volkman, B. F.; Kim, B.-M.; Markley, J. L.; Raines, R. T. Biochemistry 1997, 36, 14985-14991.
67. Turner, D. L.; Salgueiro, C. A.; Catarino, T.; LeGall, J.; Xavier, A. V. Eur. J. Biochem. 1996, 247, 723-731.
68. Salgueiro, C. A.; Turner, D. L.; Xavier, A. V. Eur. J. Biochem. 1997, 244, 721-734.
69. Louro, R. O.; Catarino, T.; Turner, D. L.; Piçarra-Pereira, M. A.; Pacheco, I.; LeGall, J.; Xavier, A. V. Biochemistry 1998, 37, 15808-15815.
70. Gayda, J.; Benosman, H.; Bertrand, P.; More, C.; Asso, M. Eur. J. Biochem. 1988, 177, 199-206.
71. Louro, R. O.; Catarino, T.; LeGall, J.; Turner, D. L.; Xavier, A. V. ChemBioChem 2001, 2, 831-837.
72. Pereira, P. M.; Pacheco, I.; Turner, D. L.; Louro, R. O. J. Biol. Inorg. Chem. 2002, 7, 815-822.
73. Eisenhaber, F.; Argos, P. J. Comput. Chem. 1993, 14, 1272-1280.
74. Eisenhaber, F.; Lijnzaad, P.; Argos, P.; Sander, C.; Scharf, M. J. Comput. Chem. 1995, 16, 273-284.
75. van Gunsteren, W. F.; Berendsen, H. J. C. Groningen Molecular Simulation (GROMOS) Library Manual; Biomos: Groningen, The Netherlands, 1987.
76. Smith, L. J.; Mark, A. E.; Dobson, C. M.; van Gunsteren, W. F. Biochemistry 1995, 34, 10918-10931.
77. Soares, C. M.; Martel, P. J.; Carrondo, M. A. J. Biol. Inorg. Chem. 1997, 2, 714-727.
78. Bashford, D.; Gerwert, K. J. Mol. Biol. 1992, 224, 473-486.
79. Bashford, D. An Object-Oriented Programming Suite for Electrostatic Effects in Biological Molecules. In Scientific Computing in ObjectOriented Parallel Environments, ISCOPE97; Ishikawa, Y., Oldehoeft, R. R., Reynders, J. V. W., Tholburn, M., Eds.; Springer: Berlin, 1997; Vol. 1343.
80. Richards, F. M. Annu. Rev. Biophys. Bioeng. 1977, 6, 151-176.
81. Gilson, M. K.; Sharp, K. A.; Honig, B. J. Comput. Chem. 1987, 9, 327-335.
82. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B. G.; Chen, W.; Wong, M. W.; Andres, J. L.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98, revision A.7; Gaussian, Inc.: Pittsburgh, PA, 1998.
83. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J. Phys. Chem. 1993, 97, 10269-10280.
84. Harbury, H. A.; Cronin, J. R.; Fanger, M. W.; Hettinger, T. P.; Murphy, A. J.; Myer, Y. P.; Vinogradov, S. N. Proc. Natl. Acad. Sci. U.S.A. 1965, 54, 1658-1664.
85. Gao, J.; Pavelites, J. J. J. Am. Chem. Soc. 1992, 114, 1912-1914.
86. Pranata, J. J. Comput. Chem. 1993, 14, 685-690.
87. Chen, J. L.; Noodleman, L.; Bashford, D. J. Phys. Chem. 1994, 98, 11059-11068.
88. Andzelm, J.; Kölmel, C. J. Chem. Phys. 1995, 103, 9312-9320.
89. Barone, V.; Cossi, M. J. Phys. Chem. A 1998, 102, 1995-2001.
90. Jean-Charles, A.; Nicholls, A.; Sharp, K.; Honig, B.; Tempczyk, A.; Hendrickson, T. F.; Still, W. C. J. Am. Chem. Soc. 1991, 113, 1454-1455.
91. Mohan, V.; Davis, M. E.; McCammon, J. A.; Pettitt, B. M. J. Phys. Chem. 1992, 96, 6428-6431.
92. Bashford, D.; Case, D. A.; Dalvit, C.; Tennant, L.; Wright, P. E. Biochemistry 1993, 32, 8045-8056.
93. Postma, J. P. M.; Berendsen, H. J. C.; Haak, J. R. Faraday Symp. Chem. Soc. 1982, 17, 55-67.
94. Gallicchio, E.; Kubo, M.; Levy, R. M. J. Phys. Chem. B 2000, 104, 6271-6285.
95. Pauling, L. The Nature of the Chemical Bond, 3rd ed.; Cornell University Press: Ithaca, NY, 1960.
96. Sitkoff, D.; Sharp, K. A.; Honig, B. J. Phys. Chem. 1994, 98, 1978-1988.
97. In the SPC model, the one used to model water in the 43A1 force field, the hydrogen atoms are "inside" the oxygen-repulsive region and have no Lennard-Jones interaction. Therefore, only the oxygen atom is needed to compute atomic radii.
98. Vorobjev, Y. N.; Scheraga, H. A.; Hitz, B.; Honig, B. J. Phys. Chem. 1994, 98, 10940-10948.
99. Press, W. H.; Teukolsky, S. A.; Vetterling, W. T.; Flannery, B. P. Numerical Recipes in C, 2nd ed.; Cambridge University Press: New York, 1992.
100. Warshel, A. Proc. Natl. Acad. Sci. U.S.A. 1978, 75, 5250-5254.
101. Warshel, A.; Russell, S. T.; Churg, A. K. Proc. Natl. Acad. Sci. U.S.A. 1984, 81, 4785-4789.
102. 13,45,46
103. Mehler, E. L.; Eichele, G. Biochemistry 1984, 23, 3887-3991.
104. 29
105. 8,20,21 by considering that the "moves" consist in that case of single-site (de)protonations within an environment of average-charged sites.
106. mod, whose value can be determined afterward as the displacement leading to best agreement with experimental data (e.g., least-RMSD of reduction potentials).
107. Warshel, A.; Sussman, F.; King, G. Biochemistry 1986, 25, 8368-8372.
108. Kenneth, M.; Merz, J. J. Am. Chem. Soc. 1991, 113, 3572-3575.
109. Simonson, T.; Carlsson, J.; Case, D. A. J. Am. Chem. Soc. 2004, 126, 4167-4180.