Computer simulation of the chemical catalysis of DNA polymerases: Discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase

Journal of the American Chemical Society

Volumn 125, Issue 27, 2003, Pages 8163-8177

  Florián, Jan ^a   Goodman, Myron F ^b   Warshel, Arieh ^b  

^a LOYOLA UNIVERSITY CHICAGO   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION ENERGY; CATALYSIS; CHEMICAL BONDS; FREE ENERGY;

POLYMERASES;

DNA;

ASPARTIC ACID DERIVATIVE; DNA POLYMERASE;

AQUEOUS SOLUTION; ARTICLE; CATALYSIS; CHEMICAL REACTION; COMPUTER SIMULATION; COVALENT BOND; ENZYME ANALYSIS; GENE INSERTION; GENE INSERTION SEQUENCE; HYDROLYSIS; IONIZATION; KINETICS; PROTON TRANSPORT; THERMODYNAMICS;

EID: 84961974064     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja028997o     Document Type: Article

References (99)

1. Steitz, T. A. J. Biol. Chem. 1999, 274, 17395-17398.
2. Doublie, S.; Sawaya, M. R.; Ellenberger, T. Structure 1999, 7, R31-R35.
3. Kool, E. T. Annu. Rev. Biochem. 2002, 71, 191-219.
4. Florián, J.; Warshel, A.; Goodman, M. F. J. Phys. Chem. B 2002, 106, 5754-5760.
5. Florián, J.; Goodman, M. F.; Warshel, A. Biopolymers, 2003, 68, 286-299.
6. Fothergill, M.; Goodman, M. F.; Petruska, J.; Warshel, A. J. A. Chem. Soc. 1995, 117, 11619-11627.
7. Langen, R.; Schweins, T.; Warshel, A. Biochemistry 1992, 31, 8691-8696.
8. Glennon, T. M.; Villà, J.; Warshel, A. Biochemistry 2000, 39, 9641-9651.
9. Glennon, T. M.; Warshel, A. J. Am. Chem. Soc. 1998, 120, 10234-10247.
10. Hansson, T.; Nordlund, P.; Aqvist, J. J. Mol. Biol. 1997, 265, 118-127.
11. Kolmodin, K.; Nordlund, P.; Aqvist, J. Proteins: Struct., Funct., Genet. 1999, 36, 370-379.
12. Warshel, A.; Russell, S. T.; Sussman, F. Israel J. Chem. 1986, 27, 217.
13. Chung, H. H.; Benson, D. R.; Schultz, P. G. Science 1993, 259, 806-809.
14. Pelletier, H.; Sawaya, M. R.; Kumar, A.; Wilson, S. H.; Kraut, J. Science 1994, 264, 1891-1903.
15. Burgers, P. M. J.; Eckstein, F. J. Biol. Chem. 1979, 254, 6889-6893.
16. Brody, R. S.; Adler, S.; Modrich, P.; Stec, W. J.; Leznikowski, Z. J.; Frey, P. A. Biochemistry 1982, 21, 2570-2572.
17. Abashkin, Y. G.; Erickson, J. W.; Burt, S. K. J. Phys. Chem. B 2001, 105, 287-292.
18. Warshel, A.; Weiss, R. M. J. Am. Chem. Soc. 1980, 102, 6218-6226.
19. Warshel, A.; Sussman, F.; Hwang, J.-K. J. Mol. Biol. 1988, 201, 139.
20. Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solutions; John Wiley & Sons: New York, 1991.
21. Evans, M. G.; Polanyi, M. Trans. Faraday Soc. 1935, 31, 875-894.
22. Eyring, H. Chem. Rev. 1935, 17, 65-77.
23. Glasstone, S.; Laidler, K. J.; Eyring, H. The Theory of Rate Processes; McGraw-Hill: New York, 1941.
24. Strajbl, M.; Florian, J.; Warshel, A. J. Am. Chem. Soc. 2000, 122, 5354-5366.
25. Warshel, A.; Parson, W. W. Q. Rev. Biophys. 2001, 34, 563-679.
26. Miertus, S.; Scrocco, E.; Tomasi, J. J. Chem. Phys. 1981, 55, 117-129.
27. Miertus, S.; Tomasi, J. Chem. Phys. 1982, 65, 239.
28. Florián, J.; Warshel, A. J. Phys. Chem. B 1997, 101, 5583-5595.
29. Florián, J.; Warshel, A. J. Phys. Chem. B 1999, 103, 10282-10288.
30. Gaussian 94, revision D.2; Gaussian, Inc.: Pittsburgh, PA, 1995.
31. Florián, J.; Warshel, A. J. Phys. Chem. B 1998, 102, 719-734.
32. Hwang, J.-K.; King, G.; Creighton, S.; Warshel, A. J. Am. Chem. Soc. 1988, 110, 5297-5311.
33. Åqvist, J.; Warshel, A. Chem. Rev. 1993, 93, 2523-2544.
34. Florián, J. J. Phys. Chem. A 2002, 106, 5046-5047.
35. Jensen, F.; Norrby, P. O. Theor. Chem. Acc. 2003, 109, 1-7.
36. Bentzien, J.; Muller, R. P.; Florián, J.; Warshel, A. J. Phys. Chem. B 1998, 102, 2293-2301.
37. Valleau, J. P.; Torrie, G. M. In Modern Theoretical Chemistry; Berne, B. J., Ed.; Plenum: New York, 1977; Vol. 5, pp 169-194.
38. Zwanzig, R. W. J. Chem. Phys. 1954, 22, 1420-1426.
39. Hummer, G.; Szabo, A. J. Chem. Phys. 1996, 105, 2004-2010.
40. Radmer, R. J.; Kollman, P. A. J. Comput. Chem. 1997, 18, 902-919.
41. Jenkins, L. A.; Bashkin, J. K.; Pennock, J. D.; Florian, J.; Warshel, A. Inorg. Chem. 1999, 38, 3215-3222.
42. Florián, J.; Åqvist, J.; Warshel, A. J. Am. Chem. Soc. 1998, 120, 11524-11525.
43. Florián, J.; Warshel, A. Phosphorus, Sulfur Silicon Relat. Elem. 1999, 146, 525-528.
44. Florián, J.; Baumruk, V.; Strajbl, M.; Bednarova, L.; Stepanek, J. J. Phys. Chem. 1996, 100, 1559-1568.
45. Florián, J.; Scheiner, S. J. Comput. Chem. 1994, 15, 553-560.
46. Serjeant, E. P.; Dempsey, B. Ionization constants of organic acids in aqueous solution; Pergamon Press: Oxford, 1979.
47. Åqvist, J.; Kolmodin, K.; Florian, J.; Warshel, A. Chem. Biol. 1999, 6, R71-R80.
48. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
49. Marelius, J.; Kolmodin, K.; Feierberg, I.; Åqvist, J. J. Mol. Graphics and Modeling 1999, 16, 213-225.
50. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
51. Doublie, S.; Tabor, S.; Long, A. M.; Richardson, C. C.; Ellenberger, T. Nature 1998, 391, 252-258.
52. Florián, J.; Goodman, M. F.; Warshel, A. J. Phys. Chem. B 2002, 106, 5739-5753.
53. Warshel, A.; King, G. Chem. Phys. Lett. 1985, 121, 124-129.
54. Lee, F. S.; Warshel, A. J. Chem. Phys. 1992, 97, 3100-3107.
55. Sham, Y. Y.; Warshel, A. J. Chem. Phys. 1998, 109, 7940-7944.
56. Warshel, A. Proc. Natl. Acad. Sci. U.S.A. 1978, 75, 5250.
57. Wolfenden, R.; Snider, R. J. Acc. Chem. Res. 2001, 34, 938-945.
58. Warshel, A. J. Biol. Chem. 1998, 273, 27035-27038.
59. Warshel, A.; Florián, J. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 5950-5955.
60. Cannon, W. R.; Benkovic, S. J. J. Biol. Chem. 1998, 273, 26257-26260.
61. Florián, J. Unpublished results.
62. Scheiner, S.; Kar, T. J. Am. Chem. Soc. 1995, 117, 6970-6975.
63. Villa, J.; Warshel, A. J. Phys. Chem. 2001, 105, 7887-7907.
64. Eigen, M. Angew. Chem., Int. Ed. Engl. 1964, 3, 1-72.
65. Bunton, C. A.; Mhala, M. M.; Oldham, K. G.; Vernon, C. A. J. Chem. Soc. 1960, 3293-3301.
66. Wolfenden, R.; Ridgway, C.; Young, G. J. Am. Chem. Soc. 1998, 120, 833-834.
67. Williams, N. H.; Wyman, P. Chem. Commun. 2001, 1268-1269.
68. Herschlag, D.; Piccirilli, J. A.; Cech, T. R. Biochemistry 1991, 30, 4844-4854.
69. Blasko, A.; Bruice, T. C. Acc. Chem. Res. 1999, 32, 475-484.
70. Kirby, A. J.; Younas, M. J. Chem. Soc. B 1970, 510-513.
71. Hengge, A. C.; Tobin, A. E.; Cleland, W. W. J. Am. Chem. Soc. 1995, 117, 5919-5926.
72. Herschlag, D.; Jencks, W. P. J. Am. Chem. Soc. 1987, 109, 4665-4674.
73. Hu, C.-H.; Brinck, T. J. Phys. Chem. A 1999, 103, 5379-5386.
74. Haake, P. C.; Westheimer, F. H. J. Am. Chem. Soc. 1961, 83, 1102-1109.
75. Kumamoto, J.; Cox, J. R., Jr.; Westheimer, F. H. J. Am. Chem. Soc. 1956, 78, 4858.
76. Dejaegere, A.; Lim, C.; Karplus, M. J. Am. Chem. Soc. 1991, 113, 4353-4355.
77. Uchimaru, T.; Tanabe, K.; Nishikawa, S.; Taira, K. J. Am. Chem. Soc. 1991, 113, 4351-4353.
78. Williams, N. H.; Cheung, W.; Chin, J. J. Am. Chem. Soc. 1998, 120, 8079-8087.
79. Steitz, T. A. Science 1998, 391, 231-232.
80. Steitz, T. A.; Smerdon, S. J.; Jager, J.; Joyce, C. M. Science 1994, 266, 2022-2025.
81. Pelletier, H. Science 1994, 266, 2025-2026.
82. Doublie, S.; Ellenberger, T. Curr. Opin. Struct. Biol. 1998, 8, 704-712.
83. Florián, J.; Strajbl, M.; Warshel, A. J. Am. Chem. Soc. 1998, 120, 7959-7966.
84. Albery, W. J.; Knowles, J. R. Biochemistry 1976, 15, 5627-5631.
85. Hunkapiller, M. W.; Forgac, M. D.; Richards, J. H. Biochemistry 1976, 15, 5581-5588.
86. Stratton, J. R.; Pelton, J. G.; Kirsch, J. F. Biochemistry 2001, 40, 10411-10416.
87. Carroll, S. S.; Benkovic, S. J. Chem. Rev. 1990, 90, 1291-1307.
88. Johnson, K. A. Annu. Rev. Biochem. 1993, 32, 685-713.
89. Arndt, J. W.; Gong, W.; Zhong, X.; Showalter, A. K.; Liu, J.; Dunlap, C. A.; Lin, Z.; Paxson, C.; Tsai, M.-D.; Chan, M. K. Biochemistry 2001, 40, 5368-5375.
90. Showalter, A. K.; Tsai, M. D. Biochemistry 2002, 41, 10571-10576.
91. Echols, H.; Goodman, M. F. Annu. Rev. Biochem. 1991, 60, 477-511.
92. Zhong, X. J.; Patel, S. S.; Werneburg, B. G.; Tsai, M. D. Biochemistry 1997, 1997, 11891-11900.
93. Yang, L.; Beard, W. A.; Wilson, S. H.; Roux, B.; Broyde, S.; Schlick, T. J. Mol. Biol. 2002, 321, 459-478.
94. Schweins, T.; Geyer, M.; Scheffzek, K.; Warshel, A.; Kalbitzer, H. R.; Wittinghofer, A. Nat. Struct. Biol. 1995, 2, 36-44.
95. Bentzien, J.; Florián, J.; Glennon, T. M.; Warshel, A. In Combined Quantum Mechanical & Molecular Mechanical Methods; ACS Symposium Series 712; Gao, J., Thompson, M. A., Eds.; American Chemical Society: Washington DC, 1998; pp 16-34.
96. Sicinska, D.; Paneth, P.; Truhlar, D. G. J. Phys. Chem. B 2002, 106, 2708-2713.
97. Kumar, J. K.; Tabor, S.; Richardson, C. C. J. Biol. Chem. 2001, 276, 34905-34912.
98. Izatt, R. M.; Rytting, J. H.; Hansen, L. D.; Christensen, J. J. J. Am. Chem. Soc. 1966, 88, 2641.
99. Sigel, H.; Bianchi, E. M.; Corfu, N. A.; Kinjo, Y.; Tribolet, R.; Martin, R. B. J. Chem. Soc., Perkin Trans. 2 2001, 507-511.