Analyzing Free Energy Relationships for Proton Translocations in Enzymes: Carbonic Anhydrase Revisited

Journal of Physical Chemistry B

Volumn 108, Issue 6, 2004, Pages 2066-2075

  Schutz, C N ^a   Warshel, A ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; CHARGE TRANSFER; COMPUTER SIMULATION; FREE ENERGY; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; MUTAGENESIS; PROTONS; REACTION KINETICS; SURFACES;

FREE ENERGY RELATIONSHIPS; PROTON TRANSLOCATIONS;

ENZYMES;

EID: 1342281185     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0366015     Document Type: Article

References (65)

1. Silverman, D. N.; Tu, C.; Chen, X.; Tanhauser, S. M.; Kresge, A. J.; Laipis, P. J. Biochemistry 1993, 34, 10757-10762.
2. Warshel, A.; Hwang, J. K.; Åqvist, J. Faraday Discuss. 1992, 93, 225-238.
3. Hammett, L. P. Physical Organic Chemistry; Reaction Rates, Equilibria, and Mechanisms; McGraw-Hill Book Company: New York, 1970.
4. Maskill, H. The Physical Basis of Organic Chemistry; Oxford University Press: Oxford, U.K., 1985; Chapter 10.
5. Albery, W. J. Annu. Rev. Phys. Chem. 1980, 31, 227-263.
6. Kong, Y. S.; Warshel, A. J. Am. Chem. Soc. 1995, 117, 6234-6242.
7. Marcus, R. A. J. Chem. Phys. 1968, 72, 891.
8. Hwang, J. K.; King, G.; Creighton, S.; Warshel, A. J. Am. Chem. Soc. 1988, 110, 5297-5311.
9. Åqvist, J.; Warshel, A. Chem. Rev. 1993, 93, 2523-2544.
10. Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solutions; John Wiley & Sons: New York, 1991.
11. 2 Mechanism; John Wiley & Sons: New York, 1992.
12. Fersht, A. R.; Leatherbarrow, R. J.; Wells, T. N. C. Nature 1986, 322, 284.
13. Warshel, A. Simulating the Energetics and Dynamics of Enzymatic Reactions. In Specificity in Biological Interactions; Proceedings of a Working Group of the Pontificiae Academiae Scientiarum Scripta Varia, Nov 9-11, 1983; Chagas, C., Pullman, B., Eds; Reidel Publishing Co.: Boston, MA, 1984; Vol. 55.
14. Hawkinson, D. C.; Pollack, R. M.; Ambulos, N. P., Jr. Biochemistry 1994, 33, 12172-12183.
15. Schweins, T.; Geyer, M.; Scheffzek, K.; Warshel, A.; Kalbitzer, H. R.; Wittinghofer, A. Nat. Struct. Biol. 1995, 2, 36-44.
16. Gerlt, J. A.; Gassman, P. G. J. Am. Chem. Soc. 1993, 115, 11552-11568.
17. Silverman, D. N. Biochim. Biophys. Acta 2000, 1458, 88-103.
18. Schweins, T.; Warshel, A. Biochemistry 1996, 35, 14232-14243.
19. Muegge, I.; Qi, P. X.; Wand, A. J.; Chu, Z. T.; Warshel, A. J. Phys. Chem. B 1997, 101, 825-836.
20. Albery, W. J.; Knowles, J. R. Biochemistry 1976, 15, 5627-5631.
21. Åqvist, J.; Feierberg, I. Biochemistry 2002, 41, 15728-15735.
22. Hwang, J.-K.; Warshel, A. J. Am. Chem. Soc. 1996, 118, 11745-11751.
23. Sham, Y.; Muegge, I.; Warshel, A. Proteins: Struct., Funct., Genet. 1999, 36, 484-500.
24. Lindskog, S.; Engberg, P.; Forsman, C.; Ibrahim, S. A.; Jonsson, B.-H.; Simonsson, I.; Tibell, L. Ann. N.Y. Acad. Sci. 1984, 429, 61-75.
25. Silverman, D. N.; Lindskog, S. Acc. Chem. Res. 1988, 21, 30-36.
26. Krebs, J. F.; Ippolito, J. A.; Christianson, D. W.; Fierke, C. A. J. Biol. Chem. 1993, 265, 27458.
27. Silverman, D. N.; Lindskog, S. Acc. Chem. Res. 1988, 21, 30-36.
28. Åqvist, J.; Fothergill, M.; Warshel, A. J. Am. Chem. Soc. 1993, 115, 631-635.
29. Åqvist, J.; Warshel, A. J. Mol. Biol. 1992, 224, 7.
30. Warshel, A.; Russell, S. T. Q. Rev. Biophys. 1984, 17, 283-421.
31. Hwang, J.-K.; King, G.; Creighton, S.; Warshel, A. J. Am. Chem. Soc. 1988, 110, 5297-5311.
32. Marcus, R. A. Annu. Rev. Phys. Chem. 1964, 15, 155.
33. King, G.; Warshel, A. J. Chem. Phys. 1990, 93, 8682-8692.
34. Warshel, A. Annu. Rev. Biophy. Biomol. Struct. 2003, 32, 425-443.
35. Warshel, A.; Weiss, R. M. J. Am. Chem. Soc. 1980, 102, 6218-6226.
36. Aqvist, J.; Warshel, A. Chem. Rev. 1993, 93, 2523-2544.
37. Vuilleumier, R.; Borgis, D. Chem. Phys. Lett. 1998, 284, 71-77.
38. Schmitt, U. W.; Voth, G. A. J. Phys. Chem. B 1998, 102, 5547-5551.
39. Villa, J.; Warshel, A. J. Phys. Chem. B 2001, 105, 7887-7909.
40. Schweins, T.; Geyer, T. M.; Kalbitzer, H. R.; Wittinghofer, A.; Warshel, A. Biochemistry 1996, 35, 14225-14231.
41. Warshel, A.; Schweins, T.; Fothergill, M. J. Am. Chem. Soc. 1994, 116, 6, 8437.
42. Warshel, A. Correlation between Structure and Efficiency of Light-Induced Proton Pumps. In Methods in Enzymology; Packer, L., Ed.; Academic Press Inc.: London, 1986; Vol. 127, pp. 578-587.
43. Warshel, A. Acc. Chem. Res. 2002, 35, 385-395.
44. Sham, Y. Y.; Chu, Z. T.; Warshel, A. J. Phys. Chem. B. 1997, 101, 4458-4472.
45. Warshel, A. Photochem. Photobiol. 1979, 30, 285-290.
46. Lee, F. S.; Chu, Z. T.; Warshel, A. J. Comput. Chem. 1993, 14, 161-185.
47. Warshel, A.; Russell, S. T.; Churg, A. K. Proc. Natl. Acad. Sci. U.S.A. 1984, 81, 4785.
48. Schutz, C. N.; Warshel, A. Proteins: Struct., Funct., Genet. 2001, 44, 400-417.
49. Johnson, E. T.; Parson, W. W. Biochemistry 2002, 41, 6483-6494.
50. Sham, Y. Y.; Muegge, I.; Warshel, A. Biophys. J. 1998, 74, 1744-1753.
51. King, G.; Warshel, A. J. Chem. Phys. 1989, 91, 3647-3661.
52. Lee, F. S.; Warshel, A. J. Chem. Phys. 1992, 97, 3100-3107.
53. Mallis, R. J.; Poland, B. W.; Chatterjee, T. K.; Fisher, A. R.; Darmawan, S.; Honzatko, R. B.; Thomas, T. A. FEES Lett. 2000, 482, 237-241.
54. Warshel, A. Biochemistry 1981, 20, 3167-3177.
55. Smedarchina, Z.; Siebrand, W.; Fernández-Ramos, A.; Cui, Q. J. Am. Chem. Soc. 2003, 125, 243-251.
56. Cui, Q.; Karplus, M. J. Phys. Chem. B 2003, 107, 1071-1078.
57. Strajbl, M.; Florián, J.; Warshel, A. J. Am. Chem. Soc. 2000, 122, 5354-5366.
58. Daggett, V.; Schröder, S.; Kollman, P. J. Am. Chem. Soc. 1991, 113, 8926-8935.
59. Schowen, R. L. Molecular Structure and Energetics. In Principles of Enzyme Activity; Liebman, J. F., Greenberg, A. D., Eds.; VCH Publishers: Weinheim, Germany, 1988; Vol. 9.
60. Åqvist, J.; Kolmodin, K.; Florian, J.; Warshel, A. Chem. Biol. 1999, 6, R71-R80.
61. Hwang, J.-K.; Warshel, A. J. Am. Chem. Soc. 1987, 109, 715-720.
62. Pollock, E. L.; Adler, B. J.; Pratt, L. R. Proc. Natl. Acad. Sci. U.S.A. 1980, 77, 49.
63. Warshel, A.; Parson, W. W. Q. Rev. Biophys. 2001, 34, 563-670.
64. Burykin, A.; Warshel, A. Biophys. J. 2003, 85.
65. Nagle, J. F.; Mille, M. J. Chem. Phys. 1981, 74, 1367-1372.