Promoting modes and demoting modes in enzyme-catalyzed proton transfer reactions: A study of models and realistic systems

Journal of Physical Chemistry B

Volumn 106, Issue 32, 2002, Pages 7927-7947

  Cui, Qiang ^a,b   Karplus, Martin ^a,c  

^a HARVARD UNIVERSITY   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c UNIVERSITÉ LOUIS PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; DECOMPOSITION; PROTEINS; PROTONS; RATE CONSTANTS;

PROTON TRANSFER REACTIONS;

ENZYMES;

EID: 0037104752     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0205057     Document Type: Article

References (102)

1. (1) (a) Fersht, A. Structure and mechanism in protein science; W.H. Freeman and Company: New York, 1999.
2. (b) Jencks, W.P. Catalysis in Chemistry and Biology; Dover: New York, 1987.
3. For recent analyses, see, for example: (a) Wu, N.; Mo, Y.R.; Gao, J.L.; Pai, E.F. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 2017.
4. (b) Warshel, A.; Strajbl, M.; Villa, J.; Florian, J. Biochem. 2000, 39, 14728.
5. See, for example: (a) Warshel, A. J. Biol. Chem. 1998, 273, 27035.
6. Cannon, W.R.; Benkovic, S.J. J. Biol. Chem. 1998, 273, 26257.
7. See, for example: Villa, J.; Strajbl, M.; Glennon, T.M.; Sham, Y.Y.; Chu, Z.T.; Warshel, A. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 11899.
8. See, for example: Cleland, W.W.; Frey, P.A.; Gerlt, J.A. J. Biol. Chem. 1998, 273, 25529.
9. (a) Karplus, M.; McCammon, J.A. Nature 1979, 277, 578.
10. (b) Welch, G.R.; Somogyi, B.; Damjanovich, S. Prog. Biophys., Mol. Biol. 1982, 39, 109.
11. For a recent enthusiastic discussion, see, for example: Wilson, E.K. Chem. Eng. News 2000, 78, 42.
12. We note that in theoretical analyses, "dynamics" typically refers to the properties of the environment that influence the transmission coefficient. In the experimental community, however, "dynamics" is often used as a general term to describe the motion of the protein, For discussions of this point, see, for example, refs 20, 34, and 65a.
13. Bruice, T.C.; Benkovic, S.J. Biochem. 2000, 39, 6267.
14. Borgis, D.; Hynes, J.T. In The Enzyme Catalysis Process; Cooper, A., Houben, J., Chien, L., Eds.; Plenum: New York, 1989; p 293.
15. Agmon, N.; Hopfield, J.J. J. Chem. Phys. 1983, 79, 2042.
16. For a recent review, see: Kohen, A.; Klinman, J. Acc. Chem. Res. 2000, 31, 397.
17. (a) Alston, W.C.; Manska, M.; Murray, C.J. Biochem. 1996, 35, 12873.
18. (b) Suteliffe, M.J.; Scrutton, N.S. Trends Biol. Sci. 2000, 25, 405.
19. (a) Kohen, A.; Cannio, R.; Bartolucci, S.; Klinman, J.P. Nature 1999, 399, 496.
20. (b) Cha, Y.; Murray, C.J.; Klinman, J.P. Science 1989, 243, 1325.
21. (c) Bahnson, B.J.; Colby, T.D.; Chin, K.J.; Goldstein, B.M.; Klinman, J.P. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 12797.
22. Grant, K.L.; Klinman, J.P. Biochemistry 1989, 28, 6597.
23. Kohen, A.; Jonsson, T.; Klinman, J.P. Biochemistry 1997, 36, 2603.
24. (a) Glickman, M.H.; Klinman, J.P. Biochemistry 1995, 34, 14077.
25. (b) Glickman, M.H.; Klinman, J.P. J. Am. Chem. Soc. 1994, 116, 793.
26. Zavodszky, P.; Kardos, J.; Svingor, J.; Petsko, G.A. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 7406.
27. Rudd, P.M.; Joao, H.C.; Coghill, E.; Fiten, P.; Saunders, M.R.; Opdenakker, G.; Dwek, R.A. Biochem. 1994, 33, 17.
28. Billeter, S.R.; Webb, S.P.; Agarwal, P.K.; Iordanov, T.; Hammes-Schiffer, S. J. Am. Chem. Soc. 2001, 123, 11262.
29. (a) Benderskii, V.A.; Markarov, D.E.; Grinevich, P. Chem. Phys. 1993, 170, 275.
30. (b) Benderskii, V.A.; Markarov, D.E.; Wight, C.A. Adv. Chem. Phys.; John Wiley & Sons: New York, 1994.
31. Miller, W.H. J. Chem. Phys. 1975, 62, 1899.
32. (a) Borgis, D.; Hynes, J.T. J. Chem. Phys. 1991, 94, 3619.
33. (b) Borgis, D.; Hynes, J.T. J. Phys. Chem. 1996, 100, 1118.
34. Suarez, A.; Silbey, R. J. Chem. Phys. 1991, 94, 4809.
35. (a) Caratzoulas, S.; Schwartz, S.D. J. Chem. Phys. 2001, 114, 2910.
36. (b) Antoniou, D.; Schwartz, S.D. J. Phys. Chem. B 2001, 105, 5553.
37. (c) Antoniou, D.; Schwartz, S.D. J. Chem. Phys. 1998, 108, 3620.
38. (d) Antoniou, D.; Schwartz, S.D. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 12360.
39. (a) Kiefer, P.M.; Hynes, J.T. J. Phys. Chem. A 2002, 106, 1834.
40. (b) Kiefer, P.M.; Hynes, J.T. J. Phys, Chem. A 2002, 106, 1850.
41. For a recent discussion in the context of VTST, see: Schenter, G.K.; Garrett, B.C.; Truhlar, D.G. J. Phys. Chem. B 2001, 105, 9672.
42. (a) Caldeira, A.O.; Leggett, A.J. Phys. Rev. Lett. 1981, 46, 211.
43. (b) Caldeira, A.O.; Leggett, A.J. Ann. Phys. 1983, 149, 374.
44. (c) Leggett, A.J.; Chakravarty, S.; Dorsey, A.T.; Fisher, M.P.A.; Garg, A.; Zwerger, W. Rev. Mod. Phys. 1987, 59, 1.
45. Wolynes, P. Phys. Rev. Lett. 1981, 47, 468.
46. Topaler, M.; Makri, N. J. Chem. Phys. 1994, 101, 7500.
47. See, for example: (a) Hänggi, P.; Pollak, E.; Grabert, H. The Quantum Kramers Problem; University of Augsburg: FRG, 1989.
48. (b) Pollak, E.; Grabert, H.; Hänggi, P. J. Chem. Phys. 1989, 91, 4073.
49. (a) For a recent review, see: Truhlar, D.G.; Garrett, B.C.; Klippenstein, S.J. J. Phys. Chem. 1996, 100, 12771.
50. (b) Truhlar, D.G.; Isaacson, A.D.; Garrett, B.C. In Theory of Chemical Reaction Dynamics; Bear, M., Ed.; CRC Press: Boca Raton, FL, 1985; Vol. 4, p 65.
51. See, for example: Garrett, B.C.; Joseph, T.; Truong, T.N.; Truhlar, D.G. Chem. Phys. 1989, 136, 271.
52. Cui, Q.; Elstner, M.; Karplus, M. J. Phys. Chem. B 2002, 106, 2721.
53. Marcus, R.A. J. Phys. Chem. 1968, 72, 891.
54. (a) Marcus, R.A. J. Chem. Phys. 1956, 24, 966.
55. (b) Marcus, R.A. Annu. Rev. Phys. Chem. 1964, 15, 155.
56. For a recent discussion, see, for example: Webb, S.P.; Agarwal, P.K.; Hammes-Schiffer, S. J. Phys. Chem. B, 2000, 104, 8884.
57. Gehlen, J.N.; Chandler, D.; Kim, H.J.; Hynes, J.T. J. Phys. Chem. 1992, 96, 1748.
58. Cui, Q.; Brumer, Y.; Reichman, D.; Karplus, M. not published.
59. Brooks, C.L., III.; Karplus, M. J. Mol. Biol. 1989, 208, 159.
60. Field, M.; Bash, P.A.; Karplus, M. J. Comput. Chem. 1990, 11, 700.
61. Gonzalez-Lafont, A.; Truong, T.N.; Truhlar, D.G. J. Phys. Chem. 1991, 95, 4618.
62. See, for example: Cho, M.; Fleming, G.; Saito, S.; Ohmine, I.; Stratt, R.M. J. Chem. Phys. 1994, 100, 6672.
63. Sagnella, D.E.; Straub, J.E. Biophys. J. 1999, 77, 70.
64. See for example: Marcus, R.A.; Coltrin, M.E. J. Chem. Phys. 1977, 67, 2609.
65. Miller, W.H.; Handy, N.C.; Adams, J.E. J. Chem. Phys. 1980, 72, 99.
66. Garrett, B.C.; Joseph, T.; Truong, T.N.; Truhlar, D.G. Chem. Phys. 1989, 136, 271.
67. For examples, see: (a) Mielke, S.L.; Allison, T.C.; Truhlar, D.G.; Schwenke, D.W. J. Phys. Chem. 1996, 100, 13588.
68. (b) Lynch, G.C.; Truhlar, D.G.; Brown, F.B.; Zhao, J.G. J. Phys. Chem. 1995, 99, 207.
69. (c) Truhlar, D.G.; Garrett, B.C.; Hipes, P.G.; Kuppermann, A. J. Chem. Phys. 1984, 81, 3542.
70. For recent examples, see: (a) Corchado, J.C.; Truhlar, D.G.; Espinosa-García, J. J. Chem. Phys. 2000, 112, 9375.
71. (b) Roberto-Neto, O.; Coitino, E.L.; Truhlar, D.G. J. Phys. Chem. A 1998, 102, 4568.
72. (c) Liu, Y.; Lu, D.; Gonzalezlafont, A.; Truhlar, D.G.; Garrett, B.C. J. Am. Chem. Soc. 1993, 115, 7806.
73. Brooks, B.R.; Burccoleri, R.E.; Olafson, B.D.; States, D.J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
74. Fischer, S.; Karplus, M. Chem. Phys. Lett. 1992, 194, 252.
75. Cui, Q.; Karplus, M. J. Am. Chem. Soc. 2002, 124, 3093.
76. POLYRATE version 8.0; Chuang, Y.; Corchado, J.C.; Fast, P.L.; Villa, J.; Coitino, E.L.; Hu, W.; Liu, Y.; Lynch, G.C.; Nguyen, K.; Jackels, C.F.; Gu, M.Z.; Rossi, I.; Clayton, S.; Melissas, V.; Stectder, R.; Garrett, B.C.; Isaacson, A.D.; Truhlar, D.G. Department of Chemistry and Supercomputer Institute, University of Minnesota: Minneapolis, MN, 1998.
77. Kim, Y.; Truhlar, D.G.; Keevoy, M.M. J. Am. Chem. Soc. 1991, 113, 7837.
78. Swain, C.G.; Stivers, E.C.; Reuwer, J.F., Jr.; Schaad, L.J. J. Am. Chem. Soc. 1958, 80, 5885.
79. (a) Goldanskii, V.I. Dokl. Akad. Nauk SSSR 1959, 124, 1261.
80. (b) Goldanskii, V.I. Dokl. Akad. Nauk SSSR 1959, 127, 1037.
81. (c) Häggi, P.; Grabert, H.; Ingold, G.L.; Weiss, U. Phys. Rev. Lett. 1985, 55, 761.
82. Page, M.; McIver, J.W., Jr. J. Chem. Phys. 1988, 88, 922.
83. Siebrand, W.; Smedarchina, Z.; Zgierski, M.Z.; Fernández-Ramos, Int. Rev. Phys. Chem. 1999, 18, 5.
84. (a) Cui, Q.; Karplus, M. J. Am. Chem. Soc. 2001, 123, 2284.
85. (b) Cui, Q.; Karplus, M. J. Phys. Chem. B 2002, 106, 1768.
86. For some recent discussions, see, for example: (a) Jang, S.; Schwieters, C.D.; Voth, G.A. J. Phys. Chem. A 1999, 103, 9526.
87. (b) Golosov, A.A.; Reichman, D.R. J. Chem. Phys. 2001, 114, 1065.
88. Skodje, R.T.; Truhlar, D.G. J. Phys. Chem. 1981, 85, 624.
89. (a) Borchert, T.V.; Abagyan, R.; Jaenicke, R.; Wierenga, R.K. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 1515.
90. (b) Åqvist, J.; Fothergill, M. J. Biol. Chem. 1996, 271, 10010.
91. For a recent review, see: New Trends in Kramers' Reaction Rate Theory, Talkener, P., Häggi, P., Eds.; Kluwer Academic: Dordrecht, The Netherlands, 1995.
92. Neria, E.; Karplus, M. Chem. Phys. Lett. 1997, 267, 23.
93. (a) Karplus, M. J. Phys. Chem. B 2000, 104, 11.
94. (b) Berezhkovskii, A.M.; Szabo, A.; Weiss, G.H.; Zhou, H.-X. J. Chem. Phys. 1999, 111, 9952.
95. (c) Doering, C.R.; Gadoua, J.C. Phys. Rev. Lett. 1992, 69, 2318.
96. Neria, E.; Karplus, M. J. Chem. Phys. 1996, 105, 10812.
97. Agarwal, P.K.; Billeter, S.; Ravi-Rajagopalan, P.T.; Benkovic, S.J.; Hammes-Schiffer, S. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 2794.
98. (b) Agarwal, P.K.; Billeter, S.; Hammes-Schiffer, S. J. Phys. Chem. B 2002, 106, 3283.
99. (a) Lakatos, S.; Halasz, G.; Zavodszky, P. Biochem. Soc. Trans. 1978, 6, 1195.
100. (b) Vihinen, M. Prot. Eng. 1987, 1, 477.
101. Kohen, A.; Klinman, J.P. J. Am. Chem. Soc. 2000, 122, 10738.
102. Daniel, R.M.; Smith, J.C.; Ferrand, M.; Héry, S.; Dunn, R.; Finney, J.L. Biophy J. 1998, 76, 2504.