Kinetic isotope effects as probes for hydrogen tunneling, coupled motion and dynamics contributions to enzyme catalysis

Progress in Reaction Kinetics and Mechanism

Volumn 28, Issue 2, 2003, Pages 119-156

  Kohen, Amnon ^a  

^a University of Iowa ^*  (United States)

Author keywords

Coupled motion; Enzyme catalysis; Enzyme dynamics; Isotope effect; Reaction rate; Temperature dependence; Tunneling

Indexed keywords

CATALYSIS; HYDROGEN; ISOTOPES; MATHEMATICAL MODELS;

ENZYME CATALYSIS; ENZYME DYNAMICS; HYDROGEN TUNNELING; ISOTOPE EFFECT;

ENZYME KINETICS;

EID: 0141828475     PISSN: 14686783     EISSN: None     Source Type: Journal    
DOI: 10.3184/007967403103165486     Document Type: Article

References (109)

1. Wolfenden R., Snider M., Ridgway C. and Miller B. J. Am. Chem. Soc., 1999, 121, 7419-7420.
2. Bruice T. C. and Benkovic S. J. Biochemistry; 2000, 39, 6267-6273.
3. Strajbl M., Florian J. and Warshel A. J. Am. Chem. Soc., 2000, 122, 5354-5366.
4. Stryer L. Biochemistry 5th edn; W.H. Freeman and Company, New York, 2002.
5. Steinfeld J. I., Francisco J. S. and Hase W. L. Chemical Kinetics and Dynamics; 2nd ed.; Prentice Hall: Upper Saddle River, N.J., 1998.
6. Kohen A. and Klinman J. P. Acc. Chem. Res., 1998, 31, 397-404.
7. Mulholland A. J. and Karplus M. Biochem. Soc. Trans., 1996, 24, 247-54.
8. Wilson E. K. Chem. Eng. News, 2000, 78, July 17, 42-45.
9. Villa J. and Warshel A. J. Phys. Chem. B, 2001, 105, 7887-7907.
10. Cui Q. and Karplus M. J. Phys. Chem. B, 2002, 106, 7927-7947.
11. Fersht A. Structure and mechanism in protein sciences: a guide to enzyme catalysis and protein folding; W. H. Freeman, New York, 1998.
12. Northrop D. B. in Enzyme mechanism from isotope effects, Cook P.F., Ed., CRC Press, Boca Raton, Fl., 1991 pp. 181-202.
13. Cleland W. W. in Enzyme Mechanism from Isotope Effects, Cook P.F., Ed., CRC Press, Boca Raton, FL, 1991 p 247-268.
14. Swain C. G., Stivers E. C., Reuwer J. F. and Schaad L. J. J. Am. Chem. Soc., 1958, 80, 5885-5893.
15. Melander L. and Saunders W. H. Reaction rates of isotopic molecules; Krieger, R. E.: Malabar, FL, 1987.
16. Bigeleisen J. International Atomic Energy Agency, Vienna, 1962; p 161.
17. Stem M. J. and Vogel P. C. J. Am. Chem. Soc., 1971, 93, 4664-4675.
18. Stem M. J. and Weston R. E. J. Chem. Phys., 1974, 60, 2803, 2808, 2814.
19. Huskey W. P. and Schowen R. L. J. Am. Chem. Soc., 1983, 105, 5704-5706.
20. Saunders W. H. J. Am. Chem. Soc., 1985, 107, 164-169.
21. Amin M., Price R. C. and Saunders W. H. J. Am. Chem. Soc., 1990, 112, 4467-4471.
22. Northrop D. B. in Isotope effects on enzyme-catalyzed reactions, Cleland W.W., O'Leary M.H., Northrop D.B., Eds., University Park Press, Baltimore, MD., 1977, pp. 122-152.
23. Cleland W. W. Adv. Enzymol., 1977, 45, 273-303.
24. Kohen A. and Klinman J. P. Chem. Biol., 1999, 6, R191-198.
25. Bigeleisen J. J. Chem. Phys., 1955, 23, 2264-2267.
26. Huskey W. P. J. Phys. Org. Chem., 1991, 4, 361-366.
27. Huskey W. P. in Enzyme mechanism from isotope effects, Cook P.F., Ed., CRC'Press, Boca Raton, Fl., 1991 p 37-72.
28. Saunders W. H. Croat. Chem. Acta, 1992, 65, 505-515.
29. Lin S. and Saunders W. H. J. Am. Chem. Soc., 1994, 116, 6107-6110.
30. Cha Y., Murray C. J. and Klinman J. P. Science, 1989, 243, 1325-1330.
31. Bahnson B. J., Park D. H., Kim K., Plapp B. V. and Klinman J. P. Biochemistry, 1993, 32, 5503-5507.
32. Kohen A., Cannio R., Bartolucci S. and Klinman J. P. Nature, 1999, 399, 496-499.
33. Alston W. C., Manska M. and Murray C. J. Biochemistry, 1996, 35, 12873-12881.
34. Streitwieser A., Jagow R. H., Faney R. C. and Suzuki F. J. Am. Client. Soc., 1958, 80, 2326-2332.
35. Kohen A. and Jensen J. H. J. Am. Chem. Soc., 2002, 124, 3858-3864.
36. Wilson E. B., Decius J. C. and Cross P. C. Molecular vibrations; Dover Publications, Inc., New York, 1955.
37. Chin J. K., Kohen A. and Klinman J. P., unpublished results.
38. Rucker J. and Klinman J. P. J. Am. Chem. Soc., 1999, 121, 1997-2006.
39. Bigeleisen J. and Mayer M. G. J. Chem. Phys., 1947, 15, 261-267.
40. Bigeleisen J. and Wolfsberg M. Adv. Chem. Phys., 1958, 1, 15-76.
41. Bell R. P. The tunnel effect in chemistry; Chapman & Hall, London & New York., 1980.
42. Sims L. B., Burton G. and Lewis D. E., 1977, Vol. BeboVib IV, Program No. 337; Quantum Chemistry Program Exchange. Department of Chemistry, Indiana University, Bloomington, IN
43. Bruice T. C. and Lightstone F. C. Acc. Chem. Res., 1999, 32, 127-136.
44. Grant K. L. and Klinman J. P. Bioorg. Chem., 1992, 20, 1-7.
45. Rubach J. K., Ramaswamy S. and Plapp B. V. Biochemistry, 2001, 40, 12686-12694.
46. Agarwal P. K., Webb S. P. and Hammes-Schiffer S. J. Am. Chem. Soc., 2000, 122, 4803-4812.
47. Alhambra C., Corchado J. C., S·nchez M. L., Gao J. and Truhlar D. J. J. Am. Chem. Soc., 2000, 122, 8197-8203.
48. Antoniou D. and Schwanz S. D. J. Phys. Chem. B, 2001, 105, 5553-5558.
49. Kraut J. Science, 1988, 242, 533-540.
50. Moiseyev N., Rucker J. and Glickman M. H. J. Am. Chem. Soc., 1997, 119, 3853-3860.
51. Knapp M. J., Rickert K. and Klinman J. P. J. Am. Chem. Soc., 2002, 124, 3865-3874.
52. Nesheim J. C. and Lipscomb J. D. Biochemistry, 1996, 35, 10240-10247.
53. Whittaker M. M., Ballou D. P. and Whittaker J. W. Biochemistry, 1998, 37, 8426-8436.
54. Basran J., Sutcliffe M. J. and Scrutton N. S. Biochemistry, 1999, 38, 3218-22.
55. Basran J., Patel S., Sutcliffe M. J. and Scrutton N. S. J. Biol. Chem., 2001, 276, 6234-6242.
56. Basran J., Sutcliffe M. J. and Scrutton N. S. J. Biol. Chem., 2001, 276, 24581-24587.
57. Harris R. J., Meskys R., Sutcliffe M. J. and Scrutton N. S. Biochemistry, 2000, 39, 1189-1198.
58. Chowdhury S. and Banerjee R. J. Am. Chem. Soc., 2000, 122, 5417-5418.
59. Abad J. L., Camps F. and Fabrias G. Angew. Chem. Int. Ed., 2000, 122, 3279-3281.
60. Francisco W. A., Knapp M. J., Blackburn N. J. and Klinman J. P. J. Am. Chem. Soc., 2002, 124, 8194-8195.
61. Grant K. L. and Klinman J. P. Biochemistry, 1989, 28, 6597-6605.
62. Jonsson T., Edmondson D. E. and Klinman J. P. Biochemistry, 1994, 33, 14871-14878.
63. Glickman M. H., Wiseman J. S. and Klinman J. P. J. Am. Chem. Soc., 1994, 116, 793-794.
64. Knapp M. J. and Klinman J. P. Eur. J. Biochem., 2002, 269, 3113-3121.
65. Scrutton N. S., Basran J. and Sutcliffe M. J. Eur. J. Biochem., 1999, 264, 666-671.
66. Sutcliffe M. J. and Scrutton N. S. Eur. J. Biochem., 2002, 269, 3096-3102.
67. Glickman M. H. and Klinman J. P. Biochemistry, 1996, 35, 12882-12892.
68. Jonsson T., Glickman M. H., Sun S. J. and Klinman J. P. J. Am. Chem. Soc., 1996, 118, 10319-10320.
69. Truhlar D. G. 2001, personal communication.
70. Glickman M. H. and Klinman J. P. Biochemistry, 1995, 34, 14077-14092.
71. Cannio R., Rossi M. and Bartolucci S. Eur. J. Biochem., 1994, 222, 345-352.
72. Truhlar D. G. and Kohen A. Proc. Nat. Acad. Sci. USA, 2001, 98, 848-851.
73. Tolman R. C. J. Am. Chem. Soc., 1920, 42, 2506-2528.
74. Tolman R. C. Statistical Mechanics with Applications to Physics and Chemistry; Chemical Catalog Co., New York, 1927.
75. Truhlar D. G. J. Chem. Educ., 1978, 55, 209-211.
76. Truhlar D. G. and Morokuma K. Transition State Modeling for Catalysis; American Chemical Society, Washington, 1999.
77. Rasmussen B. F., Stock A. M., Ringe D. and Petsko G. A. Nature, 1992, 357, 423-424.
78. Sawaya M. R. and Kraut J. Biochemistry, 1997, 36, 586-603.
79. Welch G. R., Somogyi B. and Damjanovich S. Prog. Biophys. Mol. Biol, 1982, 39, 109-146.
80. Kohen A. and Klinman J. P. J. Am. Chem. Soc., 2000, 122, 10738-10739.
81. Gregory R. B. Protein-Solvent Interactions; Marcel Dekker, Inc., New York, Basel, Hong Kong, 1995.
82. Ostermann A., Waschipkyo R., Parak F. G. and Nienhaus G. U. Nature, 2000, 404, 205-208.
83. Radkiewicz J. L. and Brooks C. L. J. Am. Chem. Soc., 2000, 122, 225-231.
84. Liebl U., Lipowski G., Négrerie M., Lambry J. C., Martin J. L. and Vos M. H. Nature, 1999, 401, 181-184.
85. Northrop D. B. J. Am. Chem. Soc., 1999, 121, 3521-3524.
86. Warshel A. and Parson W. W. Quart. Rev. Biophys., 2001, 34, 563-679.
87. Northrop D. B. and Cho Y. K. Biophys. J., 2000, 79, 1621-1628.
88. Eisenmesser E. Z., Bosco D. A., Akke M. and Kern D. Science, 2002, 295, 1520-1523.
89. Schowen R. L. Eur. J. Biochem., 2002, 269, 3095.
90. Antoniou D., Caratzoulas S., Kalyanaraman C., Mincer J. S. and Schwartz S. D. Eur. J. Biochem., 2002, 269, 3103-3112.
91. Marcus R. A. and Sutin N. Biochem. Biophys. Acta, 1985, 811, 265-322.
92. Borgis D. and Hynes J. T. J. Chem. Phys., 1991, 94, 3619-3628.
93. Borgis D. and Hynes J. T. Chem. Phys., 1993, 170, 315-346.
94. Kuznetsov A. M. and Ulstrup J. Can. J. Chem., 1999, 77, 1085-1096.
95. Warshel A. Proc. Natl. Acad. Sci. USA, 1984, 81, 444-448.
96. Cui Q. and Karplus M. J. Am. Chem. Soc., 2001, 123, 2284-2290.
97. Hwang J.-K. and Warshel A. J. Am. Chem. Soc., 1996, 118, 11745-11751.
98. Cui Q., Elstner M. and Karplus M. J. Phys. Chem. B, 2002, 106, 2721-2740.
99. Hwang J. K., Chu Z. T., Yadav A. and Warshel A. J. Phys. Chem., 1991, 95, 8445-8448.
100. Alhambra C., Sánchez M. L., Corchado J. C., Gao J. and Truhlar D. J. Client. Phys. Lett., 2001, 347, 512-518.
101. Truhlar D. G., Gao J., Alhambra C., Garcia-vilcoa M., Corchado J. C., Nchez M. L. S. and Villa J. Acc. Chem. Res., 2002, 35, 341-349.
102. Faulder P. F., Tresadem G., Chohan K. K., Scrutton N. S., Sutcliffe M. J., Hillier I. H. and Burton N. A. J. Am. Chem. Soc., 2001, 123, 8604-8605.
103. Agarwal P. K., Billeter S. R. and Hammes-Schiffer S. J. Phys. Chem. B, 2002, 106, 3283-3293.
104. Brunton G., Griller D., Barclay L. R. C. and Ingold K. U. J. Am. Chem. Soc., 1976, 98, 6803-6811.
105. Kwart H. Acc. Chem. Res., 1982, 15, 401-408.
106. Braun J., Schwesinger R., Williams P. G., Morimoto H., Wemmer D. E. and Limbach H.-H. J. Am. Chem. Soc., 1996, 118, 11101-11110.
107. Shurki A., Strajbl M., Villa J. and Warshel A. J. Am. Chem. Soc., 2002, 124, 4097-4107.
108. Prass B., Stehlik D., Chan I. Y., Trakhtenberg L. I. and Klochikhin V. L. Ber. Bunsenges. Phys. Chem., 1998, 102, 498-503.
109. Agarwal P. K., Billeter S. R., Rajagopalan P. T. R., Benkovic S. J. and Hammes-Schiffer S. Proc. Nat. Acad. Sci. U.S.A., 2002, 99, 2794-2799.