Determining transition states from kinetic isotope effects

Methods in Enzymology

Volumn 308, Issue , 1999, Pages 355-397

  Berti, Paul J ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME INHIBITOR; ISOTOPE;

ARTICLE; CATALYSIS; CHEMICAL BOND; ENERGY TRANSFER; ENZYME ANALYSIS; ENZYME MECHANISM; ENZYME SUBSTRATE COMPLEX; HYDROLYSIS; NONHUMAN; PRIORITY JOURNAL; QUANTUM MECHANICS;

EID: 0032845061     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(99)08016-7     Document Type: Article

References (95)

1. L. B. Sims and D. E. Lewis, in "Isotope Effects: Recent Developments in Theory and Experiment" (E. Buncel and C. C. Lee, eds.), Vol. 6, p. 161. Elsevier, New York, 1984.
2. P. J. Berti and V. L. Schramm, J. Am. Chem. Soc. 119, 12069 (1997).
3. P. J. Berti, S. R. Blanke, and V. L. Schramm, J. Am. Chem. Soc. 119, 12079 (1997).
4. K. A. Rising and V. L. Schramm, J. Am. Chem. Soc. 119, 27 (1997).
5. J. Scheuring and V. L. Schramm, Biochemistry 36, 4526 (1997).
6. J. Scheuring, P. J. Berti, and V. L. Schramm, Biochemistry 37, 2748 (1998).
7. J. Scheuring and V. L. Schramm, Biochemistry 36, 8215 (1997).
8. R. D. Guthrie and W. P. Jencks, Acc. Chem. Res. 22, 343 (1989).
9. P. C. Kline and V. L. Schramm, Biochemistry 34, 1153 (1995).
10. D. J. Merkler, P. C. Kline, P. Weiss, and V. L. Schramm, Biochemistry 32, 12993 (1993).
11. P. C. Kline and V. L. Schramm, Biochemistry 32, 13212 (1993).
12. B. A. Horenstein, D. W. Parkin, B. Estupinan, and V. L. Schramm, Biochemistry 30, 10788 (1991).
13. D. W. Parkin, F. Mentch, G. A. Banks, B. A. Horenstein, and V. L. Schramm, Biochemistry 30, 4586 (1991).
14. D. W. Parkin and V. L. Schramm, Biochemistry 26, 913 (1987).
15. F. Mentch, D. W. Parkin, and V. L. Schramm, Biochemistry 26, 921 (1987).
16. L. Pauling, Chem. Eng. News 24, 1375 (1946).
17. A. Radzicka and R. Wolfenden, Science 267, 90 (1995).
18. B. G. Miller, T. W. Traut, and R. Wolfenden, J. Am. Chem. Soc. 120, 2666 (1998).
19. R. Wolfenden, C. Ridgway, and G. Young, J. Am. Chem. Soc. 120, 833 (1998).
20. R. Wolfenden, X. Lu, and G. Young, J. Am. Chem. Soc. 120, 6814 (1998).
21. W. E. Buddenbaum and V. J. Shiner, Jr., Can. J. Chem. 54, 1146 (1976).
22. W. P. Huskey, in "Enzyme Mechanism from Isotope Effects" (P. F. Cook, ed.), p. 37. CRC Press, Boca Raton, FL, 1991.
23. J. Suhnel and R. L. Schowen, in "Enzyme Mechanism from Isotope Effects" (P. F. Cook, ed.), p. 3. CRC Press, Boca Raton, FL, 1991.
24. W. E. Buddenbaum and V. J. Shiner, Jr., in "Isotope Effects on Enzyme-Catalyzed Reactions" (W. W. Cleland, M. H. O'Leary, and D. B. Northrop, eds.), p. 1. University Park Press, Baltimore, MD, 1977.
25. A. Kohen and J. P. Klinman, Acc. Chem. Res. 31, 397 (1998).
26. Y. Cha, C. J. Murray, and J. P. Klinman, Science 243, 1325 (1989).
27. D. G. Truhlar, W. L. Hase, and J. T. Hynes, J. Phys. Chem. 87, 2664 (1983).
28. S. C. Tucker, D. G. Truhlar, B. C. Garrett, and A. D. Isaacson, J. Chem. Phys. 82, 4102 (1985).
29. D. G. Truhlar and B. C. Garrett, Acc. Chem. Res. 13, 440 (1980).
30. J. Bigeleisen and M. Goeppert Mayer, J. Chem. Phys. 15, 261 (1947).
31. J. Bigeleisen and M. Wolfsberg, Adv. Chem. Phys. 1, 15 (1958).
32. E. B. Wilson, Jr., J. C. Decius, and P. C. Cross, "Molecular Vibrations: The Theory of Infrared and Raman Vibrational Spectroscopy." McGraw-Hill, New York, 1955.
33. D. C. Harris and M. D. Bertolucci, "Symmetry and Spectroscopy: An Introduction to Vibrational and Electronic Spectroscopy." Dover Publications, New York, 1978.
34. H. S. Johnston, "Gas Phase Reaction Rate Theory." Ronald Press, New York, 1966.
35. G. W. Burton, L. B. Sims, J. C. Wilson, and A. Fry, J. Am. Chem. Soc. 99, 3371 (1977).
36. A. R. Fersht, "Enzyme Structure and Mechanism." Freeman, New York, 1985.
37. D. W. Parkin, in "Enzyme Mechanism from Isotope Effects" (P. F. Cook, ed.), p. 269. CRC Press, Boca Raton, FL, 1991.
38. M. H. O'Leary, Methods Enzymol 64, 83 (1980).
39. P. M. Weiss, in "Enzyme Mechanism from Isotope Effects" (P. F. Cook, ed.), p. 291. CRC Press, Boca Raton, FL, 1991.
40. B. J. Bahnson and V. E. Anderson, Biochemistry 30, 5894 (1991).
41. E. Gawlita, P. Paneth, and V. E. Anderson, Biochemistry 34, 6050 (1995).
42. D. A. Singleton and A. A. Thomas, J. Am. Chem. Soc. 117, 9357 (1995).
43. D. B. Northrop, Annu. Rev. Biochem. 50, 103 (1981).
44. I. W. Rose, Methods Enzymol. 64, 47 (1980).
45. X. Y. Chen, P. J. Berti, and V. L. Schramm, manuscript in preparation.
46. J. Rodgers, D. A. Femec, and R. L. Schowen, J. Am. Chem. Soc. 104, 3263 (1982).
47. D. E. Lewis, L. B. Sims, H. Yamataka, and J. McKenna, J. Am. Chem. Soc. 102, 7411 (1980).
48. L. B. Sims, G. W. Burton, and D. E. Lewis, "BEBOVIB-IV, QCPE No. 337," Quantum Chemistry Program Exchange, Department of Chemistry, University of Indiana, Bloomington, IN, 1977.
49. W. P. Huskey, J. Am. Chem. Soc. 118, 1663 (1996).
50. T. E. Casamassina, and W. P. Huskey, J. Am. Chem. Soc. 115, 14 (1993).
51. M. J. Stern, and M. Wolfsberg, J. Chem. Phys. 45, 4105 (1966).
52. M. J. Frisch, G. W. Trucks, H. B. Schlegel, P. M. W. Gill, B. G. Johnson, M. A. Robb, J. R. Cheeseman, T. Keith, G. A. Petersson, J. A. Montgomery, K. Raghavachari, M. A. Al-Laham, V. G. Zakrzewski, J. V. Ortiz, J. B. Foresman, J. Cioslowski, B. B. Stefanov, A. Nanayakkara, M. Challacombe, C. Y. Peng, P. Y. Ayala, W. Chen, M. W. Wong, J. L. Andres, E. S. Replogle, R. Gomperts, R. L. Martin, D. J. Fox, J. S. Binkley, D. J. Defrees, J. Baker, J. P. Stewart, M. Hend-Gordon, C. Gonzalez, and J. A. Pople, "Gaussian 94, Revision C.2, D.4." Gaussian, Pittsburgh, PA, 1995.
53. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, Jr., D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. 117, 5179 (1995).
54. S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, Jr., and P. Weiner, J. Am. Chem. Soc. 106, 765 (1984).
55. M. J. Stern, W. Spindel, and E. U. Monse, J. Chem. Phys. 52, 2022 (1970).
56. M. J. Stern, W. Spindel, and E. U. Monse, J. Chem. Phys. 48, 2908 (1968).
57. As discussed in Ref. 3, IEs are a nonlinear function of bond order, being more closely correlated with the relative change in bond order. Thus the IEs associated with a 1.06-fold increase in the N-1-C-2 bond order will be very much smaller than the 40-fold decrease in the C-1′-N-1 bond order.
58. W. E. Buddenbaum and P. E. Yankwich, J. Phys. Chem. 71, 3136 (1967).
59. G. D. Markham, D. W. Parkin, F. Mentch, and V. L. Schramm, J. Biol. Chem. 262, 5609 (1987).
60. F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, E. F. Meyer, Jr., M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi, J. Mol. Biol. 112, 535 (1977).
61. L. J. Mazzella, D. W. Parkin, P. C. Tyler, R. H. Furneaux, and V. L. Schramm, J. Am. Chem. Soc. 118, 2111 (1996).
62. V. L. Schramm, in "Enzyme Mechanism from Isotope Effects" (P. F. Cook, ed.), p. 367. CRC Press, Boca Raton, FL, 1991.
63. D. W. Parkin, B. A. Horenstein, D. R. Abdulah, B. Estupinan, and V. L. Schramm, J. Biol, Chem. 266, 20658 (1991).
64. M. L. Sinnott, Chem. Rev. 90, 1171 (1990).
65. C. F. Bernasconi, Acc. Chem. Res. 25, 9 (1992).
66. C. F. Bernasconi, Adv. Phys. Org. Chem. 27, 119 (1992).
67. P. J. Berti and V. L. Schramm, manuscript in preparation.
68. W. B. Wright and G. S. D. King, Acta Crystallogr. 7, 283 (1954).
69. F. H. Allen, J. E. Davies, J. J. Galloy, O. Johnson, O. Kennard, C. F. Macrae, E. Mitchell, G. F. Mitchell, J. M. Smith, and D. G. Watson, J. Chem. Inf. Comput. Sci. 31, 187 (1991).
70. S. L. Moodie and J. M. Thornton, Nucleic Acids Res. 21, 1369 (1993).
71. A. Gelbin, B. Schneider, L. Clowney, S. H. Hsieh, W. K. Olson, and H. M. Berman, J. Am. Chem. Soc. 118, 519 (1996).
72. J. M. Thornton and P. M. Bayley, Biopolymers 16, 1971 (1977).
73. C. Altona and M. Sundaralingam, J. Am. Chem. Soc. 95, 2333 (1973).
74. N. J. Oppenheimer, in "The Pyridine Nucleotide Coenzymes" (J. Everse, B. Anderson, and K.-S. You, eds.), p. 51. Academic Press, New York, 1982.
75. N. J. Oppenheimer, in "Pyridine Nucleotide Coenzymes" (D. Dolphin, R. Poulson, and O. Avramovic, eds.), p. 185. Wiley-Interscience, New York, 1987.
76. C. L. Perrin, K. B. Armstrong, and M. A. Fabian, J. Am. Chem. Soc. 116, 715 (1994).
77. A. J. Briggs, R. Glenn, P. G. Jones, A. J. Kirby, and P. Ramaswamy, J. Am. Chem. Soc. 106, 6200 (1984).
78. Y. Kinoshita, J. R. Ruble, and G. A. Jeffrey, Carbohydr. Res. 92, 1 (1981).
79. M. Ashwell, X. Guo, and M. L. Sinnott, J. Am. Chem. Soc. 114, 10158 (1992).
80. D. E. Sunko, I. Szele, and W. J. Hehre, J. Am. Chem. Soc. 99, 5000 (1977).
81. W. J. Hehre, Acc. Chem. Res. 8, 369 (1975).
82. Unpublished results.
83. R. G. Duggleby and D. B. Northrop, Bioorg. Chem. 17, 177 (1989).
84. W. E. DeWolf, Jr., F. A. Fullin, and V. L. Schramm, J. Biol. Chem. 254, 10868 (1979).
85. M. Boutellier, B. A. Horenstein, A. Semenyaka, V. L. Schramm, and B. Ganem, Biochemistry 33, 3994 (1994).
86. R. W. Miles, P. C. Tyler, R. H. Furneaux, C. K. Bagdassarian, and V. L. Schramm, Biochemistry 37, 8615 (1998).
87. M. Degano, S. C. Almo, J. C. Sacchettini, and V. L. Schramm, Biochemistry 37, 6277 (1998).
88. B. A. Horenstein and V. L. Schramm, Biochemistry 32, 9917 (1993).
89. B. A. Horenstein and V. L. Schramm, Biochemistry 32, 7089 (1993).
90. A. P. Scott and L. Radom, J. Phys. Chem. 100, 16502 (1996).
91. J. A. Pople, A. P. Scott, M. W. Wong, and L. Radom, Isr. J. Chem. 33, 345 (1993).
92. M. W. Wong, Chem. Phys. Lett. 256, 391 (1996).
93. iα1.
94. C. F. Bernasconi and P. J. Wenzel, J. Am. Chem. Soc. 116, 5405 (1994).
95. C. F. Bernasconi, Tetrahedron 41, 3219 (1985).