Enzymatic transition-state analysis and transition-state analogs

Methods in Enzymology

Volumn 308, Issue , 1999, Pages 301-348

  Schramm, Vern L ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ISOTOPE; NUCLEOSIDASE; NUCLEOSIDE; NUCLEOTIDE; OLIGONUCLEOTIDE; PURINE NUCLEOSIDE PHOSPHORYLASE; RNA;

ARTICLE; CATALYSIS; ENZYME ANALYSIS; ENZYME BINDING; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SYNTHESIS; NONHUMAN; PRIORITY JOURNAL; STEREOSPECIFICITY;

EID: 0032860328     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(99)08015-5     Document Type: Article

References (108)

1. W. W. Cleland, Methods Enzymol. 87, 625 (1982).
2. W. W. Cleland, Methods Enzymol. 249, 341 (1995).
3. W. W. Cleland, M. H. O'Leary, and D. B. Northrop, "Isotope Effects on Enzyme-Catalyzed Reactions." University Park Press, Baltimore, MD, 1977.
4. P. F. Cook, ed., "Enzyme Mechanisms from Isotope Effects." CRC Press, Boca Raton, FL, 1991.
5. R. D. Gandour and R. L. Schowen, eds., "Transition States of Biochemical Processes." Plenum Press, New York, 1978.
6. L. Melander and W. J. Saunders, Jr., "Reaction Rates of Isotopic Molecules." Wiley New York, 1980.
7. P. Berti, Methods Enzymol., Chapter [14] (this volume) (1999).
8. R. G. Parr and W. Yang, "Density Functional Theory of Atoms and Molecules." Oxford Univ. Press, New York, 1989.
9. 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." Gaussian, Inc., Pittsburgh, 1995.
10. L. B Sims and D. E. Lewis, in "Isotopes in Organic Chemistry" (E. Buncel and C. C. Lee, eds.), p. 161. Elsevier, New York, 1984.
11. 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, 1977.
12. W. P. Huskey, J. Am. Chem. Soc. 118, 14 (1993).
13. B. B. Braunheim and S. D. Schwartz, Methods Enzymol., Chapter [15].
14. V. L. Schramm, Annu. Rev. Biochem. 67, 693 (1998).
15. R. W. Miles, P. C. Tyler, R. H. Furneaux, C. K. Bagdassarian, and V. L. Schramm, Biochemistry 37, 8615 (1998).
16. X.-Y Chen, T. M. Link, and V. L. Schramm, Biochemistry 37, 11605 (1998).
17. C. Li, P. C. Tyler, R. H. Furneaux, G. Kicska, Y. Xu, C. Grubmeyer, M. E. Girvin, and V. L. Schramm, Nature Struct. Biol. 6, in press (1999).
18. V. L. Schramm B. A. Horenstein, and P. C. Kline, J. Biol. Chem. 269, 18259 (1994).
19. K. Liu, J. C. Polanyi, and S. Yang, J. Chem. Phys. 98, 5431 (1993).
20. N. F. Scherer, L. R. Khundkar, R. B. Bernstein, and A. H. Zewail, J. Chem. Phys. 87, 1451 (1987).
21. J. F Morrison and C. T. Walsh, Adv. Enzymol. Relat Areas Mol. Biol. 61, 201 (1988).
22. A. Radzicka and R. Wolfenden, Methods Enzymol. 249, 284 (1995).
23. L. Pauling, Am. Sci. 36, 50 (1948).
24. K. B. J. Schowen, in "Transition States of Biochemical Processes" (R. D. Gandour and R. L. Schowen, eds.), p. 225. Plenum Press, New York, 1978.
25. W. R. Cannon, S. F. Singleton, and S. J. Benkovic, Nature Struct Biol. 3, 821 (1996).
26. A. Radzicka and R. Wolfenden, Science 267, 90 (1996).
27. W. W. Cleland, Biochemistry 31, 317 (1992).
28. S.-O. Shan and D. Herschlag, Proc. Natl. Acad. Sci. U.S.A 93, 14474 (1996).
29. J. A. Gerlt and P. G. Gassman, J. Am. Chem. Soc. 115, 11552 (1993).
30. A. S. Mildvan, T. K. Harris, and C. Abeygunawardana, Methods Enzymol., Chapter [10], (this volume) (1999).
31. S.-O. Shan and D. Herschlag, Method Enzymol., Chapter [11] (this volume) (1999).
32. A. E. Aleshin, C. Zeng, H. D. Bartunik, H. J. Fromm, and R. B. Honzatko, J. Mol. Biol. 282, 345 (1998).
33. B. A. Horenstein, D. W. Parkin, B. Estupiñán, and V. L. Schramm, Biochemistry 30, 10788 (1991).
34. C. R. Muchmore, J. M. Krahn, J. H. Kim, H. Zalkin, and J. L. Smith, Prot. Sci. 7, 39 (1998).
35. M. Degano, S. C. Almo, J. C. Sacchettini, and V. L. Schramm, Biochemistry 37, 6277 (1998).
36. M. Garcia-Viloca, R. Gelabert, A. Gonzalez-Lafont, M. Moreno, and J. M. Lluch, J. Am. Chem. Soc. 120, 10203 (1998).
37. C. K. Bagdassarian, V. L. Schramm, and S. D. Schwartz, J. Am. Chem. Soc. 118, 8825 (1996).
38. J. Bigeleisen and M. Wolfsberg, Adv. Chem. Phys. 1, 15 (1958).
39. J. Suhnel and R. L. Schowen, in "Enzyme Mechanism from Isotope Effects" (P. F. Cook, ed.), p. 3. CRC Press, Boca Raton, FL, 1991.
40. W. P. Huskey, in "Enzyme Mechanism from Isotope Effects" (P. F. Cook., ed.), p. 37. CRC Press, Boca Raton, FL, 1991.
41. P. M. Weiss, in "Enzyme Mechanism from Isotope Effects" (P. F Cook., ed.), p. 291. CRC Press, Boca Raton, FL, 1991.
42. F. W. Dahlquist, T. Rand-Meier, and M. A. Raftery, Biochemistry 8, 4214 (1969).
43. D. W Parkin, H. B. Leung, and V. L. Schramm, J. Biol. Chem. 259, 9411 (1984).
44. P. J Berti and V. L Schramm, J. Am. Chem. Soc. 119, 12069 (1997).
45. P. J. Berti, S. R. Blanke, and V. L Schramm, J. Am. Chem. Soc. 119, 12079 (1997).
46. D. W. Parkin, in "Enzyme Mechanism from Isotope Effects" (P. F. Cook, ed.), p. 269. CRC Press, Boca Raton, FL, 1991.
47. D. W. Parkin and V. L. Schramm, Biochemistry 26, 913 (1987).
48. T. J. Batterham, R. K. Ghambeer, R. L. Blakley, and C. Brownson, Biochemistry 6, 1203 (1967).
49. Y. Xu, J. C. Eads, J. C. Sacchettini, and C. Grubmeyer, Biochemistry 36, 3700 (1997).
50. J. S. Blanchard and K. K. Wong, in "Enzyme Mechanism from Isotope Effects" (P. F. Cook, ed.), p. 341. CRC Press, Boca Raton, FL, 1991.
51. K. Aktories, ed., "Current Topics in Microbiology and Immunology: ADP-Ribosylating Toxins." Springer-Verlag, Berlin, 1992.
52. M. Miwa., O. Hayaishi, S. Shall, M. Smulson, and T. Sugimura, eds., "ADP-Ribosylation, DNA Repair and Cancer." Japan Scientific Societies Press, Tokyo, 1983.
53. H. C Lee, T. F Walseth, G. T. Bratt, R. N. Hayes, and D. L. Clapper, J. Biol. Chem. 264, 1608 (1989).
54. K. A. Rising and V. L. Schramm, J. Am. Chem. Soc. 116, 6531 (1994).
55. A. S. Sauve, C. Munshi, H. C. Lee, and V. L. Schramm, Biochemistry 37, 13239 (1998).
56. X.-Y. Chen, T. M. Link, and V. L. Schramm, Biochemistry 37, 11605 (1998).
57. J. Scheuring, P. J. Berti, and V. L. Schramm, Biochemistry 37, 2748 (1998).
58. D. B. Northrop, Biochemistry 14, 2644 (1975).
59. D. B. Northrop, Annu. Rev. Biochem. 50, 103 (1981).
60. D. B. Northrop, in "Isotope Effects on Enzyme-Catalyzed Reactions" (W. W. Cleland, M. H. O'Leary, and D. B. Northrop, eds.), p. 122. University Park Press, Baltimore, MD, 1977.
61. B. J. Bahnson and J. P. Klinman, Methods. Enzymol. 249, 374 (1995).
62. D. Antoniou and S. D. Schwartz, Proc. Nat. Acad. Sci. U.S.A. 94, 12360 (1997).
63. W. P. Huskey and R. L. Schowen, J. Am. Chem. Soc. 105, 5704 (1983).
64. I. A. Rose, Methods Enzymol. 249, 315 (1995).
65. P. C. Kline and V. L. Schramm, Biochemistry 32, 13212 (1993).
66. P. C. Kline and V. L. Schramm, Biochemistry 34, 1153 (1995).
67. G. D. Markham, D. W. Parkin, F. Mentch, and V. L. Schramm, J. Biol. Chem. 262, 5609 (1987).
68. M. Cohn and G. H. Reed, Annu. Rev. Biochem. 51, 365 (1982).
69. P. C. Kline and V. L. Schramm, Biochemistry 34, 1153 (1995).
70. J. T. McFarland, in "Enzyme Mechanism from Isotope Effects" (P. F. Cook, ed.), p. 151. CRC Press, Boca Raton, FL, 1991.
71. D. Northrop, J. Chem. Ed. 75, 1153 (1998).
72. R. LaReau, W. Wah, and V. Anderson, Biochemistry 28, 3619 (1989).
73. E. Gawlita, W. S. Caldwell, M. H. O'Leary, P. Paneth, and V. E. Anderson, Biochemistry 34, 2577 (1995).
74. B. Lewis and V. Schramm, unpublished results (1998).
75. R. Callender and H. Deng, Annu. Rev. Biophys. Biomol. Struct. 23, 215 (1994).
76. F. Mentch, D. W. Parkin, and V. L. Schramm, Biochemistry 26, 921 (1987).
77. D. J. Merkler, P. C. Kline, P. Weiss, and V. L. Schramm, Biochemistry 32, 12993 (1993).
78. D. J. Merkler and V. L. Schramm, Biochemistry 32, 5792 (1993).
79. S. L. Meyer, K. L. Kvalnes-Krick, and V. L. Schramm, Biochemistry 28, 8734 (1989).
80. V. L. Schramm and C. Bagdassarian, in "Comprehensive Natural Product Chemistry" (C. D. Poulter, ed.), Vol. 5, pp. 71-100. Pergamon Press, Elsevier Science, New York, 1999.
81. P. C. Kline and V. L. Schramm, Biochemistry 34, 1153 (1994).
82. D. W. Parkin, B. A. Horenstein, D. R. Abdulah, B. Estupiñán, and V. L. Schramm, J. Biol. Chem. 266, 20658 (1991).
83. M. J. S. Dewar, E. F. Zoebisch, J. J. P. Healy, and J. Stewart, J. Am. Chem. Soc. 107, 3902 (1985).
84. M. Degano, S. C. Almo, J. C. Sacchettini, and V. L. Schramm, Biochemistry 37, 6277 (1998).
85. A. Gelbin, B. Schneider, L. Clowney, S. H. Hsieh, W. K. Olson, and H. M. Berman, J. Am. Chem. Soc. 118, 519 (1996).
86. D. M. Quinn and L. D. Sutton, in "Enzyme Mechanism from Isotope Effects" (P. F. Cook, ed.), p. 72. CRC Press, Boca Raton, FL, 1991.
87. M. J. Frisch, G. W. Trucks, M. Hend-Gordon, P. M. W. Gill, M. W. Wong, J. B. Foresman, B. G. Johnson, H. B. Schlegel, M. A. Robb, E. S. Replogle, R. Gomperts, J. L. Andres, K. Raghavachari, J. S. Binkley, C. Gonzalez, R. L. Martin, D. J. Fox, D. J. DeFrees, J. Baker, J. J. P. Stewart, and J. A. Pople, "Gaussian 92 User's Guide." Gaussian Inc., Pittsburgh, 1992.
88. B. A. Horenstein and V. L. Schramm, Biochemistry 32, 7089 (1993).
89. M. S. Hershfield and B. S. Mitchell, in "The Metabolic Basis of Inherited Disease" (C. R. Scriber, A. L. Beaudet, W. S. Sly, and D. Valle, eds.), 7th ed., p. 1725. McGraw-Hill, New York, 1995.
90. S. Niwas, P. Chand, V. P. Pathak, and J. A. Montgomery, J. Med. Chem. 37, 2477 (1994).
91. G. M. Walsh, N. S. Reddy, S. Bantia, Y. S. Babu, and J. A. Montgomery, Hematol. Rev. 8, 87 (1994).
92. G. D. Markham, D. W. Parkin, F. Mentch, and V. L. Schramm, J. Biol. Chem. 262, 5609 (1987).
93. G. W. Burton, L. B. Sims, J. C. Wilson, and A. Fry, J. Am. Chem. Soc. 99, 3371 (1977).
94. A. J. Bennet and M. L. Sinnott, J. Am. Chem. Soc. 108, 7287 (1986).
95. D. E. Sunko, I. Szele, and W. J. Hehre, J. Am. Chem. Soc. 99, 5000 (1977).
96. D. W. Parkin, H. B. Leung, and V. L. Schramm, J. Biol. Chem. 259, 9411 (1984).
97. P. Politzer and G. Truhlar, eds., in "Chemical Applications of Atomic and Molecular Electrostatic Potentials." Plenum Press, New York, 1981.
98. C. A. Venanzi, C. Plant, and T. J. Vananzi, J. Med. Chem. 35, 1643 (1992).
99. P. Sjoberg and P. Politzer, J. Phys. Chem. 94, 3959 (1990).
100. S. Srebrenik, H. Weinstein, and R. Pauncz, Chem. Phys. Lett. 20, 419 (1973).
101. C. K. Bagdassarian, B. B. Brauheim, V. L. Schramm, and S. D. Schwartz, Int. J. Quant. Chem. 60, 73 (1996).
102. C. K. Bagdassarian, V. L. Schramm, and S. D. Schwartz, J. Am. Chem. Soc. 118, 8825 (1996).
103. P. A. M. Michels, A. Polisczak, K. A. Osinga, O Misset, J. Van Beeumen, R. K. Wierenga, P. Borst, and F. R. Opperdoes, EMBO J. 5, 1049 (1986).
104. M. D. Erion, J. D. Stoeckler, W. C. Guida, R. L. Walter, and S. E. Ealick, Biochemistry 36, 11735 (1997).
105. M. D. Erion, K. Takabayashi, H. B. Smith, J. Kessi, S. Wagner, S. Honger, S. L. Shames, and S. E. Ealick, Biochemistry 36, 11725 (1997).
106. B. A. Horenstein and V. L. Schramm, Biochemistry 32, 9917 (1993).
107. R. W. Miles, P. C. Tyler, R. H. Furneaux, C. K. Bagdassarian, and V. L. Schramm, Biochemistry 37, 8615 (1998).
108. D. W. Parkin, G. Limberg, P. C. Tyler, R. H. Furneaux, X.-Y. Chen, and V. L. Schramm, Biochemistry 36, 3528 (1997).