Active species for the ground-state complex of cytidine deaminase: A linear-scaling quantum mechanical investigation

Journal of the American Chemical Society

Volumn 120, Issue 22, 1998, Pages 5407-5410

  Lewis, James P ^a   Carter Jr , Charles W ^a   Hermans, Jan ^a   Pan, Wei ^b   Lee, Tai Sung ^b   Yang, Weitao ^b  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b DUKE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTIDINE DEAMINASE;

ARTICLE; CATALYSIS; ENZYME ACTIVE SITE; ENZYME SUBSTRATE COMPLEX; LIGAND BINDING; MOLECULAR DYNAMICS; PH; X RAY CRYSTALLOGRAPHY;

EID: 0032503607     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja973522w     Document Type: Article

References (55)

1. (a) Cohen, R. M.; Wolfenden, R. J. Biol. Chem. 1971, 246, 7561.
2. (b) Cohen, R. M.; Wolfenden, R. J. Biol Chem. 1971, 246, 7566.
3. (c) Marquez, V. E.; Liu, P. S.; Kelley, J. A.; Driscoll, J. S.; McCormick, J. J. J. Med. Chem. 1980, 23, 713.
4. (d) Liu, P. S.; Marquez, V. E.; Driscoll, J. S.; Fuller, R. W.; McCormick, J. J. J. Med. Chem. 1981, 24, 662.
5. (e) Ashley, G. W.; Bartlett, P. A. J. Biol. Chem. 1984, 259, 13621.
6. (f) Kim, C. H.; Marquez, V. E.; Mao, D. T.; Haines, D. R.; McCormick, J. J. J. Med. Chem. 1986, 29, 1374
7. (g) Wilson, D. K.; Rudolph, F. B.; Quiocho, F. A. Science 1991, 252, 1278.
8. (h) Betts, L.; Xiang, S.; Short, S. A.; Wolfenden, R.; Carter, Jr., C. W. J. Mol. Biol. 1994, 235, 635.
9. (i) Carlow, D.; Smith, A. A.; Yang, C. C.; Short, S. A.; Wolfenden, R. Biochemistry 1995, 34, 4220.
10. (j) Xiang, S.; Short, S. A.; Wolfenden, R.; Carter, Jr., C. W., Biochemistry 1995, 34, 4516.
11. (k) Carlow, D.; Short, S. A.; Wolfenden, R. Biochemistry 1996, 55, 948.
12. (l) Xiang, S.; Short, S. A.; Wolfenden, R.; Carter, Jr., C. W., Biochemistry 1996, 55, 1335.
13. (m) Xiang, S.; Short, S. A.; Wolfenden, R.; Carter, Jr., C. W. Biochemistry 1997, 36, 4768.
14. Frick, L.; MacNeela, J. P.; Wolfenden, R. Bioorg. Chem. 1987, 15, 100.
15. (a) Marquez, V. E. In Developments in Cancer Chemotherapy, Glazer, R. I., Ed.; CRC Press: Florida, 1984; pp 91-114 and references cited within.
16. (b) Chandrasekaren, B.; Capizzi, R. L.; Kute, T. E.; Morgan, T.; Dimling, J. Cancer Res. 1989, 49, 3259.
17. Coleman, J. E. In Zinc Enzymes; Maret, W., Zeppezauer, M., Eds.; Birkhäuser: Boston, 1986.
18. Bertini, I.; Luchinat, C.; Rosi, M.; Sgamellotti, A.; Tarantelli, F. Inorg. Chem. 1990, 29, 1460.
19. (a) Warshel, A.; Levitt, M. J. Mol. Biol. 1976, 103, 227.
20. (b) Singh, U. C.; Kollman, P. J. Comput. Chem. 1986, 7, 718.
21. (c) Field, M. J.; Bash, P. A.; Karplus, M. J. Comput. Chem. 1990, 11, 700.
22. (d) Gao, J.; Xia, X. Science 1992, 258, 631.
23. (a) Warshel, A. Curr. Opin. Struct. Biol. 1992, 2, 230.
24. (b) Stanton, R. V.; Hartsough, D. S.; Merz Jr., K. M. J. Phys. Chem. 1993, 97, 11868.
25. (c) Wei, D.; Salahub, D. R. Chem. Phys. Lett. 1994, 224, 291.
26. (d) Thery, V.; Rinaldi, D.; Rivail, J.-L. J. Comput. Chem. 1994, 15, 269.
27. (e) Gao, J. Review in Computational Chemistry; VCH: New York, 1995; Vol. 7, p 119.
28. (f) Thompson, M. A.; Schenter, G. K. J. Phys. Chem. 1995, 99, 6374.
29. (g) Maseras, F.; Morokuma, K. J. Comput. Chem. 1995, 16, 1170.
30. (h) Humbel, S.; Sieber, S.; Morokuma, K. J. Chem. Phys. 1996, 105, 1959.
31. (i) Assfeld, X.; Rivail, J.-L. Chem. Phys. Lett. 1996, 263, 100.
32. (j) Merz Jr., K. M.; Band, L. J. Am. Chem. Soc. 1997, 119, 863.
33. (k) Peräkyla, M.; Kollmann, P. A. J. Am. Chem. Soc. 1997, 119, 1189.
34. (a) Baroni, S.; Giannozzi, P. Europhys. Lett. 1992, 17, 547.
35. (b) Galli, G.; Parinello, M. Phys. Rev. Lett. 1992, 69, 3547.
36. (c) Mauri, F.; Galli, G.; Car, R. Phys. Rev. B 1993, 47, 9973.
37. (d) Li, X.-P.; Nunes, W.; Vanderbilt, D. Phys. Rev. B 1993, 47, 10891.
38. (e) Daw, M. S. Phys. Rev. B 1993, 47, 10899.
39. (f) Ordejón, P.; Drabold, D. A.; Grumbach, M. P.; Martin, R. M. Phys. Rev. B1993, 48, 14646.
40. (g) Stechel, E. B.; Williams, A. P.; Feibleman, P. J. Phys. Rev. B 1993, 49, 3898.
41. (h) Drabold, D. A.; Sankey, O. F. Phys. Rev. Lett. 1993, 70, 3631.
42. (i) Kohn, W. Chem. Phys. Lett. 1993, 208, 167.
43. (j) Goedecker, S.; Colombo, L. Phys. Rev. Lett. 1994, 73, 122.
44. (k) Hierse, W.; Stechel, E. B. Phys. Rev. B 1994, 50, 17811.
45. (l) Ordejón, P.; Drabold, D. A.; Martin, R. M.; Grumbach, M. P. Phys. Rev. B 1995, 51, 1456.
46. (m) Hemandez, E.; M. J. Gillan. Phys. Rev. B 1995, 51, 10157.
47. (n) Kim, J.; Mauri, F.; Galli, G. Phys. Rev. B 1995, 52, 1640.
48. (o) Stewart, J. P. P. Int. J. Quantum Chem. 1996, 58, 133.
49. (a) Yang, W. Phys. Rev. Lett. 1991, 66, 438.
50. (b) Zhao, Q.; Yang, W. J. Chem. Phys. 1995, 102, 9598.
51. (a) Yang, W.; Lee, T.-S. J. Chem. Phys. 1995, 103, 5674.
52. (b) Lee, T.-S.; York, D. M.; Yang, W. J. Chem. Phys. 1996, 105, 2744.
53. Pan, W.; Lee, T.-S.; Yang, W. J. Comput. Chem., in press.
54. (a) Stewart, J. J. P. J. Comput. Chem. 1989, 10, 221.
55. (b) Stewart, J. J. P. J. Comput. Chem. 1991, 12, 320.