Nitric oxide binding to ferric cytochrome P450: A computational study

Inorganic Chemistry

Volumn 39, Issue 11, 2000, Pages 2352-2359

  Scherlis, Damián A ^a   Cymeryng, Cora B ^a   Estrin, Darío A ^a  

^a UNIVERSIDAD DE BUENOS AIRES   (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME P450; NITRIC OXIDE; FERRIC ION; PROTEIN; WATER;

ARTICLE; CATALYSIS; CHEMICAL BINDING; ELECTRON TRANSPORT; ENZYME ACTIVE SITE; ENZYME BINDING; GEOMETRY; QUANTUM CHEMISTRY; THERMODYNAMICS; BINDING SITE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; DRUG ANTAGONISM; METABOLISM; X RAY CRYSTALLOGRAPHY;

BINDING SITES; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; CYTOCHROME P-450 ENZYME SYSTEM; FERRIC COMPOUNDS; MODELS, CHEMICAL; MOLECULAR CONFORMATION; NITRIC OXIDE; PROTEINS; THERMODYNAMICS; WATER;

EID: 0034729030     PISSN: 00201669     EISSN: None     Source Type: Journal    
DOI: 10.1021/ic991191d     Document Type: Article

References (77)

1. Hereafter, we will adopt the usual designation of P450 to denote cytochrome P450.
2. (a) Lewis, D. F.; Pratt, J. M. Drug Metab. Rev. 1998, 30, 739.
3. (b) Poulos, T. L. Curr. Opin. Struct. Biol. 1995, 5, 767.
4. Ortiz de Montellano, P. R. Cytochrome P-450: Structure, Mechanism and Biochemistry; Plenum Press: New York, 1995.
5. Guengerich, F. P.; MacDonald, T. L. FASEB J. 1990, 4, 2453.
6. Dawson, J. H.; Sono, M. Chem. Rev. 1987, 87, 1255.
7. (a) Hanke, C. J.; Drewett, J. G.; Myers, C. R.; Campbell, W. B. Endocrinology 1998, 139, 4053.
8. (b) del Punta, K.; Charreau, E. H.; Pignataro, O. Endocrinology 1996, 137, 5337.
9. (c) Van Voorhis, B. J.; Dunn, M. S.; Snyder, G. D.; Weiner, C. P. Endocrinology 1994, 135, 1799.
10. Minamiyama, Y.; Takemura, S.; Imaoka, S.; Funae, Y.; Tanimoto, Y.; Inoue, M. J. Pharmacol. Exp. Ther. 1997, 283, 1479.
11. Marques, H. M.; Munro, O. Q.; Grimmer, N. E.; Levendis, D. C.; Marsicano, F.; Pattrick, G.; Markoulides, T. J. Chem. Soc., Faraday Trans. 1995, 91, 1741.
12. (a) Ghosh, A.; Almlof, J.; Lawrence, Q., Jr. J. Phys. Chem. 1994, 98, 5576.
13. (b) Ghosh, A.; Bocian, D. F. J. Phys. Chem. 1996, 100, 6363.
14. (c) Matsuzawa, N.; Ata, M.; Dixon, D. A. J. Phys. Chem. 1995, 99, 7698.
15. Jones, D. H.; Hinman, A. S.; Ziegler, T. Inorg. Chem. 1993, 32, 2092.
16. (a) Havlin, R. H.; Godbout, N.; Salzmann, R.; Wojdelski, M.; Arnold, W.; Schulz, C. E.; Oldfield, E. J. Am. Chem. Soc. 1998, 120, 3144.
17. (b) Spiro, G. T.; Kozlowski, P. M. J. Am. Chem. Soc. 1998, 120, 4524.
18. (a) Green, M. T. J. Am. Chem. Soc. 1998, 120, 10772.
19. (b) Green, M. T. J. Am. Chem. Soc. 1999, 121, 7939.
20. Harris, D.; Loew, G. H.; Komornicki, A. J. Phys. Chem. A 1997, 101, 3959.
21. Harris, D.; Loew, G. H.; Waskell, L. J. Am. Chem. Soc. 1998, 120, 4308.
22. Henson, N. J.; Hay, P. J.; Redondo, A. Inorg. Chem. 1999, 38, 1618.
23. (a) Rovira, C.; Kunc, K.; Hutter, J.; Ballone, P.; Parrinello, M. J. Phys. Chem. A 1997, 101, 8914.
24. (b) Rovira, C.; Parrinello, M. Int. J. Quantum Chem. 1998, 70, 387.
25. (c) Rovira, C.; Ballone, P.; Parrinello, M. Chem. Phys. Lett. 1997, 271, 246.
26. de Groot, M. J.; Havenith, R. W. A.; Vinkers, H. M.; Zwaans, R.; Vermeulen, N. P. E.; van Lenthe, J. H. J. Comput.-Aided Mol. Des. 1998, 12, 183.
27. Yeom, H.; Sligar, S. G.; Li, H.; Poulos, T. L.; Fulco, A. J. Biochemistry 1995, 34, 14733.
28. HyperChem, Release 5.1 Pro; Hypercube, Inc.: Gainesville, FL, 1997.
29. Branden, C.; Tooze, J. Introduction to Protein Structure; Garland Publishing, Inc.: New York and London, 1991.
30. (a) AMPAC 5.0, 1994 Semichem: Shawnee, KS, 1994.
31. (b) Holder, A. J.; Ward, R. Abstr. Pap-Am. Chem. Soc. 1998, 216, 174.
32. (c) White, D. A.; Holder, A. J.; Jie, C. Abstr. Pap-Am. Chem. Soc. 1998, 216, 182.
33. (a) Estrin, D.; Hamra, O. Y.; Paglieri, L.; Slep, L.; Olabe, J. Inorg. Chem. 1996, 35, 6832.
34. (b) Estrin, D.; Baraldo, L.; Slep, L.; Barja, B.; Olabe, J.; Paglieri, L.; Corongiu, G. Inorg. Chem. 1996, 35, 3897.
35. Taylor, J. C.; Mueller, M. H.; Hitterman, R. L. Acta Crystallogr. 1974, A26, 559.
36. Bottomley, F.; White, P. S. Acta Crystallogr. 1979, B35, 2193.
37. Bray, M.; Deeth, R.; Paget, V.; Sheen, P. Int. J. Quantum Chem. 1996, 61, 85.
38. (a) Lang, G.; Spartalian, K.; Reed, C. A.; Collman, L. J. Chem. Phys. 1978, 69, 5424.
39. (b) Goff, H.; La Mar, G. N.; Reed, C. A. J. Am. Chem. Soc. 1977, 99, 3641.
40. Estrin, D. A.; Corongiu, G.; Clementi, E. In METECC, Methods and Techniques in Computational Chemistry; Clementi, E., Ed.; Stef: Cagliari, Italy, 1993.
41. Kohn, W.; Sham, L. J. Phys. Rev. 1965, A140, 1133.
42. Becke, A. D. J. Chem. Phys. 1988, 88, 1053.
43. Godbout, N.; Salahub, D. R.; Andzelm, J.; Wimmer, E. Can. J. Chem. 1992, 70, 560.
44. Andzelm, J.; Radzio, E.; Salahub, D. R. J. Comput. Chem. 1985, 6, 520.
45. (a) Sim, F.; Salahub, D. R.; Chin, S.; Dupuis, M. J. Chem. Phys. 1991, 95, 4317.
46. (b) Sim, F.; St.-Amant, A.; Papai, I.; Salahub, D. R. J. Am. Chem. Soc. 1992, 114, 4391.
47. Vosko, S. H.; Wilk, L.; Nusair, M. Can. J. Phys. 1980, 58, 1200.
48. (a) Perdew, P. W. Phys. Rev. 1986, B33, 8800; 1986, B34, 7406 (erratum).
49. (a) Perdew, P. W. Phys. Rev. 1986, B33, 8800; 1986, B34, 7406 (erratum).
50. (b) Becke, A. D. Phys. Rev. 1988, A38, 3098.
51. (a) Elola, M. D.; Laria, D.; Estrin, D. A. J. Phys. Chem. A 1999, 103, 5105.
52. (b) Stanton, R. V.; Little, L. R.; Merz, K. M. J. Phys. Chem. 1995, 99, 17344.
53. (a) Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765.
54. (b) Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. J. Comput. Chem. 1986, 7, 230.
55. Parr, R. G.; Yang, W. Density-Functional Theory of Atoms and Molecules; Oxford University Press: New York, 1990.
56. (a) Fukui, K. Theory of Orientation and Stereoselection; SpringerVerlag: Berlin, 1975.
57. (b) Fukui, K. Science 1987, 218, 747.
58. (c) Fukui, K.; Yonezawa, T.; Shingu, H. J. Chem. Phys. 1952, 20, 722.
59. (d) Fukui, K.; Yonezawa, T.; Nagata, C.; Shingu, H. J. Chem. Phys. 1954, 22, 1433.
60. Vasquez, G. B.; Ji, X.; Pechik, I.; Fronticelli, C.; Gilliland, G. L. X-ray Structure of Alpha-Oxy, Beta-(C1 12g)deoxy Human Hemoglobin. PDB Code: 1GBV. Protein Data Bank at the National Library of Medicine. URL: http://www.ncbi.nlm.nih.gov.
61. (a) Collman, J. P.; Sorrell, T. N.; Hoffman, B. M. J. Am. Chem. Soc. 1975, 97, 913.
62. (b) Collman, J. P.; Sorrell, T. N.; Hodgson, K. O.; Kulshrestha, A. K.; Strouse, C. E. J. Am. Chem. Soc. 1977, 99, 5180.
63. (c) English, D. R.; Hendrickson, D. N.; Suslick, K. S.; Eigenbrot, C. W.; Scheldt, W. R. J. Am. Chem. Soc. 1984, 106, 7258.
64. Scheidt, W. R.; Ellison, M. K. Acc. Chem. Res. 1999, 32, 350.
65. Enemark, J. H.; Feltham, R. D. Coord. Chem. Rev. 1974, 13, 339.
66. (a) Hoffmann, R.; Chen, M. M. L.; Elian, M.; Rossi, A. R.; Mingo, D. M. P. Inorg. Chem. 1974, 13, 2666.
67. (b) Wayland, B. B.; Olson, L. W. J. Am. Chem. Soc. 1974, 96, 6037.
68. Wong, M. W.; Wiberg, K. B.; Frisch, M. J. J. Am. Chem. Soc. 1992, 114, 1645.
69. Hoshino, M.; Maeda, M.; Konishi, R.; Seki, H.; Ford, P. J. Am. Chem. Soc. 1996, 118, 5702.
70. Ziegler, T. Chem. Rev. 1991, 91, 651.
71. (a) Li, H.; Poulos, T. L. Acta Crystallogr. 1995, D51, 21.
72. (b) Schlichting, I.; Jung, C.; Schulze, H. FEBS Lett. 1997, 3, 253.
73. (c) Sundaramoorthy, M.; Terrer, J.; Poulos, T. L. Structure (London) 1995, 3, 1367.
74. (a) Peng, S. M.; Ibers, J. A. J. Am. Chem. Soc. 1976, 98, 8032.
75. (b) Scheidt, W. R.; Prisse, M. E. J. Am. Chem. Soc. 1975, 97, 17.
76. (c) Jameson, G. B.; Rodley, G. A.; Robinson, W. T.; Gagne, R. R.; Reed, C. A.; Collman, J. P. Inorg. Chem. 1978, 17, 850.
77. Momenteau, M.; Reed, C. A. Chem. Rev. 1994, 94, 659.