Dissecting the thermodynamics and cooperativity of ligand binding in cytochrome P450eryF

Journal of the American Chemical Society

Volumn 129, Issue 7, 2007, Pages 2015-2024

  Muralidhara, B K ^a   Negi, Surendra S ^a   Halpert, James R ^a  

^a University of Texas Medical Branch School of Medicine   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENTROPY-ENTHALPY COMPENSATION; ISOTHERMAL TITRATION CALORIMETRY (ITC); LIGAND BINDING;

CATALYST ACTIVITY; COMPUTER SIMULATION; HYDROPHOBICITY; MOLECULAR STRUCTURE; PARAMETER ESTIMATION; THERMODYNAMICS; TITRATION;

ENZYMES;

1 PYRENEBUTANOL; 4 (4 CHLOROPHENYL)IMIDAZOLE; 4 PHENYLPYRIDINE; 9 AMINOPHENANTHRENE; ALPHA NAPHTHOFLAVONE; BUTANOL; CYTOCHROME P450; CYTOCHROME P450ERYF; IMIDAZOLE DERIVATIVE; PHENANTHRENE DERIVATIVE; PYRENE DERIVATIVE; PYRIDINE DERIVATIVE; UNCLASSIFIED DRUG;

ALLOSTERISM; ARTICLE; BINDING AFFINITY; BINDING SITE; ENTHALPY; ENTROPY; HYDROPHOBICITY; ISOTHERMAL TITRATION CALORIMETRY; LIGAND BINDING; MOLECULAR RECOGNITION; SIMULATION; STOICHIOMETRY; THERMODYNAMICS;

BINDING SITES; BINDING, COMPETITIVE; CALORIMETRY; COMPUTER SIMULATION; CYTOCHROME P-450 ENZYME SYSTEM; KINETICS; LIGANDS; MIXED FUNCTION OXYGENASES; MODELS, MOLECULAR; SPECTROPHOTOMETRY, ULTRAVIOLET; THERMODYNAMICS;

EID: 33847326238     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja066303w     Document Type: Article

References (62)

1. Poulos, T. L.; Johnson, E. F. Cytochrome P450: Structure, Mechanism and Biochemistry, 3rd ed.; Ortiz de Montellano, P. R., Ed.; Plenum Publishers: New York, 2005; pp 87-114.
2. Cupp-Vickery, J.; Anderson, R.; Hatziris, Z. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 3050-3055.
3. de Groot, M. J. Drug Discovery Today 2006, 11, 601-606.
4. Scott, E. E.; He, Y. A.; Wester, M. R.; White, M. A.; Chin, C. C.; Halpert, J. R.; Johnson, E. F.; Stout, D. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13196-13201.
5. Scott, E. E.; White, M. A.; He, Y. A.; Johnson, E. F.; Stout, D.; and Halpert, J. R. J. Biol. Chem. 2004, 279, 27294-27301.
6. Wester, M. R.; Yano, J. K.; Schoch, G. A.; Yang, C.; Griffin, K. J.; Stout, C. D.; Johnson, E. F. J. Biol. Chem. 2004, 279, 35630-35637.
7. Williams, P. A.; Cosme, J.; Angove, H. C.; Vinkovic, D. M.; Jhoti, H. Nature 2003, 424, 464-468.
8. Williams, P. A.; Cosme, J.; Vinkovic, D. M.; Ward, A.; Angove, H. C.; Day, P. J.; Vonrhein, C.; Tickle, I. J.; Jhoti, H. Science 2004, 305, 683-686.
9. Zhao, Y.; White, W. A.; Muralidhara, B. K.; Sun, L.; Halpert, J. R.; Stout, C. D. J. Biol. Chem. 2006, 281, 5973-5981.
10. Shou, M.; Grogan, J.; Mancewicz, J. A.; Krausz, K. W.; Gonzalez, F. J.; Gelboin, H. V.; Korzekwa, K. R. Biochemistry 1994, 33, 6450-6455.
11. Korzekwa, K. R.; Krishnamachary, N.; Shou, M.; Ogai, A.; Parise, R. A.; Rettie, A. E.; Gonzalez, F. J.; Tracy, T. S. Biochemistry 1998, 37, 4137-4147.
12. Ueng, Y. F.; Kuwabara, T.; Chun, Y. J.; Guengerich, F. P. Biochemistry 1997, 36, 370-381.
13. Miller, G. P.; Guengerich, F. P. Biochemistry 2001, 40, 7262-7272.
14. Atkins, W. M. Drug Discovery Today 2004, 9, 478-484.
15. Harlow, G. R.; Halpert, J. R. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 6636-6641.
16. Schrag, M. L.; Wienkers, L. C. Drug Metab. Dispos. 2000, 28, 1198-1201.
17. Atkins, W. M.; Wang, R. W.; Lu, A. Y. H. Chem. Res. Toxicol. 2001, 14, 338-347.
18. Roberts, A. G.; Campbell, A. P.; Atkins, W. M. Biochemistry 2005, 44, 1353-1366.
19. Baas, B. J.; Denisov, I. G.; Sligar, S. G. Arch. Biochem. Biophy.s. 2004, 430, 218-228.
20. Davydov, D. R.; Fernando, F.; Baas, B. J.; Sugar, S. G.; Halpert, J. R. Biochemistry 2005, 44, 13902-13913.
21. Koley, A. P.; Buters, J. T.; Robinson, R. C.; Markowitz, A.; Friedman, F. K. J. Biol. Chem. 272, 3149-3159.
22. Davydov, D. R.; Fernando, F.; Halpert, J. R. Biophys. Chem. 2006, 123, 77-83.
23. Fernando, F.; Halpert, J. R.; Davydov, D. R. Biochemistry 2006, 45, 4199-4209.
24. Khan, K. K.; Liu, H.; Halpert, J. R. Drug Metab. Dispos. 2003, 31, 356-359.
25. Khan, K. K.; He, Y. A.; He, Y. Q.; Halpert, J. R. Chem. Res. Toxicol. 2002, 15, 843-853.
26. Davydov, D. R.; Kumar, S.; Halpert, J. R. Biochem. Biophys. Res. Commun. 2002, 294, 806-812.
27. Davydov, D. R.; Botchkareva, A. E.; Kumar, S.; Ile, Y. Q.; Halpert, J. R. Biochemistry 2004, 43, 6475-6485.
28. Davydov, D. R.; Botchkareva, A. E.; Davydova, N. E.; Halpert, J. R. Biophys. J. 2005, 89, 418-432.
29. Roberts, A. G.; Diaz, M. D.; Lampe, J. N.; Shireman, L. M.; Grinstead, J. S.; Dabrowski, M. J.; Pearson, J. T.: Bowman, M. K.; Atkins, W. M.; Campbell, A. P. Biochemistry 2006, 45, 1673-1684
30. Leavitt, S.; Freire, E. Curr. Opin. Struct. Biol. 2001, 11, 560-566.
31. Lopez, M. M.; Makhatadze, G. I. Methods Mol. Biol. 2002, 173, 121-126.
32. Weber, P. C.; Salemme, F. R. Curr. Opin. Struct. Biol. 2003, 13, 115-121.
33. Muralidhara, B. K.; Wittung-Stafshede, P. Biochemistry 2003, 42, 13074-13080.
34. Muralidhara, B. K.; Chen, M.; Ma, J.; Wittung-Stafshede, P. J. Mol. Biol. 2005, 349, 89-97.
35. Ohtaka, H.; Velazquez-Compoy, A.; Xie, D.; Freire, E. Protein Sci. 2002, 11, 1908-1916.
36. Turnbull, W. B.; Daranas, A. H. J. Am. Chem. Soc. 2003, 125, 14859-14866.
37. Muralidhara, B. K.; Wittung-Stafshede, P. Biochemistry 2004, 43, 12855-12864.
38. Muralidhara, B. K.; Negi, S.; Chin, C. C.; Braun, W.; Halpert, J. R. J. Biol. Chem. 2006, 281, 8051-8061.
39. Lebowitz, J.; Lewis, M. S.; Schuck, P. Protein Sci. 2002, 11, 2067-2079.
40. Wiseman, T.; Williston, S.; Brandts, J. F.; Lin, L-N. Anal. Biochem. 1989, 179, 131-137.
41. Dam, T. K.; Roy, R.; Page, D.; Brewer, C. F. Biochemistry 2002, 41, 1359-1363.
42. Sali, A.; Blundell, T. L. J. Mol. Biol. 1993, 234, 779-815.
43. Kalé, K.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. J. Comput. Phys. 1999, 151, 283-312.
44. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Bellew, R. K.; Olson, A. J. J. Comput. Chem. 1998, 19, 1639-1662.
45. Helms, V.; Wade, R. C. Biophys. J. 1995, 69, 810-824.
46. van Aalten, D. M.; Bywater, R.; Findlay, J. B.; Hendlich, M.; Hooft, R. W.; Vriend, G. J. Comput. Aided Mol. Des. 1996, 10, 255-262.
47. Cupp-Vickery, J. R.; Garcia, C.; Hofacre, A.; McGee-Estrada, K. J Mol. Biol. 2001, 311, 101-110.
48. Nagano, S.; Cupp-Vickery, J. R.; Poulos, T. L. J. Biol. Chem. 2005, 280, 22102-22107.
49. Yoon, M. Y.; Campbell, A. P.; Atkins, W. M. Drug Metab. Rev. 2004, 36, 219-230.
50. Hutzler, J. M.; Hauer, M. J.; Tracy, T. S. Drug Metab. Dispos. 2001, 29, 1029-1034.
51. Luque, I.; Freire, E. PROTEINS: Str. Fun. Gen. 2002, 49, 181-190.
52. Raag, R.; Poulos, T. L. Biochemistry 1989, 28, 917-922.
53. Raag, R.; Poulos, T. L. Biochemistry 1991, 30, 2674-2684.
54. Fraczkiewicz, R.; Braun, W. J. Comp. Chem. 1998, 19, 319-333.
55. Dabrowski, M. J.; Schrag, M. L.; Wienkers, L. C.; Atkins, W. M. J. Am. Chem. Soc. 2002, 124, 11866-11867.
56. Jushchyshyn, M.; Hutzler, M. J.; Schrag, M. L.; Wienkers, L. C. Arch. Biochem. Biophys. 2005, 438, 21-28.
57. Domanski, T. L.; He, Y. A.; Khan, K. K.; Roussel, F.; Wang, Q.; Halpert, J. R. Biochemistry 2001, 40, 10150-10160.
58. He, Y. A.; Roussel, F.; Halpert, J. R. Arch. Biochem. Biophys. 2003, 409, 92-101.
59. Tsalkova, T. N.; Davydova, N.; Halpert, J. R.; Davydov, D. R. Biochemistry 2007, 46, 106-119.
60. Wade R. C.; Gabdoulline R. R.; Ludemann, S. K.; Lounnas, V. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 5942-5949.
61. Davydov, D. R.; Hui Bon Hoa, G.; Peterson, J. A. Biochemistry 1999, 38, 751-761.
62. Delano, W. L. The PyMol User's Manual; Delano Scientific: San Carlos, CA, 2004.