Evaluation of comparative cytochrome P450 2B4 model by photoaffinity labeling

General Physiology and Biophysics

Volumn 23, Issue 4, 2004, Pages 467-488

  Hodek, Petr ^a   Sopko, B ^a   Antonovic L ^b   Sulc M ^a,c   Novak P ^c   Strobel, H W ^b  

^a CHARLES UNIVERSITY   (Czech Republic)

^b UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

^c INSTITUTE OF MICROBIOLOGY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME P450 2B; CYTOCHROME P450 2C; HEME; IRON;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; HYDROXYLATION; NONHUMAN; PHOTOAFFINITY LABELING; PREDICTION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; SPECTROSCOPY; STRUCTURE ANALYSIS; VALIDATION PROCESS; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ARYL HYDROCARBON HYDROXYLASES; BINDING SITES; COMPUTER SIMULATION; ISOENZYMES; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR PROBE TECHNIQUES; MOLECULAR SEQUENCE DATA; PHOTOAFFINITY LABELS; PROTEIN BINDING; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY, AMINO ACID; SPECTRUM ANALYSIS;

BACTERIA (MICROORGANISMS); MAMMALIA; ORYCTOLAGUS CUNICULUS;

EID: 14844363869     PISSN: 02315882     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (62)

1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. (1990): Basic local alignment search tool. J. Mol. Biol. 215, 403-410
2. Antonovič L., Hodek P., Smrček S., Novák P., Šulc M., Strobel H. W. (1999): Heterobifunctional photoaffinity probes for cytochrome P450 2B. Arch. Biochem. Biophys. 370, 208-215
3. Bayley H. (1983): Photogenerated reagents in biochemistry. In: Laboratory Techniques in Biochemistry and Molecular Biology (Eds. T. S. Work and R. H. Burdon), pp. 168-180, (2nd ed.), Elsevier Science, Amsterdam
4. Brooks B. R., Bruccoleri R. E., Olafson B. D., States D. J., Swaminathan S., Karplus M. (1983): CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4 187-217
5. Chang Y.-T., Stiffelman O. B., Vakser I. A., Loew G. H., Bridges A., Waskell L. (1997): Construction of a 3D model of cytochrome P450 2B4. Protein Eng. 10, 119-129
6. Conley A., Mapes S., Corbin C. J., Greger D., Walters K., Trant J., Graham S. (2001): A comparative approach to structure-function studies of mammalian aromatases. J. Steroid. Biochem. Mol. Biol. 79 289-297
7. Cupp-Vickery J. R., Poulos T. L. (1995): Structure of cytochrome P450eryF involved in erythromycin biosynthesis. Nat. Struct. Biol. 2, 144-153
8. Cvrk T., Strobel H. W. (1998): Photoaffinity labeling of cytochrome P4501A1 with azidocumene: identification of cumene hydroperoxide binding region. Arch. Biochem. Biophys. 349, 95-104
9. Cvrk T., Hodek P., Strobel H. W. (1996): Identification and characterization of cytochrome P4501A1 amino acid residues interacting with a radiolabeled photoaffinity diazido-benzphetamine analogue. Arch. Biochem. Biophys. 330, 142-152
10. Dai R., Pincus M. R., Friedman F. K. (1998): Molecular modeling of cytochrome P450 2B1: mode of membrane insertion and substrate specificity. J. Protein Chem. 17, 121-129
11. Domanski T. L., Halpert J. R. (2001): Analysis of mammalian cytochrome P450 structure and function by site-directed mutagenesis. Curr. Drug Metab. 2, 117-137 (and references therein)
12. Ekins S., Wrighton S. A. (1999): The role of CYP2B6 in human xenobiotic metabolism. Drug Metab. Rev. 31, 719-754
13. Ekins S., De Groot M. J., Jones J. P. (2001): Pharmacophore and three-dimensional quantitative structure activity relationship methods for modeling cytochrome P450 active sites. Drug Metab. Dispos. 29, 936-944
14. Fiser A., Do R. K., Sali A. (2000): Modeling of loops in protein structures. Protein Sci. 9, 1753-1773
15. Gartner C. A. (2003): Photoaffinity ligands in the study of cytochrome P450 active site structure. Curr. Med. Chem. 10, 671-689
16. Guengerich F. P. (1977): Separation and purification of multiple forms of microsomal cytochrome P-450. Activities of different forms of cytochrome P-450 towards several compounds of environmental interest. J. Biol. Chem. 252, 3970-3979
17. Guex N., Peitsch M. C. (1997): SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18, 2714-2723
18. Hasemann C. A., Ravichandran K. G., Peterson J. A., Deisenhofer J. (1994): Crystal structure and refinement of cytochrome P450terp at 2.3 Å resolution. J. Mol. Biol. 236, 1169-1185
19. Haugen D. A., Coon M. J. (1976): Properties of electrophoretically homogeneous phenobarbital-inducible and beta-naphthoflavone-inducible forms of liver microsomal cytochrome P-450. J. Biol. Chem. 251, 7929-7939
20. Hodek P., Strobel H. W. (1994): Synthesis and characterization of azidobenzphetamine analogs of the cytochrome-P450 substrate benzphetamine. Bioorg. Chem. 22, 253-267
21. Hodek P., Janščák P., Anzenbacher P., Burkhard J., Janků J., Vodička, L. (1988): Metabolism of diamantane by rat liver microsomal cytochromes P-450. Xenobiotica 18, 1109-1118
22. Hodek P., Burkhard J., Janků J. (1995): Probing the cytochrome P-450 2B1 active site with diamantoid compounds. Gen. Physiol. Biophys. 14, 225-239
23. Ito S., Matsuoka T., Watanabe I., Kagasaki T., Serizawa N., Hata T. (1999): Crystallization and preliminary X-ray diffraction analysis of cytochrome P450sca-2 from Streptomyces carbophilus involved in production of pravastatin sodium, a tissue-selective inhibitor of HMG-CoA reductase. Acta Crystallogr., D. Biol. Crystallogr. 55, 1209-1211
24. Kent U. M., Juschyshyn M. I., Hollenberg P. F. (2001): Mechanism-based inactivators as probes of cytochrome P450 structure and function. Curr. Drug Metab. 2, 215-243
25. Kirton S. B., Baxter C. A., Sutcliffe M. J. (2002): Comparative modelling of cytochromes P450. Adv. Drug Deliv. Rev. 54 385-406
26. Laemmli U. K. (1970): Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680-685
27. Laskowski R. A., MacArthur M. W., Moss D. S., Thornton J. M. (1993): PROCHECK - a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283-291
28. Lewis D. F. (1998): The CYP2 family: models, mutants and interactions. Xenobiotica 28, 617-661
29. Lewis D. F. (2002): Homology modelling of human CYP2 family enzymes based on the CYP2C5 crystal structure. Xenobiotica 32, 305-323
30. Leys D., Mowat C. G., McLean K. J., Richmond A., Chapman S. K., Walkinshaw M. D., Munro A. W. (2003): Atomic structure of Mycobacterium tuberculosis CYP121 to 1.06 Å reveals novel features of cytochrome P450. J. Biol. Chem. 278, 5141-5147
31. Morris G. M., Goodsell D. S., Halliday R. S., Huey R., Hart W. E., Belew R. K., Olson A. J. (1998): Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comp. Chem. 19, 1639-1662
32. Nelson D. R., Strobel H. W. (1988): On the membrane topology of vertebrate cytochrome P-450 proteins. J. Biol. Chem. 263, 6038-6050
33. Ohnishi T., Miura S., Ichikawa Y. (1993): Photoaffinity labeling of cytochrome P-45011 beta with methyltrienolone as a probe for the substrate binding region. Biochim. Biophys. Acta 1161, 257-264
34. Omura T., Sato R. (1964): The carbon monoxide-binding pigment of liver microsomes. I. Evidence for its hemoprotein nature. J. Biol. Chem. 239, 2370-2378
35. Park S. Y., Shimizu H., Adachi S., Nakagawa A., Tanaka I., Nakahara K., Shoun H., Obayashi E., Nakamura H., Iizuka T., Shiro Y. (1997): Crystal structure of nitric oxide reductase from denitrifying fungus Fusarium. oxysporum. Nat. Struct. Biol. 4, 827-832
36. Paulsen M. D., Bass M. B., Ornstein R. L. (1991): Analysis of active site motions from a 175 picosecond molecular dynamics simulation of camphor-bound cytochrome P450cam. J. Biomol. Struct. Dyn. 9, 187-203
37. Peterson J. A., Graham S. E. (1998): A close family resemblance: the importance of structure in understanding cytochromes P450. Structure 6, 1079-1085
38. Podust L. M., Poulos T. L., Waterman M. R. (2001): Crystal structure of cytochrome P450 14alpha-sterol demethylase (CYP51) from Mycobacterium tuberculosis in complex with azole inhibitors. Proc. Natl. Acad. Sci. U.S.A. 98, 3068-3073
39. Podust L. M., Kim Y., Arase M., Neely B. A., Beck B. J., Bach H., Sherman D. H., Lamb D. C., Kelly S. L., Waterman M. R. (2003): The 1.92-Å structure of Streptomyces coelicolor A3(2) CYP154C1. A new monooxygenase that functionalizes macrolide ring systems. J. Biol. Chem. 278, 12214-12221
40. Porter T. D., Coon M. J. (1991): Cytochrome P-450. Multiplicity of isoforms, substrates, and catalytic and regulatory mechanisms. J. Biol. Chem. 266, 13469-13472
41. Poulos T. L., Howard A. J. (1987): Crystal structures of metyrapone- and phenylimidazole-inhibited complexes of cytochrome P-450cam. Biochemistry 26, 8165-8174
42. Poulos T. L., Finzel B. C., Gunsalus I. C., Wagner G. C., Kraut J. (1985): The 2.6-Å crystal structure of Pseudomonas putida cytochrome P-450. J. Biol. Chem. 260, 16122-16130
43. Poulos T. L., Finzel B. C., Howard A. J. (1987): High-resolution crystal structure of cytochrome P450cam. J. Mol. Biol. 195, 687-700
44. Raag R., Li H., Jones B. C., Poulos T. L. (1993): Inhibitor-induced conformational change in cytochrome P-450CAM. Biochemistry 32, 4571-4578
45. Ravichandran K. G., Boddupalli S. S., Hasermann C. A., Peterson J. A., Deisenhofer J. (1993): Crystal structure of hemoprotein domain of P450BM-3, a prototype for microsomal P450's. Science 261, 731-736
46. Sali A., Blundell T. L. (1993): Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815
47. Schenkman J. B., Remmer H., Estabrook R. W. (1967): Spectral studies of drug interaction with hepatic microsomal cytochrome. Mol. Pharmacol. 3, 113-123
48. Schlichting I., Berendzen J., Chu K., Stock A. M., Maves S. A., Benson D. E., Sweet R. M., Ringe D., Petsko G. A., Sligar S. G. (2000): The catalytic pathway of cytochrome p450cam at atomic resolution. Science 287, 1615-1622
49. Scott E. E., He Y. Q., Halpert J. R. (2002): Substrate routes to the buried active site may vary among cytochromes P450: mutagenesis of the F-G region in P450 2B1. Chem. Res. Toxicol. 15, 1407-1413
50. Scott E. E., He Y. Q., Wester M. R., White M. A., Chin C. C., Halpert J. R., Johnson E. F., Stout C. D. (2003): A open conformation of mammalian cytochrome P450 2B4 at 1.6-Å resolution. Proc. Natl. Acad. Sci. U.S.A. 100, 13196-13201
51. Sevrioukova I. F., Li H., Zhang H., Peterson J. A., Poulos T. L. (1999): Structure of a cytochrome P450-redox partner electron-transfer complex. Proc. Natl. Acad. Sci. U.S.A. 96, 1863-1868
52. Shevchenko A., Wilm M., Vorm O., Mann M. (1996): Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal. Chem. 68, 850-858
53. Szklarz G. D., Ornstein R. L., Halpert J. R. (1994): Application of 3-dimensional homology modeling of cytochrome P450 2B1 for interpretation of site-directed mutagenesis results. J. Biomol. Struct. Dyn. 12, 61-78
54. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. (1997): The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882
55. Wang Q., Halpert J. R. (2002): Combined three-dimensional quantitative structure-activity relationship analysis of cytochrome P450 2B6 substrates and protein homology modeling. Drug Metab. Dispos. 30 86-95
56. Wester M. R., Johnson E. F., Marques-Soares C., Dijols S., Dansette P. M., Mansuy D., Stout C. D. (2003): Structure of mammalian cytochrome P450 2C5 complexed with diclofenac at 2.1 Å resolution: evidence for an induced fit model of substrate binding. Biochemistry 42, 9335-9345
57. Wiechelman K. J., Braun R. D., Fitzpatrick J. D. (1988): Investigation of the bicinchoninic acid protein assay: identification of the groups responsible for color formation. Anal. Biochem. 175, 231-237
58. Williams P. A., Cosme J., Sridhar V., Johnson E. F., McRee D. E. (2000a): Mammalian microsomal cytochrome P450 monooxygenase: structural adaptations for membrane binding and functional diversity. Mol. Cell 5, 121-131
59. Williams P. A., Cosme J., Sridhar V., Johnson E. F., McRee D. E. (2000b): Microsomal cytochrome P450 2C5: comparison to microbial P450s and unique features. J. Inorg. Biochem. 81, 183-190
60. Williams P. A., Cosme J., Ward A., Angove H. C., Vinkovic D. M., Jhoti H. (2003): Crystal structure of human cytochrome P450 2C9 with bound warfarin. Nature 424, 464-468
61. Yano J. K., Koo L. S., Schuller D. J., Li H., Ortiz de Montellano P. R., Poulos T. L. (2000): Crystal structure of a thermophilic cytochrome P450 from the archaeon Sulfolobus solfataricus. J. Biol. Chem. 275, 31086-31092
62. Zerbe K., Pylypenko, O., Vitali F., Zhang W., Rouset S., Heck M., Vrijbloed J. W., Bischoff D., Bister B., Sussmuth R. D., Pelzer S., Wohlleben W., Robinson J. A., Schlichting I. (2002): Crystal structure of OxyB, a cytochrome P450 implicated in an oxidative phenol coupling reaction during vancomycin biosynthesis. J. Biol. Chem. 277, 47476-47485