Molecular modeling of mammalian cytochromes P450: Application of study enzyme function

Vitamins and Hormones

Volumn 58, Issue , 2000, Pages 53-87

  Szklarz, Grazyna D ^a   Graham, Sandra E ^b   Paulsen, Mark D ^c  

^a WEST VIRGINIA UNIVERSITY   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^c NORTHERN MICHIGAN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME P450;

AMINO ACID SEQUENCE; ANIMAL; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; MOLECULAR GENETICS; PHYSIOLOGY; REVIEW; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; CYTOCHROME P-450 ENZYME SYSTEM; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; SEQUENCE HOMOLOGY;

EID: 0033630119     PISSN: 00836729     EISSN: None     Source Type: Book Series    
DOI: 10.1016/s0083-6729(00)58021-2     Document Type: Review

References (67)

1. 5 augments the 17,20-lyase activity of human P450c17 without direct electron transfer J. Biol. Chem. 273 1998 3158 3165
2. H.-J. Bohm LUDI: Rule-based automatic design of new substituents for enzyme-inhibitor leads J. Comput.-Aided Mol. Des. 6 1992 593 606
3. A. Bridges L. Gruenke Y.-T. Chang I.A. Vakser G. Loew L. Waskell Identification of the binding sites on cytochrome P450 2B4 for cytochrome b5 and cytochrome P450 reductase J. Biol. Chem. 273 1998 17036 17049
4. Y.-T. Chang O.B. Stiffelman I.A. Vakser G.H. Loew A. Bridges L. Waskell Construction of a 3D model of cytochrome P450 2B4 Protein Eng. 10 1997 119 129
5. J.R. Cupp-Vickery T.L. Poulos Structure of cytochrome P450eryF involved in erythromycin biosynthesis Struct. Biol. 2 1995 144 153
6. M.J. de Groot N.P.E. Vermeulen J.D. Kramer F.A.A. van Acker G.M. Donne-Op den Kelder A three-dimensional protein model for human cytochrome P450 2D6 based on the crystal structures of P450 101, P450 102, and P450 108 Chem. Res. Toxicol. 9 1996 1079 1091
7. J.J. De Voss P.R. Ortiz de Montellano Computer-assisted, structure-based prediction of substrates for cytochrome P450cam J. Am. Chem. Soc. 117 1995 4185 4186
8. T.L. Domanski J. Liu G.R. Harlow J.R. Halpert Analysis of four residues within substrate recognition site 4 of human cytochrome P450 3A4: Role in steroid hydroxylase activity and α-naphthoflavone stimulation Arch. Biochem. Biophys. 350 1998 223 232
9. D. Eisenberg R. Luthy J. Bowie VERIFY3D: Assessment of protein models with three-dimensional profiles C.W. Carter Jr. R.M. Sweet Methods in Enzymology Vol. 277 1997 Academic Press San Diego, CA 396 404
10. G.D. Fasman The development of the prediction of protein structure G.D. Fasman Prediction of Protein Structure and Principles of Protein Conformation 1989 Plenum New York 193 301
11. D.S. Goodsell G.M. Morris A.J. Olson Automated docking of flexible ligands: applications of AutoDock J. Mol. Recognition 9 1996 1 5
12. O. Gotoh Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences J. Biol. Chem. 267 1992 83 90
13. S. Graham-Lorence J.A. Peterson E.R. Simpson A three-dimensional model of aromatase cytochrome P450 Protein Sci. 4 1995 1065 1080
14. S. Graham-Lorence G. Truan J.A. Peterson J.R. Falck S. Wei C. Helvig J.H. Capdevila An active site substitution F87V, converts cytochrome P450 BM-3 into a regio- and stereoselective (14S,15R_-arachidonic acid epoxygenase J. Biol. Chem. 272 1997 1127 1135
15. L.M. Gregoret F.E. Cohen A novel method for the rapid evaluation of packing in protein structures J. Mol. Biol. 211 1990 959 974
16. F.P. Guengerich Metabolic reactions: Types of reactions of cytochrome P450 enzymes Handb. Exp. Pharmacol. 105 1993 89 103
17. G.R. Harlow J.R. Halpert Alanine-scanning mutagenesis of a putative substrate recognition site in human cytochrome P450 3A4. Role of residues 210 and 211 in flavonoid activation and substrate specificity J. Biol. Chem. 272 1997 5396 5402
18. G.R. Harlow J.R. Halpert Analysis of human cytochrome P450 3A4 cooper-activity: Construction and characterization of a site-directed mutant that displays hyperbolic steroid hydroxylation kinetics Proc. Natl. Acad. Sci. U.S.A. 95 1998 6636 6641
19. terp at 2.3 Å resolution J. Mol. Biol. 236 1994 1169 1185
20. C.A. Hasemann R.G. Kurumbail S.S. Boddupalli J.A. Peterson J. Deisenhofer Structure and function of cytochromes P450: A comparative analysis of three crystal structures Structure 3 1995 41 62
21. K. He Y.A. He G.D. Szklarz J.R. Halpert M.A. Correia Secobarbital-mediated inactivation of cytochrome P450 2B1 and its active site mutants. Partitioning between heme and protein alkylation and epoxidation J. Biol. Chem. 271 1996 25864 25872
22. Y.A. He Y.Q. He G.D. Szklarz J.R. Halpert Identification of three key residues in substrate recognition site 5 of human cytochrome P450 3A4 by cassette and site-directed mutagenesis Biochemistry 36 1997 8831 8839
23. Y.Q. He G.R. Harlow G.D. Szklarz J.R. Halpert Structural determinants of progesterone hydroxylation by cytochrome P450 2B5: The role of nonsubstrate recognition site residues Arch. Biochem. Biophys. 350 1998 333 339
24. U.M. Kent I.H. Hanna G.D. Szklarz A.N.D. Vaz J.R. Halpert J.R. Bend P.F. Hollenberg Significance of glycine 478 in the metabolism of N -benzyl-1-aminobenzotriazole to reactive intermediates by cytochrome P450 2B1 Biochemistry 36 1997 11707 11716
25. Y. Kobayashi X. Fang G.D. Szklarz J.R. Halpert Probing the active site of cytochrome P450 2B1: Metabolism of 7-alkoxycoumarins by the wild type and five site-directed mutans Biochemistry 37 1998 6679 6688
26. L.M.H. Koymans N.P.E. Vermeulen A. Baarslag G.M. Donne-Op den Kelder A preliminary 3D model for cytochrome P450 2D6 constructed by homology model building J. Comput.-Aided Mol. Des. 7 1993 281 289
27. I.D. Kuntz J.M. Blaney S.J. Oatley R. Langridge T.E. Ferrin A geometric approach to macromolecule-ligand interactions J. Mol. Biol. 161 1982 269 288
28. C.A. Laughton M.J.J.M. Zvelebil S.J. Neidle A detailed molecular model for human aromatase J. Steroid Biochem. Mol. Biol. 44 1993 399 407
29. B. Lee F.M. Richard The interpretation of protein structures: Estimation of static accessibility J. Mol. Biol. 55 1971 379 400
30. bm3) Xenobiotica 25 1995 333 366
31. D.F.V. Lewis B.G. Lake Molecular modeling of members of the P4502A subfamily: Application to studies of enzyme specificity Xenobiotica 25 1995 585 598
32. D.F.V. Lewis B.G. Lake Molecular modeling of CYP1A subfamily members based on an alignment with CYP102: Rationalization of CYP1A substrate specificity in terms of active site amino acid residues Xenobiotica 26 1996 723 753
33. O. Lichtarge H.R. Bourne F.E. Cohen An evolutionary trace method defines binding surfaces common to protein families J. Mol. Biol. 257 1996 342 358
34. αβγ binding surfaces support a model of the G protein-receptor complex Proc. Natl. Acad. Sci. U.S.A. 93 1996 7507 7511
35. J.J. Lozano E. Lopez-de-Brinas N.B. Centeno R. Guigo F. Sanz Three-dimensional modeling of human cytochrome P450 1A2 and its interaction with caffeine and MeIQ J. Comput.-Aided Mol. Des. 11 1997 395 408
36. 450 2D6 based on homology modeling and NMR studies of substrate binding Biochemistry 35 1996 4540 4550
37. A. Muller J.J. Muller Y.A. Muller H. Uhlmann R. Bernhardt U. Heinemann New aspects of electron transfer revealed by the crystal structure of a truncated bovine adrenodoxin, Adx(4–108) Structure 6 1998 269 280
38. L.O. Narhi A.J. Fulco Characterization of a catalytically self-sufficient 119,000-dalton cytochrome P-450 monooxygenase induced by barbiturates in Bacillus megaterium J. Biol. Chem. 261 1986 7160 7169
39. D.R. Nelson L. Koymans T. Kamataki J.J. Stegeman R. Feyereisen D.J. Waxman M.R. Waterman O. Gotoh M.J. Coon R.W. Estabrook I.C. Gunsalus D.W. Nebert P450 superfamily: Update on new sequences, gene mapping, accession numbers and nomenclature Pharmacogenetics 6 1996 1 42
40. S.Y. Park H. Shimizu S. Adachi A. Nakagawa I. Tanaka K. Nakahara H. Shoun E. Obayashi H. Nakamura T. Iizuka Y. Shiro Crystal structure of nitric oxide reductase from denitrifying fungus Fusarium oxysporum Nat. Struct. Biol. 4 1997 827 832
41. cam Proteins 11 1991 184 204
42. M.D. Paulsen R.L. Ornstein Predicting the product specificity and coupling of cytochrome P450cam J. Comput.-Aided Mol. Des. 6 1992 449 460
43. M.D. Paulsen R.L. Ornstein Binding free energy calculations for P450cam-substrate complexes Protein Eng. 9 1996 567 571
44. M.D. Paulsen D. Filipovic S.G. Sligar R.L. Ornstein Controlling the regiospecificity and coupling of cytochrome P450cam: T185F mutant increases coupling and abolishes 3-hydroxynorcamphor product Protein Sci. 2 1993 357 365
45. M.D. Paulsen J.I. Manchester R.L. Ornstein Using molecular modeling and molecular dynamics simulations to predict P450 oxidation products E.F. Johnson M.R. Waterman Methods in Enzymology Vol. 272 1996 Academic Press Sam Diego, CA 347 357
46. J.A. Peterson S.E. Graham A close family resemblance: The importance of structure in understanding cytochromes P450 Structure 6 1998 1079 1085
47. T.L. Poulos B.C. Finzel I.C. Gunsalus G.C. Wagner J. Kraut The 2.6-Å crystal structure of Pseudomonas putida cytochrome P450 J. Biol. Chem. 260 1985 16122 16130
48. T.L. Poulos B.C. Finzel A.J. Howard High-resolution crystal structure of cytochrome P450cam J. Mol. Biol. 195 1987 687 700
49. K.G. Ravichandran S.S. Boddupalli C.A. Hasemann J.A. Peterson J. Deisenhofer Crystal structure of hemoprotein domain of P450BM-3, a prototype for microsomal P450's Science 261 1993 731 736
50. I. Sevrioukova G. Truan J.A. Peterson Reconstitution of the fatty acid hydroxylase activity of cytochrome P450BM-3 utilizing its functional domains Biochemistry 35 1996 7528 7535
51. I. Sevrioukova H. Li H. Zhang J.A. Peterson T. Poulos Structure of a cytochrome P450-redox partner electron transfer complex Proc. Natl. Acad. Sci. U.S.A. 96 1999 1863 1868
52. G.C. Smith D.G. Tew C.R. Wolf Dissection of NADPH-cytochrome P450 oxidoreductase into distinct functional domains Proc. Natl. Acad. Sci. U.S.A. 91 1994 8710 8714
53. S.M. Strobel G.D. Szklarz Y. He M. Foroozesh W.L. Alworth E.S. Roberts P.F. Hollenberg J.R. Halpert Identification of mechanism-based inactivators of cytochromes P450 2B4 and 2B5, and determination of the molecular basis of differential susceptibility J. Pharm. Exp. Ther. 290 1999 445 451
54. G.D. Szklarz J.R. Halpert Use of homology modeling in conjunction with site-directed mutagenesis for analysis of structure-function relationships of mammalian cytochromes P450 Life Sci. 61 1997 2507 2520
55. G.D. Szklarz J.R. Halpert Molecular modeling of cytochrome P450 3A4 J. Comput.-Aided Mol. Des. 11 1997 265 272
56. G.D. Szklarz R.L. Ornstein J.R. Halpert Application of 3-dimensional homology modeling of cytochrome P450 2B1 for interpretation of site-directed mutagenesis results J. Biomol. Struct. Dyn. 12 1994 61 78
57. G.D. Szklarz Y.A. He J.R. Halpert Site-directed mutagenesis as a tool for molecular modeling of cytochrome P450 2B1 Biochemistry 34 1995 14312 14322
58. G.D. Szklarz Y.Q. He K.M. Kedzie J.R. Halpert V.L. Burnett Elucidation of amino acid residues critical for unique activities of rabbit cytochrome P450 2B5 using hybrid enzymes and reciprocal site-directed mutagenesis with rabbit cytochrome P450 2B4 Arch. Biochem. Biophys. 327 1996 308 318
59. 5, its functions, structure and membrane topology Biochimie 77 1995 604 620
60. scc Biochim. Biophys. Acta 1160 1992 281 286
61. C. von Wachenfeldt E.F. Johnson Structures of eukaryotic cytochrome P450 enzymes P.R. Ortiz de Montellano Cytochrome P450: Structure, Mechanism and Biochemistry 2nd ed. 1995 Plenum New York 183 223
62. H. Wang R. Dick H. Yin E. Licad-Coles D.L. Kroetz G. Szklarz G. Harlow J.R. Halpert M.A. Correia Structure-function relationships of human liver cytochromes P450 3A: Aflatoxin B1 metabolism as a probe Biochemistry 37 1998 12536 12545
63. M. Wang D.L. Roberts R. Paschke T.M. Shea B.S.S. Masters J.-J.P. Kim Three-dimensional structure of NADPH-cytochrome P450 reductase: Prototype for FMN- and FAD-containing enzymes Proc. Natl. Acad. Sci. U.S.A. 94 1997 8411 8416
64. S.A. Wrighton J.C. Stevens The human hepatic cytochromes P450 involved in drug metabolism Crit. Rev. Toxicol. 22 1992 1 21
65. H. Yamazaki W.W. Johnson Y.-F. Ueng T. Shimada P.F. Gueugerich Lack of electron transfer from cytochrome b5 in stimulation of catalytic activities of cytochrome P450 3A4. Characterization of a reconstituted cytochrome P450 3A4/NADPH-cytochrome P450 reductase system and studies with apo-cytochrome b5 J. Biol. Chem. 271 1996 27438 27444
66. D. Zhou K.R. Korekwa T. Poulos S. Chen A site-directed mutagenesis study of human placental aromatase J. Biol. Chem. 267 1992 762 768
67. M.J.J.M. Zvelebil C.R. Wolf M.J.E. Sternberg A predicted three-dimensional structure of human cytochrome P450: Implications for substrate specificity Protein Eng. 4 1991 271 282