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Volumn 45, Issue 31, 2006, Pages 9393-9407

Computational solvent mapping reveals the importance of local conformational changes for broad substrate specificity in mammalian cytochromes P450

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; CRYSTALLIZATION; DRUG INTERACTIONS; ENZYMES; FREE ENERGY; PROTEINS; SUBSTRATES;

EID: 33747130722     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi060343v     Document Type: Article
Times cited : (32)

References (39)
  • 2
    • 3943081412 scopus 로고    scopus 로고
    • Structural aspects of ligand binding to and electron transfer in bacterial and fungal P450s
    • Pylypenko, O., and Schlichting, I. (2004) Structural aspects of ligand binding to and electron transfer in bacterial and fungal P450s, Annu. Rev. Biochem. 73, 991-1018.
    • (2004) Annu. Rev. Biochem. , vol.73 , pp. 991-1018
    • Pylypenko, O.1    Schlichting, I.2
  • 3
    • 7944223628 scopus 로고    scopus 로고
    • Cytochrome P450 conformational diversity
    • Stout, C. D. (2004) Cytochrome P450 conformational diversity, Structure 12, 1921-1922.
    • (2004) Structure , vol.12 , pp. 1921-1922
    • Stout, C.D.1
  • 4
    • 0036028698 scopus 로고    scopus 로고
    • Sequence alignments, variabilities, and vagaries
    • Graham, S. E., and Peterson, J. A. (2002) Sequence alignments, variabilities, and vagaries, Methods Enzymol. 357, 15-28.
    • (2002) Methods Enzymol. , vol.357 , pp. 15-28
    • Graham, S.E.1    Peterson, J.A.2
  • 5
    • 0037007068 scopus 로고    scopus 로고
    • Computational mapping identifies the binding sites of organic solvents on proteins
    • Dennis, S., Kortvelyesi, T., and Vajda, S. (2002) Computational mapping identifies the binding sites of organic solvents on proteins, Proc. Natl. Acad. Sci. U.S.A. 99, 4290-4295.
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 4290-4295
    • Dennis, S.1    Kortvelyesi, T.2    Vajda, S.3
  • 8
    • 0029868304 scopus 로고    scopus 로고
    • Locating and characterizing binding sites on proteins
    • Mattos, C., and Ringe, D. (1996) Locating and characterizing binding sites on proteins, Nat. Biotechnol. 14, 595-599.
    • (1996) Nat. Biotechnol. , vol.14 , pp. 595-599
    • Mattos, C.1    Ringe, D.2
  • 10
    • 13444265957 scopus 로고    scopus 로고
    • Exploring the binding site structure of the PPAR-γ ligand binding domain by computational solvent mapping
    • Sheu, S.-H., Kaya, T., Waxman, D. J., and Vajda, S. (2005) Exploring the binding site structure of the PPAR-γ ligand binding domain by computational solvent mapping, Biochemistry 44, 1193-1209.
    • (2005) Biochemistry , vol.44 , pp. 1193-1209
    • Sheu, S.-H.1    Kaya, T.2    Waxman, D.J.3    Vajda, S.4
  • 11
    • 0034681465 scopus 로고    scopus 로고
    • Convergent solutions to binding at a protein-protein interface
    • DeLano, W. L., Ultsch, M. H., de Vos, A. M., and Wells, J. A. (2000) Convergent solutions to binding at a protein-protein interface, Science 287, 1279-1283.
    • (2000) Science , vol.287 , pp. 1279-1283
    • DeLano, W.L.1    Ultsch, M.H.2    De Vos, A.M.3    Wells, J.A.4
  • 14
    • 0033587727 scopus 로고    scopus 로고
    • A systematic study of low-resolution recognition in protein-protein complexes
    • Vakser, I. A., Matar, O. G., and Lam, C. F. (1999) A systematic study of low-resolution recognition in protein-protein complexes, Proc. Natl. Acad. Sci. U.S.A. 96, 8477-8482.
    • (1999) Proc. Natl. Acad. Sci. U.S.A. , vol.96 , pp. 8477-8482
    • Vakser, I.A.1    Matar, O.G.2    Lam, C.F.3
  • 15
    • 0012227656 scopus 로고    scopus 로고
    • A comprehensive analytical treatment of continuum electrostatics
    • Schaefer, M., and Karplus, M. A. (1996) A comprehensive analytical treatment of continuum electrostatics, J. Phys. Chem. 100, 1578-1599.
    • (1996) J. Phys. Chem. , vol.100 , pp. 1578-1599
    • Schaefer, M.1    Karplus, M.A.2
  • 17
    • 0028922586 scopus 로고
    • LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
    • Wallace, A. C., Laskowski, R. A., and Thornton, J. M. (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions, Protein Eng. 8, 127-134.
    • (1995) Protein Eng. , vol.8 , pp. 127-134
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 18
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald, I. K., and Thornton, J. M. (1994) Satisfying hydrogen bonding potential in proteins, J. Mol. Biol. 238, 777-793.
    • (1994) J. Mol. Biol. , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 21
    • 0031013972 scopus 로고    scopus 로고
    • The structure of the cytochrome P450 BM-3 haem domain complexed with the fatty acid substrate, palmitoleic acid
    • Li, H., and Poulos, T. L. (1997) The structure of the cytochrome P450 BM-3 haem domain complexed with the fatty acid substrate, palmitoleic acid, Nat. Struct. Biol. 4, 140-146.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 140-146
    • Li, H.1    Poulos, T.L.2
  • 22
    • 0022919721 scopus 로고
    • Crystal structure of substrate-free Pseudomonas putida cytochrome P-450
    • Poulos, T. L., Finzel, B. C., and Howard, A. J. (1986) Crystal structure of substrate-free Pseudomonas putida cytochrome P-450, Biochemistry 25, 5314-5322.
    • (1986) Biochemistry , vol.25 , pp. 5314-5322
    • Poulos, T.L.1    Finzel, B.C.2    Howard, A.J.3
  • 24
    • 0033970047 scopus 로고    scopus 로고
    • Mammalian microsomal cytochrome P450 monooxygenase: Structural adaptations for membrane binding and functional diversity
    • Williams, P. A., Cosme, J., Sridhar, V., Johnson, E. F., and McRee. D. E. (2000) Mammalian microsomal cytochrome P450 monooxygenase: structural adaptations for membrane binding and functional diversity, Mol. Cell 5, 121-131.
    • (2000) Mol. Cell , vol.5 , pp. 121-131
    • Williams, P.A.1    Cosme, J.2    Sridhar, V.3    Johnson, E.F.4    McRee, D.E.5
  • 25
    • 0042573727 scopus 로고    scopus 로고
    • Structure of mammalian cytochrome P450 2C5 complexed with diclofenac at 2.1 Å resolution: Evidence for an induced fit model of substrate binding
    • Wester, M. R., Johnson, E. F., Marques-Soares, C., Dijols, S., Dansette, P. M., Mansuy, D., and 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.
    • (2003) Biochemistry , vol.42 , pp. 9335-9345
    • Wester, M.R.1    Johnson, E.F.2    Marques-Soares, C.3    Dijols, S.4    Dansette, P.M.5    Mansuy, D.6    Stout, C.D.7
  • 26
    • 0037672866 scopus 로고    scopus 로고
    • Structure of a substrate complex of mammalian cytochrome P450 2C5 at 2.3 Å resolution: Evidence for multiple substrate binding modes
    • Wester, M. R., Johnson, E. F., Marques-Soares, C., Dansette, P. M., Mansuy, D., and Stout, C. D. (2003) Structure of a substrate complex of mammalian cytochrome P450 2C5 at 2.3 Å resolution: evidence for multiple substrate binding modes, Biochemistry 42, 6370-6379.
    • (2003) Biochemistry , vol.42 , pp. 6370-6379
    • Wester, M.R.1    Johnson, E.F.2    Marques-Soares, C.3    Dansette, P.M.4    Mansuy, D.5    Stout, C.D.6
  • 27
    • 0026542989 scopus 로고
    • Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences
    • Gotoh, O. (1992) 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, 83-90.
    • (1992) J. Biol. Chem. , vol.267 , pp. 83-90
    • Gotoh, O.1
  • 28
    • 3042553224 scopus 로고    scopus 로고
    • Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9-Å resolution: Insight into the range of P450 conformations and the coordination of redox partner binding
    • Scott, E. E., White, M. A., He, Y. A., Johnson, E. F., Stout, C. D., Halpert, J. R. (2004) Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9-Å resolution: insight into the range of P450 conformations and the coordination of redox partner binding, J. Biol. Chem. 279, 27294-27301.
    • (2004) J. Biol. Chem. , vol.279 , pp. 27294-27301
    • Scott, E.E.1    White, M.A.2    He, Y.A.3    Johnson, E.F.4    Stout, C.D.5    Halpert, J.R.6
  • 30
    • 0042265520 scopus 로고    scopus 로고
    • Crystal structure of human cytochrome P450 2C9 with bound warfarin
    • Williams, P. A., Cosme, J., Ward, A., Angove, H. C., Vinkovic, D. M., and Jhoti, H. (2003) Crystal structure of human cytochrome P450 2C9 with bound warfarin, Nature 424, 464-468.
    • (2003) Nature , vol.424 , pp. 464-468
    • Williams, P.A.1    Cosme, J.2    Ward, A.3    Angove, H.C.4    Vinkovic, D.M.5    Jhoti, H.6
  • 31
    • 4143143372 scopus 로고    scopus 로고
    • The structure of human cytochrome P450 2C9 complexed with flurbiprofen at 2.0-Å resolution
    • Wester, M. R., Yano, J. K., Schoch, G. A., Yang, C., Griffin, K. J., Stout, C. D., and Johnson, E. F. (2004) The structure of human cytochrome P450 2C9 complexed with flurbiprofen at 2.0-Å resolution, J. Biol. Chem. 279, 35630-35637.
    • (2004) J. Biol. Chem. , vol.279 , pp. 35630-35637
    • Wester, M.R.1    Yano, J.K.2    Schoch, G.A.3    Yang, C.4    Griffin, K.J.5    Stout, C.D.6    Johnson, E.F.7
  • 32
    • 12344307441 scopus 로고    scopus 로고
    • Conformational changes observed in enzyme crystal structures upon substrate binding
    • Gutteridge, A., and Thornton, J. (2005) Conformational changes observed in enzyme crystal structures upon substrate binding, J. Mol. Biol. 346, 21-28.
    • (2005) J. Mol. Biol. , vol.346 , pp. 21-28
    • Gutteridge, A.1    Thornton, J.2
  • 33
    • 0000633429 scopus 로고
    • Regulation of steroidogenic and related P450s
    • (Ortiz deMontellano, P. R., Ed.) 2nd ed. Plenum Press, New York
    • Kagawa, N., and Waterman, M. R.(1995) Regulation of steroidogenic and related P450s, in Cytochrome P450: Structure, Mechanism, and Biochemistry (Ortiz deMontellano, P. R., Ed.) 2nd ed., pp 419-442, Plenum Press, New York.
    • (1995) Cytochrome P450: Structure, Mechanism, and Biochemistry , pp. 419-442
    • Kagawa, N.1    Waterman, M.R.2
  • 34
    • 0032985950 scopus 로고    scopus 로고
    • Cytochrome P450 substrate specificities, substrate structural templates and enzyme active site geometries
    • Lewis, D. F., Dickins, M., Eddershaw, P. J., Tarbit, M. H., and Goldfarb, P. S. (1999) Cytochrome P450 substrate specificities, substrate structural templates and enzyme active site geometries, Drug Metab. Drug Interact. 15, 1-49.
    • (1999) Drug Metab. Drug Interact. , vol.15 , pp. 1-49
    • Lewis, D.F.1    Dickins, M.2    Eddershaw, P.J.3    Tarbit, M.H.4    Goldfarb, P.S.5
  • 35
    • 0035893819 scopus 로고    scopus 로고
    • Differences in flexibility of active sites of cytochromes P450 probed by resonance Roman and UV-Vis absorption spectroscopy
    • Anzenbacher, P., and Hudecek, J. (2001) Differences in flexibility of active sites of cytochromes P450 probed by resonance Roman and UV-Vis absorption spectroscopy, J. Inorg. Biochem. 87, 209-213.
    • (2001) J. Inorg. Biochem. , vol.87 , pp. 209-213
    • Anzenbacher, P.1    Hudecek, J.2
  • 36
    • 0037228099 scopus 로고    scopus 로고
    • Substrate selectivity of human cytochrome P450 2C9: Importance of residues 476, 365, and 114 in recognition of diclofenac and sulfaphenazole and in mechanism-based inactivation by tienilic acid
    • Melet, A., Assrir, N., Mansuy, D., et al. (2003) Substrate selectivity of human cytochrome P450 2C9: importance of residues 476, 365, and 114 in recognition of diclofenac and sulfaphenazole and in mechanism-based inactivation by tienilic acid, Arch. Biochem. Biophys. 409, 80-91.
    • (2003) Arch. Biochem. Biophys. , vol.409 , pp. 80-91
    • Melet, A.1    Assrir, N.2    Mansuy, D.3
  • 37
    • 0034956877 scopus 로고    scopus 로고
    • Dapsone activation of CYP2C9 mediated metabolism: Evidence for activation of multiple substrates and a two-site model
    • Hutzler, J. M., Hauer, M. J., and Tracy, T. S. (2001) Dapsone activation of CYP2C9 mediated metabolism: evidence for activation of multiple substrates and a two-site model, Drug Metab. Dispos. 29, 1029-1034.
    • (2001) Drug Metab. Dispos. , vol.29 , pp. 1029-1034
    • Hutzler, J.M.1    Hauer, M.J.2    Tracy, T.S.3
  • 38
    • 0037325958 scopus 로고    scopus 로고
    • Activation of cytochrome P450 2C9-mediated metabolism: Mechanistic evidence in support of kinetic observations
    • Hutzler, J. M., Wienkers, L. C., Wahhlstrom, J. L., Carlson, T. J., and Tracy, T. S. (2003) Activation of cytochrome P450 2C9-mediated metabolism: mechanistic evidence in support of kinetic observations, Arch. Biochem. Biophys. 410, 16-24.
    • (2003) Arch. Biochem. Biophys. , vol.410 , pp. 16-24
    • Hutzler, J.M.1    Wienkers, L.C.2    Wahhlstrom, J.L.3    Carlson, T.J.4    Tracy, T.S.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.