Selected references on theoretical models of P450s

Selected references on on theoretical models of P450s

Compiled by Kirill Degtyarenko

Last modified: Thu Sep 18 16:08:00 BST 2003

Ahmed, S. (1996) Molecular modelling study of pyrrolidine-2,5-dione based aromatase inhibitors and other known inhibitors. Drug Des. Discov. 14, 77-89.
Ahmed, S. (1997) The mechanism of a P-450 enzyme-aromatase; a molecular modelling perspective for the removal of the C¹⁹ methyl and aromatisation of the steroid A ring. J. Enzyme Inhib. 12, 59-70.
Ahmed, S. (1998) Review of the molecular modelling studies of the cytochrome P-450 estrogen synthetase enzyme, aromatase. Drug Des. Discov. 15, 239-252.
Ahmed, S. (1999) A novel molecular modelling study of inhibitors of the 17-hydroxylase component of the enzyme system 17-hydroxylase/17,20-lyase (P-450₁₇). Bioorg. Med. Chem. 7, 1487-1496.
Ahmed, S., Davis, P.J. and Owen, C.P. (1996) Molecular modelling study of the binding of inhibitors of aromatase to the cytochrome P-450 heme. Drug Des. Discov. 14, 91-102.
Arnold, G.E. and Ornstein, R.L. (1997) Molecular dynamics study of time-correlated protein-domain motions and molecular flexibility: Cytochrome P450BM-3. Biophys. J. 73, 1147-1159.
Auchus, R.J. and Miller, W.L. (1999) Molecular modeling of human P450c17 (17-hydroxylase/17,20-lyase): insights into reaction mechanisms and effects of mutations. Mol. Endocrinol. 13, 1169-1182.
Afzelius, L., Zamora, I., Ridderström, M., Andersson, T.B., Karlén, A. and Masimirembwa, C.M. (2001) Competitive CYP2C9 inhibitors: enzyme inhibition studies, protein homology modeling, and three-dimensional quantitative structure-activity relationship analysis. Mol. Pharmacol. 59, 909-919.
Bapiro, T.E., Hasler, J.A., Ridderström, M. and Masimirembwa, C.M. (2002) The molecular and enzyme kinetic basis for the diminished activity of the cytochrome P450 2D6.17 (CYP2D6.17) variant. Potential implications for CYP2D6 phenotyping studies and the clinical use of CYP2D6 substrate drugs in some African populations. Biochem. Pharmacol. 64, 1387-1398.
Bass, M.B., Paulsen, M.D. and Ornstein, R.L. (1992) Substrate mobility in a deeply buried active site: analysis of norcamphor bound to cytochrome P-450cam as determined by a 201-psec molecular dynamics simulation. Proteins 13, 26-37.
Baudry, J., Li, W., Pan, L., Berenbaum, M.R. and Schuler, M.A. (2003) Molecular docking of substrates and inhibitors in the catalytic site of CYP6B1, an insect cytochrome P450 monooxygenase. Protein Engineering 16, 577-587.
Boscott, P.E. and Grant, G.H. (1994) Modeling cytochrome P450 14 demethylase (Candida albicans) from P450cam. J. Mol. Graph. 12, 185-192, 195.
Braatz, J.A., Bass, M.B. and Ornstein, R.L. (1994) An evaluation of molecular models of the cytochrome P450 Streptomyces griseolus enzymes P450SU1 and P450SU2. J. Comput. Aided Mol. Design 8, 607-622.
Brickmann, J. and Vollhardt, H. (1996) Virtual reality on the World Wide Web: a paradigm shift in molecular modeling? Trends Biotechnol. 14, 167-172.
Bridges, A., Gruenke, L., Chang, Y.T., Vakser, I.A., Loew, G. and Waskell, L. (1998) Identification of the binding site on cytochrome P450 2B4 for cytochrome b₅ and cytochrome P450 reductase. J. Biol. Chem. 273, 17036-17049.
Buczko, E., Koh, Y., Miyagawa, Y. and Dufau, M.L. (1995) The rat 17-hydroxylase-17,20-desmolase (CYP17) active site: computerized homology modeling and site directed mutagenesis. J. Steroid Biochem. Mol. Biol. 52, 209-218.
Burke, D.F., Laughton, C.A. and Neidle, S. (1997) Homology modelling of the enzyme P450 17-hydroxylase/17,20-lyase - a target for prostate cancer chemotherapy - from the crystal structure of P450BM-3. Anticancer Drug Design 12, 113-123.
Cardozo, T., Totrov, M. and Abagyan, R. (1995) Homology modeling by the ICM method. Proteins 23, 403-414.
Chang, Y.-T. and Loew, G.H. (1996) Construction and evaluation of a three-dimensional structure of cytochrome P450choP enzyme (CYP105C1). Protein Engineering 9, 755-766.
Chang, Y.-T. and Loew, G.H. (1999a) Homology modeling and substrate binding study of human CYP4A11 enzyme. Proteins 34, 403-415.
Chang, Y.-T. and Loew, G.H. (1999b) Molecular dynamics simulations of P450 BM3 - Examination of substrate-induced conformational change. J. Biomol. Struct. Dyn. 16, 1189-1203.
Chang, Y.-T. and Loew, G.H. (2000) Homology modeling, molecular dynamics simulations, and analysis of CYP119, a P450 enzyme from extreme acidothermophilic archaeon Sulfolobus solfataricus. Biochemistry 39, 2484-2498.
Chang, Y.-T., Stiffelman, O.B. and Loew, G.H. (1996) Computer modelling of 3D structures of cytochrome P450s. Biochimie 78, 771-779.
Chang, Y.-T., Stiffelman, O.B., Vakser, I.A., Loew, G.H., Bridges, A. and Waskell, L. (1997) Construction of a 3D model of cytochrome P450 2B4. Protein Engineering 10, 119-129.
Dai, R., Pincus, M.R. and Friedman, F.K. (2000) Molecular modeling of mammalian cytochrome P450s. Cell. Mol. Life Sci. 57, 487-499.
Das, B., Helms, V., Lounnas, V. and Wade, R.C. (2000) Multicopy molecular dynamics simulations suggest how to reconcile crystallographic and product formation data for camphor enantiomers bound to cytochrome P-450cam. J. Inorg. Biochem. 81, 121-131.
de Groot, M.J., Vermeulen, N.P.E., Kramer, J.D., van Acker, F.A.A. and Donné-Op den Kelder, G.M. (1996) 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, 1079-1091. [Supplementary Material]
de Groot, M.J., Alex, A.A. and Jones, B.C. (2002) Development of a combined protein and pharmacophore model for cytochrome P450 2C9. J. Med. Chem. 45, 1983-1993.
de Visser, S.P. and Shaik, S. (2003) A proton-shuttle mechanism mediated by the porphyrin in benzene hydroxylation by cytochrome P450 enzymes. J. Am. Chem. Soc. 125, 7413-7424. [Supplementary Material]
de Visser, S.P., Ogliaro, F. and Shaik, S. (2001) How does ethene inactivate cytochrome P450 en route to its epoxidation? A density functional study. Angew. Chem. Int. Ed. 40, 2871-2874.
De Voss, J.J. and Ortiz de Montellano, P.R. (1996) Substrate docking algorithms and the prediction of substrate specificity. Methods Enzymol. 272, 336-347.
De Voss, J.J., Sibbesen, O., Zhang, Z. and Ortiz de Montellano, P.R. (1997) Substrate docking algorithms and prediction of the substrate specificity of cytochrome P450_cam and its L244A mutant. J. Am. Chem. Soc. 119, 5489-5498.
Ekins, S., de Groot, M.J. and 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.
Exner, T., Keil, M., Moeckel, G. and Brickmann, J. (1998) Identification of substrate channels and protein cavities. J. Mol. Model. 4, 340-343.
Ferenczy, G.G. and Morris, G.M. (1989) The active site of cytochrome P-450 nifedipine oxidase: a model-building study. J. Mol. Graph. 7, 206-211.
Gill, D.S., Roush, D.J. and Willson, R.C. (1994) Tertiary structure of the heme-binding domain of rat cytochrome b₅ based on homology modeling. J. Biomol. Struct. Dyn. 11, 1003-1015.
Graham-Lorence, S. and Peterson, J.A. (1996) Structural alignments of P450s and extrapolations to the unknown. Methods Enzymol. 272, 315-326.
Graham-Lorence, S., Amarneh, B., White, R.E., Peterson, J.A. and Simpson, E.R. (1995) A three-dimensional model of aromatase cytochrome P450. Protein Science 4, 1065-1080.
Green, M.T. (1998) Role of the axial ligand in determining the spin state of resting cytochrome P450. J. Am. Chem. Soc. 120, 10772-10773.
Guallar, V., Harris, D.L., Batista, V.S. and Miller, W.H. (2002) Proton-transfer dynamics in the activation of cytochrome P450eryF. J. Am. Chem. Soc. 124, 1430-1437.
Handschuh, S. and Gasteiger, J. (2000) The search for the spatial and electronic requirements of a drug. J. Mol. Model. 6, 358-378.
Harris, D.L. (2002) Oxidation and electronic state dependence of proton transfer in the enzymatic cycle of cytochrome P450eryF. J. Inorg. Biochem. 91, 568-585.
Harris, D. and Loew, G. (1996) Comparative study of free energies of solvation of phenylimidazole inhibitors of cytochrome P-450cam by free energy simulation, AMSOL, and Poisson-Boltzmann methods. J. Comp. Chem. 17, 273-288.
Harris, D. and Loew, G. (1996) Investigation of the proton-assisted pathway to formation of the catalytically active, ferryl species of P450s by molecular dynamics studies of P450eryF. J. Am. Chem. Soc. 118, 6377-6387.
Harris, D.L. and Loew, G.H. (1998) Theoretical investigation of the proton assisted pathway to formation of cytochrome P450 compound I. J. Am. Chem. Soc. 120, 8941-8948.
Harris, D., Loew, G. and Waskell, L. (1998) Structure and spectra of ferrous dioxygen and reduced ferrous dioxygen model cytochrome P450. J. Am. Chem. Soc. 120, 4308-4318.
Harris, D., Loew, G. and Waskell, L. (2001) Calculation of the electronic structure and spectra of model cytochrome P450 compound I. J. Inorg. Biochem. 83, 309-318.
Helms, V. and Wade, R.C. (1995) Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study. Biophys. J. 69, 810-824.
Jean, P., Pothier, J., Dansette, P.M., Mansuy, D. and Viari, A. (1997) Automated multiple analysis of protein structures: Application to homology modeling of cytochromes P450. Proteins 28, 388-404.
Ji, H., Zhang, W., Zhou, Y., Zhang, M., Zhu, J., Song, Y. and Lu, J. (2000) A three-dimensional model of lanosterol 14-demethylase of Candida albicans and its interaction with azole antifungals. J. Med. Chem. 43, 2493-2505.
Jones, J.P. and Korzekwa, K.R. (1996) Predicting the rates and stereoselectivity of reactions mediated by the P450 superfamily. Methods Enzymol. 272, 326-335.
Jones, J.P., Shou, M. and Korzekwa, K.R. (1995) Stereospecific activation of the procarcinogen benzo[a]pyrene: a probe for the active sites of the cytochrome P450 superfamily. Biochemistry 34, 6956-6961.
Jones, J.P., Shou, M. and Korzekwa, K.R. (1996) Predicting the regioselectivity and stereoselectivity of cytochrome P450-mediated reactions: structural models for bioactivation reactions. Adv. Exp. Med. Biol. 387, 355-360.
Keserü, G.M. (2001) A virtual high throughput screen for high affinity cytochrome P450cam substrates. Implications for in silico prediction of drug metabolism. J. Comput. Aided Mol. Design 15, 649-657.
Keserü, G.M., Kolossváry, I. and Bertók, B. (1997) Cytochrome P450 catalyzed insecticide metabolism. Prediction of regio and stereoselectivity in the primer metabolism of carbofuran: A theoretical study. J. Am. Chem. Soc. 119, 5126-5131.
Korzekwa, K.R., Grogan, J., DeVito, S. and Jones, J.P. (1996) Electronic models for cytochrome P450 oxidations. Adv. Exp. Med. Biol. 387, 361-369.
Koymans, L.M., Vermeulen, N.P.E., Baarslag, A. and Donné-Op den Kelder, G.M. (1993) A preliminary 3D model for cytochrome P450 2D6 constructed by homology model building. J. Comput. Aided Mol. Design 7, 281-289.
Koymans, L.M., Moereels, H. and Vanden Bossche, H. (1995) A molecular model for the interaction between vorozole and other non-steroidal inhibitors and human cytochrome P450 19 (P450 aromatase). J. Steroid Biochem. Mol. Biol. 53, 191-197.
Laughton, C.A. (1994) A study of simulated annealing protocols for use with molecular dynamics in protein structure prediction. Protein Engineering 7, 235-241.
Laughton, C.A., Neidle, S., Zvelebil, M.J.J.M. and Sternberg, M.J.E. (1990) A molecular model for the enzyme cytochrome P450(17), a major target for the chemotherapy of prostatic cancer. Biochem. Biophys. Res. Commun. 171, 1160-1167.
Laughton, C.A., Zvelebil, M.J.J.M. and Neidle, S. (1993) A detailed molecular model for human aromatase. J. Steroid Biochem. Mol. Biol. 44, 399-407.
Lewis, D.F.V. (1995) Three-dimensional models of human and other mammalian microsomal P450s constructed from an alignment with P450 102 (P450bm3). Xenobiotica 25, 333-366.
Lewis, D.F.V. (1998) The CYP2 family: models, mutants and interactions. Xenobiotica 28, 617-661.
Lewis, D.F.V. (2002a) Homology modelling of human CYP2 family enzymes based on the CYP2C5 crystal structure. Xenobiotica 32, 305-323.
Lewis, D.F.V. (2002b) Modelling human cytochromes P450 involved in drug metabolism from the CYP2C5 crystallographic template. J. Inorg. Biochem. 91, 502-514.
Lewis, D.F.V. (2003) Essential requirements for substrate binding affinity and selectivity toward human CYP2 family enzymes. Arch. Biochem. Biophys. 409, 32-44.
Lewis, D.F.V. and Lake, B.G. (1995) Molecular modelling of members of the P4502A subfamily: Application to studies of enzyme specificity. Xenobiotica 25, 585-598.
Lewis, D.F.V. and Lake, B.G. (1999) Molecular modelling of CYP4A subfamily members based on sequence homology with CYP102. Xenobiotica 29, 763-781.
Lewis, D.F.V. and Lee-Robichaud, P. (1998) Molecular modelling of steroidogenic cytochromes P450 from families CYP11, CYP17, CYP19 and CYP21 based on the CYP102 crystal structure. J. Steroid Biochem. Mol. Biol. 66, 217-233.
Lewis, D.F.V., Eddershaw, P.J., Goldfarb, P.S. and Tarbit, M.H. (1996) Molecular modelling of CYP3A4 from an alignment with CYP102: identification of key interactions between putative active site residues and CYP3A-specific chemicals. Xenobiotica 26, 1067-1086.
Lewis, D.F.V., Eddershaw, P.J., Goldfarb, P.S. and Tarbit, M.H. (1997) Molecular modelling of cytochrome P4502D6 (CYP2D6) based on an alignment with CYP102: structural studies on specific CYP2D6 substrate metabolism. Xenobiotica 27, 319-339.
Lewis, D.F.V., Lake, B.G., Dickins, M., Eddershaw, P.J., Tarbit, M.H. and Goldfarb, P.S. (1999a) Molecular modelling of CYP2B6, the human CYP2B isoform, by homology with the substrate-bound CYP102 crystal structure: evaluation of CYP2B6 substrate characteristics, the cytochrome b5 binding site and comparisons with CYP2B1 and CYP2B4. Xenobiotica 29, 361-393.
Lewis, D.F.V., Wiseman, A. and Tarbit, M.H. (1999b) Molecular modelling of lanosterol 14-demethylase (CYP51) from Saccharomyces cerevisiae via homology with CYP102, a unique bacterial cytochrome P450 isoform: quantitative structure-activity relationships (QSARs) within two related series of antifungal azole derivatives. J. Enzyme Inhib. 14, 175-192.
Lewis, D.F.V., Lake, B.G., George, S.G., Dickins, M., Eddershaw, P.J., Tarbit, M.H., Beresford, A.P., Goldfarb, P.S. and Guengerich, F.P. (1999c) Molecular modelling of CYP1 family enzymes CYP1A1, CYP1A2, CYP1A6 and CYP1B1 based on sequence homology with CYP102. Toxicology 139, 53-79.
Lewis, D.F.V., Modi, S. and Dickins, M. (2001) Quantitative structure-activity relationships (QSARs) within substrates of human cytochromes P450 involved in drug metabolism. Drug Metabol. Drug Interact. 18, 221-242.
Lewis, D.F.V., Lake, B.G., Dickins, M. and Goldfarb, P.S. (2002) Molecular modelling of CYP2B6 based on homology with the CYP2C5 crystal structure: analysis of enzyme-substrate interactions. Drug Metabol. Drug Interact. 19, 115-135.
Lewis, D.F.V., Sams, C. and Loizou, G.D. (2003a) A quantitative structure-activity relationship analysis on a series of alkyl benzenes metabolized by human cytochrome P450 2E1. J. Biochem. Mol. Toxicol. 17, 47-52.
Lewis, D.F.V., Lake, B.G., Bird, M.G., Loizou, G.D., Dickins, M. and Goldfarb, P.S. (2003b) Homology modelling of human CYP2E1 based on the CYP2C5 crystal structure: investigation of enzyme-substrate and enzyme-inhibitor interactions. Toxicol. In Vitro 17, 93-105.
Lewis, D.F.V., Lake, B.G., Dickins, M., Ueng, Y.F. and Goldfarb, P.S. (2003c) Homology modelling of human CYP1A2 based on the CYP2C5 crystallographic template structure. Xenobiotica 33, 239-254.
Lewis, D.F.V., Lake, B.G., Dickins, M. and Goldfarb, P.S. (2003d) Homology modelling of CYP2A6 based on the CYP2C5 crystallographic template: enzyme-substrate interactions and QSARs for binding affinity and inhibition. Toxicol. In Vitro 17, 179-190.
Lewis, D.F.V., Gillam, E.M., Everett, S.A. and Shimada, T. (2003e) Molecular modelling of human CYP1B1 substrate interactions and investigation of allelic variant effects on metabolism. Chem. Biol. Interact. 145, 281-295.
Li, H. and Poulos, T.L. (1995) Modeling protein-substrate interactions in the heme domain of cytochrome P450_BM-3. Acta Crystallogr. D51, 21-32.
Lin, Y.Z., Deng, H. and Ruan, K.H. (2000) Topology of catalytic portion of prostaglandin I₂ synthase: Identification by molecular modeling-guided site-specific antibodies. Arch. Biochem. Biophys. 379, 188-197.
Lounnas, V. and Wade, R.C. (1997) Exceptionally stable salt bridges in cytochrome P450cam have functional roles. Biochemistry 36, 5402-5417.
Lozano, J.J., Lopez de Brinas, E., Centeno, N.B., Guigo, R. and Sanz, F. (1997) Three-dimensional modelling of human cytochrome P450 1A2 and its interaction with caffeine and MeIQ. J. Comput. Aided Mol. Design 11, 395-408.
Lüdemann, S.K., Lounnas, V. and Wade, R.C. (2000a) How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms. J. Mol. Biol. 303, 773-795.
Lüdemann, S.K., Lounnas, V. and Wade, R.C. (2000b) How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways. J. Mol. Biol. 303, 813-830.
Mackman, R., Tschirret-Guth, R.A., Smith, G., Hayhurst, G.P., Ellis, S.W., Lennard, M.S., Tucker, G.T., Wolf, C.R. and Ortiz de Montellano, P.R. (1996) Active site topologies of human CYP2D6 and its aspartate-301 glutamate, asparagine, and glycine mutants. Arch. Biochem. Biophys. 331, 134-140.
Manchester, J.I. and Ornstein, R.L. (1995a) Enzyme-catalyzed dehalogenation of pentachloroethane: Why F87W-cytochrome P450cam is faster than wild type. Protein Engineering 8, 801-807.
Manchester, J.I. and Ornstein, R.L. (1995b) Molecular dynamics simulations indicate that F87W, T185F-cytochrome P450cam may reductively dehalogenate 1,1,1-trichloroethane. J. Biomol. Struct. Dyn. 13, 413-422.
Manchester, J.I. and Ornstein, R.L. (1996) Rational approach to improving reductive catalysis by cytochrome P450cam. Biochimie 78, 714-722.
Mathieu, A.P., LeHoux, J.-G. and Auchus, R.J. (2003) Molecular dynamics of substrate complexes with hamster cytochrome P450c17 (CYP17): mechanistic approach to understanding substrate binding and activities. Biochim. Biophys. Acta 1619, 291-300.
Modi, S., Paine, M.J., Sutcliffe, M.J., Lian, L.-Y., Primrose, W.U., Wolf, C.R. and Roberts, G.C.K. (1996) A model for human cytochrome P₄₅₀2D6 based on homology modeling and NMR studies of substrate binding. Biochemistry 35, 4540-4550.
Mosimann, S., Meleshko, R. and James, M.N.G. (1995) A critical assessment of comparative molecular modeling of tertiary structures of proteins. Proteins 23, 301-317.
Müller, J.J., Müller, A., Rottmann, M., Bernhardt, R. and Heinemann, U. (1999) Vertebrate-type and plant-type ferredoxins: crystal structure comparison and electron transfer pathway modelling. J. Mol. Biol. 294, 501-513.
Ogliaro, F., Harris, N., Cohen, S., Filatov, M., de Visser, S.P. and Shaik, S. (2000) A model "rebound" mechanism of hydroxylation by cytochrome P450: stepwise and effectively concerted pathways, and their reactivity patterns. J. Am. Chem. Soc. 122, 8977-8989.
Ogliaro, F., de Visser, S.P., Groves, J.T. and Shaik, S. (2001) Chameleon states: high-valent metal-oxo species of cytochrome P450 and its ruthenium analogue. Angew. Chem. Int. Ed. 40, 2874-2878 [published erratum Angew. Chem. Int. Ed. 40, 3503 (2001)].
Ogliaro, F., de Visser, S.P., Cohen, S., Sharma, P.K. and Shaik, S. (2002a) Searching for the second oxidant in the catalytic cycle of cytochrome P450: a theoretical investigation of the iron(III)-hydroperoxo species and its epoxidation pathways. J. Am. Chem. Soc. 124, 2806-2817.
Ogliaro, F., de Visser, S.P. and Shaik, S. (2002b) The ‘push’ effect of the thiolate ligand in cytochrome P450: a theoretical gauging. J. Inorg. Biochem. 91, 554-567.
Oprea, T.I., Hummer, G. and García, A.E. (1997) Identification of a functional water channel in cytochrome P450 enzymes. Proc. Natl. Acad. Sci. USA 94, 2133-2138.
Park, J.-Y. and Harris, D. (2003) Construction and assessment of models of CYP2E1: predictions of metabolism from docking, molecular dynamics, and density functional theoretical calculations. J. Med. Chem. 46, 1645-1660.
Paulsen, M.D. and Ornstein, R.L. (1991) A 175-psec molecular dynamics simulation of camphor-bound cytochrome P-450cam. Proteins 11, 184-204.
Paulsen, M.D. and Ornstein, R.L. (1992) Predicting the product specificity and coupling of cytochrome P450cam. J. Comput. Aided Mol. Design 6, 449-460.
Paulsen, M.D. and Ornstein, R.L. (1993) Substrate mobility in thiocamphor-bound cytochrome P450cam: an explanation of the conflict between the observed product profile and the X-ray structure. Protein Engineering 6, 359-365.
Paulsen, M.D. and Ornstein, R.L. (1994) Active-site mobility inhibits reductive dehalogenation of 1,1,1-trichloroethane by cytochrome P450cam. J. Comput. Aided Mol. Design 8, 389-404.
Paulsen, M.D. and Ornstein, R.L. (1995) Dramatic differences in the motions of the mouth of open and closed cytochrome P450BM-3 by molecular dynamics simulations. Proteins 21, 237-243.
Paulsen, M.D. and Ornstein, R.L. (1996) Binding free energy calculations for P450cam-substrate complexes. Protein Engineering 9, 567-571.
Paulsen, M.D., Bass, M.B. and 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.
Paulsen, M.D., Manchester, J.I. and Ornstein, R.L. (1996) Using molecular modeling and molecular dynamics simulation to predict P450 oxidation products. Methods Enzymol. 272, 347-357.
Payne, V.A., Chang, Y.-T. and Loew, G.H. (1999a) Homology modeling and substrate binding study of human CYP2C9 enzyme. Proteins 37, 176-190.
Payne, V.A., Chang, Y.-T. and Loew, G.H. (1999b) Homology modeling and substrate binding study of human CYP2C18 and CYP2C19 enzymes. Proteins 37, 204-217.
Pochapsky, T.C., Lyons, T.A., Kazanis, S., Arakaki, T. and Ratnaswamy, G. (1996) A structure-based model for cytochrome P450_cam-putidaredoxin interactions. Biochimie 78, 723-733.
Poulos, T.L. (1991) Modeling of mammalian P450s on basis of P450cam X-ray structure. Methods Enzymol. 206, 11-30.
Poulos, T.L. and Mauk, A.G. (1983) Models for the complexes formed between cytochrome b₅ and the subunits of methemoglobin. J. Biol. Chem. 258, 7369-7373.
Roitberg, A.E. (1997) A molecular dynamics study of Fe₂S₂ putidaredoxin: Multiple conformations of the C-terminal region. Biophys. J. 73, 2138-2148.
Roitberg, A.E., Holden, M.J., Mayhew, M.P., Kurnikov, I.V., Beratan, D.L. and Vilker, V.L. (1998) Binding and electron transfer between putidaredoxin and cytochrome P450cam. Theory and experiments. J. Am. Chem. Soc. 120, 8927-8932.
Ruan, K.-H., Milfeld, K., Kulmacz, R.J. and Wu, K.K. (1994) Comparison of the construction of a 3-D model for human thromboxane synthase using P450cam and BM-3 as templates: implications for the substrate binding pocket. Protein Engineering 7, 1345-1351.
Sagot, M.-F., Viari, A., Pothier, J. and Soldano, H. (1995) Finding flexible patterns in a text: an application to three-dimensional molecular matching. CABIOS 11, 59-70.
Schappach, A. and Holtje, H.D. (2001) Molecular modelling of 17-hydroxylase-17,20-lyase. Pharmazie 56, 435-442.
Scherlis, D.A., Cymeryng, C.B. and Estrin, D.A. (2000) Nitric oxide binding to ferric cytochrome P450: A computational study. Inorg. Chem. 39, 2352-23592.
Skrzypczak-Jankun, E. and Kurumbail, R.G. (1996) 1-trityl-4-nitroimidazole. Acta Crystallogr. C52, 189-191.
Smith, S.V., Koley, A.P., Dai, R., Robinson, R.C., Leong, H., Markowitz, A. and Friedman, F.K. (2000) Conformational modulation of human cytochrome P450 2E1 by ethanol and other substrates: a CO flash photolysis study. Biochemistry 39, 5731-5737.
Sopková-de Oliveira Santos, J., Smith, J.C., Delaforge, M., Virelizier, H. and Jankowski, C.K. (1998) Oxidation of tetrahydro-ß-carboline by cytochrome P-450_cam. Determination and rationalisation of product distribution. Eur. J. Biochem. 251, 398-404 [published erratum Eur. J. Biochem. 256, 251 (1998)].
Spatzenegger, M., Wang, Q., He, Y.Q., Wester, M.R., Johnson, E.F. and Halpert, J.R. (2001) Amino acid residues critical for differential inhibition of CYP2B4, CYP2B5, and CYP2B1 by phenylimidazoles. Mol. Pharmacol. 59, 475-484.
Szklarz, G.D. and Halpert, J.R. (1997a) Molecular modeling of cytochrome P450 3A4. J. Comput. Aided Mol. Design 11, 265-272.
Szklarz, G.D. and Halpert, J.R. (1997b) Use of homology modeling in conjunction with site-directed mutagenesis for analysis of structure-function relationships of mammalian cytochromes P450. Life Sci. 61, 2507-2520.
Szklarz, G.D. and Halpert, J.R. (1998) Molecular basis of P450 inhibition and activation: implications for drug development and drug therapy. Drug Metab. Dispos. 26, 1179-1184.
Venhorst, J., ter Laak, A.M., Commandeur, J.N.M., Funae, Y., Hiroi, T. and Vermeulen, N.P.E. (2003) Homology modeling of rat and human cytochrome P450 2D (CYP2D) isoforms and computational rationalization of experimental ligand-binding specificities. J. Med. Chem. 46, 74-86.
Vijayakumar, S. and Salerno, J.C. (1992) Molecular modeling of the 3-D structure of cytochrome P-450scc. Biochim. Biophys. Acta 1160, 281-286.
Wang, Q. and 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.
Winn, P.J., Lüdemann, S.K., Gauges, R., Lounnas, V. and Wade, R.C. (2002) Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a novel functional role for a buried arginine. Proc. Natl. Acad. Sci. USA 99, 5361-5366.
Yin, H., Anders, M.W., Korzekwa, K.R., Higgins, L., Thummel, K.E., Kharasch, E.D. and Jones, J.P. (1995) Designing safer chemicals: predicting the rates of metabolism of halogenated alkanes. Proc. Natl. Acad. Sci. USA 92, 11076-11080.
Zvelebil, M.J.J.M., Wolf, C.R. and Sternberg, M.J.E. (1991) A predicted three-dimensional structure of human cytochrome P450: implications for substrate specificity. Protein Engineering 4, 271-282.

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