Dynamics of CYP51: implications for function and inhibitor design
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Rebecca C Wade | Ghulam Mustafa | R. Wade | O. Salo-Ahen | G. Mustafa | G. Lepesheva | Vlad Cojocaru | Outi M H Salo-Ahen | Xiaofeng Yu | Vlad Cojocaru | Galina I Lepesheva | Xiaofeng Yu
[1] M. Waterman,et al. Structural Insights into Inhibition of Sterol 14α-Demethylase in the Human Pathogen Trypanosoma cruzi* , 2010, The Journal of Biological Chemistry.
[2] S. Kawato,et al. Dynamic structures of adrenocortical cytochrome P-450 in proteoliposomes and microsomes: protein rotation study. , 1992, Biochemistry.
[3] D. Tieleman,et al. The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.
[4] S. Sligar,et al. Structural differences between soluble and membrane bound cytochrome P450s. , 2012, Journal of inorganic biochemistry.
[5] M. Waterman,et al. Crystal Structures of Trypanosoma brucei Sterol 14α-Demethylase and Implications for Selective Treatment of Human Infections*♦ , 2009, The Journal of Biological Chemistry.
[6] Jeremy C. Smith,et al. Coupled flexibility change in cytochrome P450cam substrate binding determined by neutron scattering, NMR, and molecular dynamics simulation. , 2012, Biophysical journal.
[7] Berk Hess,et al. GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .
[8] R. Larson,et al. The MARTINI Coarse-Grained Force Field: Extension to Proteins. , 2008, Journal of chemical theory and computation.
[9] Karel Berka,et al. Dynamics and hydration of the active sites of mammalian cytochromes P450 probed by molecular dynamics simulations. , 2012, Current drug metabolism.
[10] Y. Yoshida. Cytochrome P450 of fungi: primary target for azole antifungal agents. , 1988, Current topics in medical mycology.
[11] William L. Jorgensen,et al. Quantum and statistical mechanical studies of liquids. 25. Solvation and conformation of methanol in water , 1983 .
[12] K. Berka,et al. Behavior of human cytochromes P450 on lipid membranes. , 2013, The journal of physical chemistry. B.
[13] A. Mark,et al. Coarse grained model for semiquantitative lipid simulations , 2004 .
[14] M. Waterman,et al. Structural complex of sterol 14α-demethylase (CYP51) with 14α-methylenecyclopropyl-Δ7-24, 25-dihydrolanosterol[S] , 2012, Journal of Lipid Research.
[15] Victor Guallar,et al. Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450 , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[16] T. Blundell,et al. Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.
[17] J Deisenhofer,et al. Structure and function of cytochromes P450: a comparative analysis of three crystal structures. , 1995, Structure.
[18] D. Nelson,et al. Cytochrome P450 and the individuality of species. , 1999, Archives of biochemistry and biophysics.
[19] Gerrit Groenhof,et al. GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..
[20] Piotr Cieplak,et al. The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building. , 2010, Physical chemistry chemical physics : PCCP.
[21] Emad Tajkhorshid,et al. Characterizing the Membrane-Bound State of Cytochrome P450 3A4: Structure, Depth of Insertion, and Orientation , 2013, Journal of the American Chemical Society.
[22] I. Pikuleva. Putative F–G loop is involved in association with the membrane in P450scc (P450 11A1) , 2004, Molecular and Cellular Endocrinology.
[23] O. Gotoh,et al. Sterol 14-demethylase P450 (CYP51) provides a breakthrough for the discussion on the evolution of cytochrome P450 gene superfamily. , 2000, Biochemical and biophysical research communications.
[24] V. Hornak,et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.
[25] S D Black,et al. Membrane topology of liver microsomal cytochrome P450 2B4 determined via monoclonal antibodies directed to the halt-transfer signal. , 1994, Biochemistry.
[26] Rebecca C Wade,et al. The ins and outs of cytochrome P450s. , 2007, Biochimica et biophysica acta.
[27] Andrei L. Lomize,et al. OPM: Orientations of Proteins in Membranes database , 2006, Bioinform..
[28] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[29] Laxmikant V. Kalé,et al. Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..
[30] P. Kollman,et al. A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .
[31] Carsten Kutzner,et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.
[32] Alessandra Magistrato,et al. Influence of the Membrane Lipophilic Environment on the Structure and on the Substrate Access/Egress Routes of the Human Aromatase Enzyme. A Computational Study , 2012, J. Chem. Inf. Model..
[33] T. Yuen,et al. Structure–phenotype correlations of human CYP21A2 mutations in congenital adrenal hyperplasia , 2013, Proceedings of the National Academy of Sciences.
[34] L. Waskell,et al. Theoretical study of the ligand–CYP2B4 complexes: Effect of structure on binding free energies and heme spin state , 2004, Proteins.
[35] Andrzej J. Rzepiela,et al. Reconstruction of atomistic details from coarse‐grained structures , 2010, J. Comput. Chem..
[36] L. Waskell,et al. Probing the Transmembrane Structure and Topology of Microsomal Cytochrome-P450 by Solid-State NMR on Temperature-Resistant Bicelles , 2013, Scientific Reports.
[37] P. Kollman,et al. Automatic atom type and bond type perception in molecular mechanical calculations. , 2006, Journal of molecular graphics & modelling.
[38] T. Ost,et al. Phe393 mutants of cytochrome P450 BM3 with modified heme redox potentials have altered heme vinyl and propionate conformations. , 2004, Biochemistry.
[39] J. Baudry,et al. Active-site hydration and water diffusion in cytochrome P450cam: a highly dynamic process. , 2011, Biophysical journal.
[40] Xavier Periole,et al. Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition. , 2009, Journal of chemical theory and computation.
[41] E. Szczesna-Skorupa,et al. Identification of membrane-contacting loops of the catalytic domain of cytochrome P450 2C2 by tryptophan fluorescence scanning. , 2006, Biochemistry.
[42] N. Grishin,et al. PROMALS3D: a tool for multiple protein sequence and structure alignments , 2008, Nucleic acids research.
[43] M. Waterman,et al. CYP51 structures and structure-based development of novel, pathogen-specific inhibitory scaffolds. , 2012, International journal for parasitology. Drugs and drug resistance.
[44] Nathan A. Baker,et al. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations , 2004, Nucleic Acids Res..
[45] S. Sligar,et al. Single-molecule height measurements on microsomal cytochrome P450 in nanometer-scale phospholipid bilayer disks , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[46] Peter M. Kasson,et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..
[47] A. Frey,et al. Determination of the membrane topology of the phenobarbital-inducible rat liver cytochrome P-450 isoenzyme PB-4 using site-specific antibodies , 1987, The Journal of cell biology.
[48] Balázs Jójárt,et al. Performance of the general amber force field in modeling aqueous POPC membrane bilayers , 2007, J. Comput. Chem..
[49] William J. Allen,et al. GridMAT‐MD: A grid‐based membrane analysis tool for use with molecular dynamics , 2009, J. Comput. Chem..
[50] O. Gotoh,et al. Sterol 14-demethylase P450 (P45014DM*) is one of the most ancient and conserved P450 species. , 1996, Journal of biochemistry.
[51] D. van der Spoel,et al. GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .
[52] W. David Nes,et al. CYP51: A Major Drug Target in the Cytochrome P450 Superfamily , 2008, Lipids.
[53] Junmei Wang,et al. Development and testing of a general amber force field , 2004, J. Comput. Chem..
[54] M. Waterman,et al. VNI cures acute and chronic experimental Chagas disease. , 2013, The Journal of infectious diseases.
[55] M. Wilce,et al. The F-G loop region of cytochrome P450scc (CYP11A1) interacts with the phospholipid membrane. , 2003, Biochimica et biophysica acta.
[56] Mark S. P. Sansom,et al. Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9 , 2011, PLoS Comput. Biol..
[57] Piotr Cieplak,et al. R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments , 2011, Nucleic Acids Res..
[58] M. Waterman,et al. CYP51—the omnipotent P450 , 2004, Molecular and Cellular Endocrinology.
[59] W. Delano. The PyMOL Molecular Graphics System , 2002 .
[60] R. Stroud,et al. Architecture of a single membrane spanning cytochrome P450 suggests constraints that orient the catalytic domain relative to a bilayer , 2014, Proceedings of the National Academy of Sciences.
[61] M. Waterman,et al. Sterol 14alpha-demethylase (CYP51) as a therapeutic target for human trypanosomiasis and leishmaniasis. , 2011, Current topics in medicinal chemistry.
[62] M. Waterman,et al. Substrate Preferences and Catalytic Parameters Determined by Structural Characteristics of Sterol 14α-Demethylase (CYP51) from Leishmania infantum* , 2011, The Journal of Biological Chemistry.
[63] N. Vermeulen,et al. Structural rationalization of novel drug metabolizing mutants of cytochrome P450 BM3 , 2008, Proteins.
[64] O. Gotoh,et al. Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences. , 1992, The Journal of biological chemistry.
[65] Karel Berka,et al. Membrane Position of Ibuprofen Agrees with Suggested Access Path Entrance to Cytochrome P450 2C9 Active Site , 2011, The journal of physical chemistry. A.
[66] Antonín Pavelka,et al. CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures , 2012, PLoS Comput. Biol..