QM and QM/MM Methods Compared: Case Studies on Reaction Mechanisms of Metalloenzymes.
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Matthew G. Quesne | Tomasz Borowski | Maciej Szaleniec | T. Borowski | M. Szaleniec | Matthew Quesne | M. Quesne
[1] Jing Zhang,et al. Drug metabolism by cytochrome p450 enzymes: what distinguishes the pathways leading to substrate hydroxylation over desaturation? , 2015, Chemistry.
[2] M. Crestoni,et al. A comprehensive test set of epoxidation rate constants for iron(iv)–oxo porphyrin cation radical complexes , 2014, Chemical science.
[3] M. Szaleniec,et al. Asymmetric reduction of ketones and β-keto esters by (S)-1-phenylethanol dehydrogenase from denitrifying bacterium Aromatoleum aromaticum , 2014, Applied Microbiology and Biotechnology.
[4] S. D. de Visser,et al. Long-range electron transfer triggers mechanistic differences between iron(IV)-oxo and iron(IV)-imido oxidants. , 2014, Journal of the American Chemical Society.
[5] J. Heider,et al. Mechanistic basis for the enantioselectivity of the anaerobic hydroxylation of alkylaromatic compounds by ethylbenzene dehydrogenase. , 2014, Journal of inorganic biochemistry.
[6] R. Reinhardt,et al. Anaerobic Activation of p-Cymene in Denitrifying Betaproteobacteria: Methyl Group Hydroxylation versus Addition to Fumarate , 2014, Applied and Environmental Microbiology.
[7] P. Siegbahn,et al. Role of substrate positioning in the catalytic reaction of 4-hydroxyphenylpyruvate dioxygenase-A QM/MM Study. , 2014, Journal of the American Chemical Society.
[8] Benedetta Mennucci,et al. Geometry Optimization in Polarizable QM/MM Models: The Induced Dipole Formulation. , 2014, Journal of chemical theory and computation.
[9] Andrew W. Munro,et al. Structure and Biochemical Properties of the Alkene Producing Cytochrome P450 OleTJE (CYP152L1) from the Jeotgalicoccus sp. 8456 Bacterium* , 2014, The Journal of Biological Chemistry.
[10] M. Blomberg,et al. Quantum chemical studies of mechanisms for metalloenzymes. , 2014, Chemical reviews.
[11] Matthew G. Quesne,et al. Computational modelling of oxygenation processes in enzymes and biomimetic model complexes. , 2014, Chemical communications.
[12] Matthew G. Quesne,et al. Quantum mechanics/molecular mechanics study on the oxygen binding and substrate hydroxylation step in AlkB repair enzymes. , 2014, Chemistry.
[13] R. Hille,et al. The mononuclear molybdenum enzymes. , 1996, Chemical reviews.
[14] Matthew G. Quesne,et al. Secondary Coordination Sphere Influence on the Reactivity of Nonheme Iron(II) Complexes: An Experimental and DFT Approach , 2013, Journal of the American Chemical Society.
[15] Walter Thiel,et al. Quantum mechanical/molecular mechanical study on the enantioselectivity of the enzymatic Baeyer-Villiger reaction of 4-hydroxycyclohexanone. , 2013, The journal of physical chemistry. B.
[16] DudzikAgnieszka,et al. The reaction mechanism of chiral hydroxylation of p-OH and p-NH2 substituted compounds by ethylbenzene dehydrogenase , 2013 .
[17] G. Fuchs,et al. Molybdoenzyme That Catalyzes the Anaerobic Hydroxylation of a Tertiary Carbon Atom in the Side Chain of Cholesterol* , 2012, The Journal of Biological Chemistry.
[18] J. Essigmann,et al. Exocyclic Carbons Adjacent to the N6 of Adenine are Targets for Oxidation by the Escherichia coli Adaptive Response Protein AlkB , 2012, Journal of the American Chemical Society.
[19] Tomasz Borowski,et al. Quantum chemical modeling studies of ethylbenzene dehydrogenase activity , 2012 .
[20] Walter Thiel,et al. Quantum mechanical/molecular mechanical study on the mechanism of the enzymatic Baeyer-Villiger reaction. , 2012, Journal of the American Chemical Society.
[21] M. Jung,et al. Oxidized cytosine metabolites offer a fresh perspective for active DNA demethylation. , 2011, Angewandte Chemie.
[22] J. Heider,et al. Microbial degradation of aromatic compounds — from one strategy to four , 2011, Nature Reviews Microbiology.
[23] Hong Sun,et al. X-ray absorption spectroscopy structural investigation of early intermediates in the mechanism of DNA repair by human ABH2. , 2011, Biochemistry.
[24] G. Grogan. Cytochromes P450: exploiting diversity and enabling application as biocatalysts. , 2011, Current opinion in chemical biology.
[25] Nuclear resonance vibrational spectroscopy on the Fe(IV)=O S=2 non-heme site in TMG3tren: experimentally calibrated insights into reactivity. , 2011, Angewandte Chemie.
[26] W. Thiel,et al. Theoretical study on the mechanism of the oxygen activation process in cysteine dioxygenase enzymes. , 2011, Journal of the American Chemical Society.
[27] N. Turner,et al. Cytochromes P450 as useful biocatalysts: addressing the limitations. , 2011, Chemical communications.
[28] K. Morokuma,et al. Protein Free Energy Corrections in ONIOM QM:MM Modeling: A Case Study for Isopenicillin N Synthase (IPNS). , 2011, Journal of chemical theory and computation.
[29] Pär Söderhjelm,et al. On the Convergence of QM/MM Energies. , 2011, Journal of chemical theory and computation.
[30] Frank Neese,et al. Nonheme oxo-iron(IV) intermediates form an oxyl radical upon approaching the C–H bond activation transition state , 2011, Proceedings of the National Academy of Sciences.
[31] Andreas Schirmer,et al. Terminal Olefin (1-Alkene) Biosynthesis by a Novel P450 Fatty Acid Decarboxylase from Jeotgalicoccus Species , 2011, Applied and Environmental Microbiology.
[32] P. Siegbahn,et al. Comparison of QM-only and QM/MM models for the mechanism of tyrosinase. , 2011, Faraday discussions.
[33] T. Pan,et al. The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-methoxycarbonylmethyluridine at the wobble position of tRNA. , 2010, Angewandte Chemie.
[34] Michael T. Green,et al. Cytochrome P450 Compound I: Capture, Characterization, and C-H Bond Activation Kinetics , 2010, Science.
[35] P. Siegbahn,et al. Mechanism of selective halogenation by SyrB2: a computational study. , 2010, Journal of the American Chemical Society.
[36] Polina Georgieva,et al. Quantum chemical modeling of enzymatic reactions: The case of histone lysine methyltransferase , 2010, J. Comput. Chem..
[37] Devesh Kumar,et al. What factors influence the rate constant of substrate epoxidation by compound I of cytochrome P450 and analogous iron(IV)-oxo oxidants? , 2010, Journal of the American Chemical Society.
[38] Tomasz Borowski,et al. Ab initio modeling of ethylbenzene dehydrogenase reaction mechanism. , 2010, Journal of the American Chemical Society.
[39] P. R. Montellano. Hydrocarbon hydroxylation by cytochrome P450 enzymes. , 2010 .
[40] S. D. de Visser,et al. Effect of porphyrin ligands on the regioselective dehydrogenation versus epoxidation of olefins by oxoiron(IV) mimics of cytochrome P450. , 2009, The journal of physical chemistry. A.
[41] D. Nelson. The Cytochrome P450 Homepage , 2009, Human Genomics.
[42] Ulf Ryde,et al. Do quantum mechanical energies calculated for small models of protein-active sites converge? , 2009, The journal of physical chemistry. A.
[43] J. Hunt,et al. Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB , 2009, Proceedings of the National Academy of Sciences.
[44] Maciej Szaleniec,et al. Quantitative structure enantioselective retention relationship for high-performance liquid chromatography chiral separation of 1-phenylethanol derivatives. , 2009, Journal of chromatography. A.
[45] Cai-Guang Yang,et al. A non-heme iron-mediated chemical demethylation in DNA and RNA. , 2009, Accounts of chemical research.
[46] Haining Liu,et al. A DFT study of nucleobase dealkylation by the DNA repair enzyme AlkB. , 2009, The journal of physical chemistry. B.
[47] Walter Thiel,et al. QM/MM methods for biomolecular systems. , 2009, Angewandte Chemie.
[48] Maciej Szaleniec,et al. Quantum chemical modelling of the C–H cleavage mechanism in oxidation of ethylbenzene and its derivates by ethylbenzene dehydrogenase , 2008 .
[49] S. D. de Visser,et al. Comparative quantum mechanics/molecular mechanics (QM/MM) and density functional theory calculations on the oxo-iron species of taurine/alpha-ketoglutarate dioxygenase. , 2008, The journal of physical chemistry. A.
[50] Yin-Ru Chiang,et al. Study of Anoxic and Oxic Cholesterol Metabolism by Sterolibacterium denitrificans , 2007, Journal of bacteriology.
[51] Fahmi Himo,et al. Quantum chemical modeling of enzymatic reactions: the case of 4-oxalocrotonate tautomerase. , 2007, Bioorganic chemistry.
[52] Keiji Morokuma,et al. Protein environment facilitates O2 binding in non-heme iron enzyme. An insight from ONIOM calculations on isopenicillin N synthase (IPNS). , 2007, The journal of physical chemistry. B.
[53] Maciej Szaleniec,et al. Kinetics and mechanism of oxygen-independent hydrocarbon hydroxylation by ethylbenzene dehydrogenase. , 2007, Biochemistry.
[54] A. Munro,et al. Variations on a (t)heme--novel mechanisms, redox partners and catalytic functions in the cytochrome P450 superfamily. , 2007, Natural product reports.
[55] U. Yasar,et al. Inhibitory effect of valproic acid on cytochrome P450 2C9 activity in epilepsy patients , 2007, Basic & clinical pharmacology & toxicology.
[56] J. Heider. Adding handles to unhandy substrates: anaerobic hydrocarbon activation mechanisms. , 2007, Current opinion in chemical biology.
[57] Walter Thiel,et al. QM/MM studies of enzymes. , 2007, Current opinion in chemical biology.
[58] G. Schulz,et al. Crystal structure of ethylbenzene dehydrogenase from Aromatoleum aromaticum. , 2006, Structure.
[59] Tomasz Borowski,et al. Modeling enzymatic reactions involving transition metals. , 2006, Accounts of chemical research.
[60] Sam P. de Visser,et al. Propene activation by the oxo-iron active species of taurine/α- ketoglutarate dioxygenase (TauD) enzyme. How does the catalysis compare to heme-enzymes? , 2006 .
[61] Thom Vreven,et al. Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM. , 2006, Journal of chemical theory and computation.
[62] Y. Mishina,et al. Oxidative dealkylation DNA repair mediated by the mononuclear non-heme iron AlkB proteins. , 2006, Journal of inorganic biochemistry.
[63] P. Weber,et al. Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB , 2006, Nature.
[64] Y. Mishina,et al. Direct reversal of DNA alkylation damage. , 2006, Chemical reviews.
[65] P. O'Brien. Catalytic promiscuity and the divergent evolution of DNA repair enzymes. , 2006, Chemical reviews.
[66] R. Reinhardt,et al. Crystal structure and enzyme kinetics of the (S)-specific 1-phenylethanol dehydrogenase of the denitrifying bacterium strain EbN1. , 2006, Biochemistry.
[67] Ilme Schlichting,et al. Structure and chemistry of cytochrome P450. , 2005, Chemical reviews.
[68] Sason Shaik,et al. Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes. , 2005, Chemical reviews.
[69] Sason Shaik,et al. Mechanism of oxidation reactions catalyzed by cytochrome p450 enzymes. , 2004, Chemical reviews.
[70] P. O’Neill,et al. Knowledge of the proposed chemical mechanism of action and cytochrome p450 metabolism of antimalarial trioxanes like artemisinin allows rational design of new antimalarial peroxides. , 2004, Accounts of chemical research.
[71] D. Richardson,et al. Architecture of NarGH reveals a structural classification of Mo-bisMGD enzymes. , 2004, Structure.
[72] Tomasz Borowski,et al. Mechanism of dioxygen activation in 2-oxoglutarate-dependent enzymes: a hybrid DFT study. , 2004, Chemistry.
[73] S. Shaik,et al. Radical clock substrates, their C-H hydroxylation mechanism by cytochrome P450, and other reactivity patterns: what does theory reveal about the clocks' behavior? , 2004, Journal of the American Chemical Society.
[74] Michael Kube,et al. The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1 , 2004, Archives of Microbiology.
[75] J. Groves. The bioinorganic chemistry of iron in oxygenases and supramolecular assemblies , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[76] Takashi Kamachi,et al. A theoretical study on the mechanism of camphor hydroxylation by compound I of cytochrome p450. , 2003, Journal of the American Chemical Society.
[77] Erling Seeberg,et al. AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli , 2002, Nature.
[78] Robert P. Hausinger,et al. Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage , 2002, Nature.
[79] M. Reiher,et al. Reparameterization of hybrid functionals based on energy differences of states of different multiplicity , 2001 .
[80] J. S. Wang,et al. In vitro evaluation of valproic acid as an inhibitor of human cytochrome P450 isoforms: preferential inhibition of cytochrome P450 2C9 (CYP2C9). , 2001, British journal of clinical pharmacology.
[81] S. Shaik,et al. How Does Ethene Inactivate Cytochrome P450 En Route to Its Epoxidation? A Density Functional Study. , 2001, Angewandte Chemie.
[82] Alfred M. Spormann,et al. Isolation and Characterization of Anaerobic Ethylbenzene Dehydrogenase, a Novel Mo-Fe-S Enzyme , 2001, Journal of bacteriology.
[83] J. Heider,et al. Ethylbenzene Dehydrogenase, a Novel Hydrocarbon-oxidizing Molybdenum/Iron-Sulfur/Heme Enzyme* , 2001, The Journal of Biological Chemistry.
[84] F. Guengerich,et al. Common and uncommon cytochrome P450 reactions related to metabolism and chemical toxicity. , 2001, Chemical research in toxicology.
[85] P. Ortiz de Montellano,et al. Roles of the proximal heme thiolate ligand in cytochrome p450(cam). , 2001, Journal of the American Chemical Society.
[86] J Berendzen,et al. The catalytic pathway of cytochrome p450cam at atomic resolution. , 2000, Science.
[87] R. Prince,et al. Structure of the Molybdenum Site of Dimethyl Sulfoxide Reductase , 1999 .
[88] J. Peterson,et al. Dynamics of protein-bound water in the heme domain of P450BM3 studied by high-pressure spectroscopy: comparison with P450cam and P450 2B4. , 1999, Biochemistry.
[89] J. Heider,et al. Initial reactions of anaerobic metabolism of alkylbenzenes in denitrifying and sulfate-reducing bacteria , 1998, Archives of Microbiology.
[90] A. Parkinson,et al. Isozyme-selective metabolism of ethyl carbamate by cytochrome P450 (CYP2E1) and carboxylesterase (hydrolase A) enzymes in murine liver microsomes. , 1998, Drug metabolism and disposition: the biological fate of chemicals.
[91] A. Rettie,et al. Human CYP2C9 and CYP2A6 mediate formation of the hepatotoxin 4-ene-valproic acid. , 1997, The Journal of pharmacology and experimental therapeutics.
[92] P. Forkert,et al. Metabolism of ethyl carbamate by pulmonary cytochrome P450 and carboxylesterase isozymes: involvement of CYP2E1 and hydrolase A. , 1997, Toxicology and applied pharmacology.
[93] J. Dawson,et al. Heme-Containing Oxygenases. , 1996, Chemical reviews.
[94] Feliu Maseras,et al. IMOMM: A new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states , 1995, J. Comput. Chem..
[95] K. Bachmann,et al. The influence of anesthetic agents on rat hepatic cytochromes P450 in vivo. , 1995, Pharmacology.
[96] T. Baillie,et al. CYP4 isozyme specificity and the relationship between omega-hydroxylation and terminal desaturation of valproic acid. , 1995, Biochemistry.
[97] A. Becke. Density-functional thermochemistry. III. The role of exact exchange , 1993 .
[98] M. Karplus,et al. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations , 1990 .
[99] A. Fulco,et al. Coding nucleotide, 5' regulatory, and deduced amino acid sequences of P-450BM-3, a single peptide cytochrome P-450:NADPH-P-450 reductase from Bacillus megaterium. , 1989, The Journal of biological chemistry.
[100] T. Baillie,et al. Cytochrome P-450-catalyzed desaturation of valproic acid in vitro. Species differences, induction effects, and mechanistic studies. , 1988, The Journal of biological chemistry.
[101] Parr,et al. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.
[102] S. Sligar,et al. Metabolic switching in cytochrome P-450cam: Deuterium isotope effects on regiospecificity and the monooxygenase/oxidase ratio , 1987 .
[103] T. Baillie,et al. Cytochrome P-450--catalyzed formation of delta 4-VPA, a toxic metabolite of valproic acid. , 1987, Science.
[104] Ortiz de Montellano,et al. Cytochrome P-450: Structure, Mechanism, and Biochemistry , 1986 .
[105] B C Finzel,et al. The 2.6-A crystal structure of Pseudomonas putida cytochrome P-450. , 1985, The Journal of biological chemistry.
[106] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[107] M. Gelb,et al. Stereochemistry and deuterium isotope effects in camphor hydroxylation by the cytochrome P450cam monoxygenase system. , 1982, Biochemistry.
[108] M. Levitt,et al. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.
[109] T. Omura,et al. A new cytochrome in liver microsomes. , 1962, The Journal of biological chemistry.
[110] Matthew G. Quesne,et al. Proceedings of the Chemical Society. June 1958 , 1958 .