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QM/MM Simulation on P450 BM3 Enzyme Catalysis Mechanism

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Mixedab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide

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The High-Valent Compound of Cytochrome P450: The Nature of the Fe−S Bond and the Role of the Thiolate Ligand as an Internal Electron Donor

inferredcites →https://doi.org/10.1002/jcc.20292openalex-snapshot

Integrated Modeling Program, Applied Chemical Theory (IMPACT)

inferredcites →https://doi.org/10.1002/jcc.20398openalex-snapshot

Systematic QM/MM investigation of factors that affect the cytochrome P450‐catalyzed hydrogen abstraction of camphor

inferredcites →https://doi.org/10.1002/prot.20104openalex-snapshot

Free energy surfaces of β‐hairpin and α‐helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model

inferredcites →https://doi.org/10.1016/0022-2836(87)90190-2openalex-snapshot

HIGH-RESOLUTION CRYSTAL STRUCTURE OF CYTOCHROME P450-CAM

inferredcites →https://doi.org/10.1016/0891-5849(96)83807-xopenalex-snapshot

Cytochrome P450: Structure, mechanism, and biochemistry

inferredcites →https://doi.org/10.1016/j.ddtec.2004.11.008openalex-snapshot

Combined quantum and molecular mechanics (QM/MM)

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Computational Modeling of the Catalytic Reaction in Triosephosphate Isomerase

inferredcites →https://doi.org/10.1016/s0009-2614(00)00289-xopenalex-snapshot

Frozen orbital QM/MM methods for density functional theory

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Replica-exchange molecular dynamics method for protein folding

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How iron-containing proteins control dioxygen chemistry: a detailed atomic level description via accurate quantum chemical and mixed quantum mechanics/molecular mechanics calculations

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Cytochrome P-450. Multiplicity of isoforms, substrates, and catalytic and regulatory mechanisms

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Reactions and significance of cytochrome P-450 enzymes

inferredcites →https://doi.org/10.1021/bi011197qopenalex-snapshot

Pivotal Role of Water in the Mechanism of P450BM-3

inferredcites →https://doi.org/10.1021/cr030722jopenalex-snapshot

Theoretical Perspective on the Structure and Mechanism of Cytochrome P450 Enzymes

inferredcites →https://doi.org/10.1021/ja003583lopenalex-snapshot

Hydroxylation of Camphor by Reduced Oxy-Cytochrome P450cam: Mechanistic Implications of EPR and ENDOR Studies of Catalytic Intermediates in Native and Mutant Enzymes

inferredcites →https://doi.org/10.1021/ja005619fopenalex-snapshot

Medium Polarization and Hydrogen Bonding Effects on Compound I of Cytochrome P450: What Kind of a Radical Is It Really?

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A Theoretical Study on the Mechanism of Camphor Hydroxylation by Compound I of Cytochrome P450

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What Factors Affect the Regioselectivity of Oxidation by Cytochrome P450? A DFT Study of Allylic Hydroxylation and Double Bond Epoxidation in a Model Reaction

inferredcites →https://doi.org/10.1021/ja036123bopenalex-snapshot

Cytochrome P450CAM Enzymatic Catalysis Cycle: A Quantum Mechanics/Molecular Mechanics Study

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Mixed Quantum Mechanical/Molecular Mechanical (QM/MM) Study of the Deacylation Reaction in a Penicillin Binding Protein (PBP) versus in a Class C β-Lactamase

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Quantum Mechanical/Molecular Mechanical Investigation of the Mechanism of C−H Hydroxylation of Camphor by Cytochrome P450cam: Theory Supports a Two-State Rebound Mechanism

inferredcites →https://doi.org/10.1021/ja0438314openalex-snapshot

Observation of Ligand Binding to Cytochrome P450 BM-3 by Means of Solid-State NMR Spectroscopy

inferredcites →https://doi.org/10.1021/ja049847bopenalex-snapshot

Substrate Hydroxylation in Methane Monooxygenase: Quantitative Modeling via Mixed Quantum Mechanics/Molecular Mechanics Techniques

inferredcites →https://doi.org/10.1021/ja0524604openalex-snapshot

Thermal Equilibrium of High- and Low-Spin Forms of Cytochrome P450 BM-3: Repositioning of the Substrate?

inferredcites →https://doi.org/10.1021/ja058196wopenalex-snapshot

The Effect of Heme Environment on the Hydrogen Abstraction Reaction of Camphor in P450cam Catalysis: A QM/MM Study

inferredcites →https://doi.org/10.1021/ja058465iopenalex-snapshot

Conformational Equilibrium of Cytochrome P450 BM-3 Complexed with N-Palmitoylglycine: A Replica Exchange Molecular Dynamics Study

inferredcites →https://doi.org/10.1021/ja0672371openalex-snapshot

Conformational Dynamics of Substrate in the Active Site of Cytochrome P450 BM-3/NPG Complex: Insights from NMR Order Parameters

inferredcites →https://doi.org/10.1021/ja0685654openalex-snapshot

Proton Assisted Oxygen−Oxygen Bond Splitting in Cytochrome P450

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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy

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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening

inferredcites →https://doi.org/10.1021/jm050540copenalex-snapshot

Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects

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Impact of Plasticity and Flexibility on Docking Results for Cytochrome P450 2D6: A Combined Approach of Molecular Dynamics and Ligand Docking

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Localized Orbital Corrections for the Calculation of Ionization Potentials and Electron Affinities in Density Functional Theory

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Crystal structure of human cytochrome P450 2C9 with bound warfarin

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A localized orbital analysis of the thermochemical errors in hybrid density functional theory: Achieving chemical accuracy via a simple empirical correction scheme

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Density functional localized orbital corrections for transition metals

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A malleable catalyst dominates the metabolism of drugs

inferredcites →https://doi.org/10.1073/pnas.0732000100openalex-snapshot

Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450

inferredcites →https://doi.org/10.1074/jbc.m312516200openalex-snapshot

Structure of Human Microsomal Cytochrome P450 2C8

inferredcites →https://doi.org/10.1093/oxfordjournals.jbchem.a123562openalex-snapshot

Xenobiotic Responsive Element in the 5′-Upstream Region of the Human P-450c Gene1

inferredcites →https://doi.org/10.1096/fasebj.6.2.1537463openalex-snapshot

Cytochrome P450 and the arachidonate cascade 1

inferredcites →https://doi.org/10.1110/ps.062224407openalex-snapshot

Combining substrate dynamics, binding statistics, and energy barriers to rationalize regioselective hydroxylation of octane and lauric acid by CYP102A1 and mutants

inferredcites →https://doi.org/10.1126/science.1099736openalex-snapshot

Crystal Structures of Human Cytochrome P450 3A4 Bound to Metyrapone and Progesterone

inferredcites →https://doi.org/10.1126/science.287.5458.1615openalex-snapshot

The Catalytic Pathway of Cytochrome P450cam at Atomic Resolution

inferredcites →https://doi.org/10.1146/annurev.physchem.55.091602.094410openalex-snapshot

AB INITIO QUANTUM CHEMICAL AND MIXED QUANTUM MECHANICS/MOLECULAR MECHANICS (QM/MM) METHODS FOR STUDYING ENZYMATIC CATALYSIS

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/cctc.201701088openalex-snapshot

Selective Oxidations of Cyperenoic Acid by Slightly Reshaping the Binding Pocket of Cytochrome P450 BM3

inferred← citeshttps://doi.org/10.1002/cctc.201801829openalex-snapshot

P450 Monooxygenases Enable Rapid Late‐Stage Diversification of Natural Products via C−H Bond Activation

inferred← citeshttps://doi.org/10.1002/chem.201103170openalex-snapshot

Rate‐Controlling Isomerizations in Fatty Acid Oxidations by a Cytochrome P450 Compound I

inferred← citeshttps://doi.org/10.1002/cjoc.201300427openalex-snapshot

Catalytic Mechanism of Cytochrome P450 2D6 for 4‐Hydroxylation of Aripiprazole: A QM/MM Study

inferred← citeshttps://doi.org/10.1002/jcc.70127openalex-snapshot

Adaptive Restraints to Accelerate Geometry Optimizations of Large Biomolecular Systems

inferred← citeshttps://doi.org/10.1002/pro.2819openalex-snapshot

Successful application of the DBLOC method to the hydroxylation of camphor by cytochrome p450

inferred← citeshttps://doi.org/10.1002/qua.24481openalex-snapshot

Jaguar: A high‐performance quantum chemistry software program with strengths in life and materials sciences

inferred← citeshttps://doi.org/10.1007/s00894-012-1552-7openalex-snapshot

Insight into substituent effects in Cal-B catalyzed transesterification by combining experimental and theoretical approaches

inferred← citeshttps://doi.org/10.1007/s43393-026-00508-xopenalex-snapshot

Horseradish peroxidase and engineered P450BM3: progress and perspectives in biocatalytic nitration

inferred← citeshttps://doi.org/10.1016/j.jmgm.2014.05.012openalex-snapshot

Mechanistic insights into the catalytic reaction of plant allene oxide synthase (pAOS) via QM and QM/MM calculations

inferred← citeshttps://doi.org/10.1016/j.molcatb.2010.01.017openalex-snapshot

Oxidation of human cytochrome P450 1A2 substrates by Bacillus megaterium cytochrome P450 BM3

inferred← citeshttps://doi.org/10.1016/j.molcatb.2013.12.004openalex-snapshot

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Deciphering Reaction Determinants of Altered-Activity CYP2D6 Variants by Well-Tempered Metadynamics Simulation and QM/MM Calculations

inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00542openalex-snapshot

Mechanistic Insights into the P450 TleB-Catalyzed Unusual Intramolecular C–N Bond Formation Involved in the Biosynthesis of Indolactam V

inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00779openalex-snapshot

QM/MM Modeling Aided Enzyme Engineering in Natural Products Biosynthesis

inferred← citeshttps://doi.org/10.1021/acs.jcim.5c00115openalex-snapshot

Mechanism of Regio- and Enantioselective Hydroxylation of Arachidonic Acid Catalyzed by Human CYP2E1: A Combined Molecular Dynamics and Quantum Mechanics/Molecular Mechanics Study

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Computational Characterization of the Reactivity of Compound I in Unspecific Peroxygenases

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inferred← citeshttps://doi.org/10.1021/acs.jpcb.6b09923openalex-snapshot

Hydrogen Abstraction of Camphor Catalyzed by Cytochrome P450cam: A QM/MM Study

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Regio- and Enantioselective Oxidation of Eicosapentaenoic and Arachidonic Acids by Human CYP2E1: A Comparative Mechanistic Study

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IDSite: An Accurate Approach to Predict P450-Mediated Drug Metabolism

inferred← citeshttps://doi.org/10.1021/ct2006693openalex-snapshot

Development of Accurate DFT Methods for Computing Redox Potentials of Transition Metal Complexes: Results for Model Complexes and Application to Cytochrome P450

inferred← citeshttps://doi.org/10.1021/ct300329hopenalex-snapshot

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Compound I Reactivity Defines Alkene Oxidation Selectivity in Cytochrome P450cam

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Peer Review #1 of "In silico screening of 393 mutants facilitates enzyme engineering of amidase activity in CalB (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj.145v0.1/reviews/2openalex-snapshot

Peer Review #2 of "In silico screening of 393 mutants facilitates enzyme engineering of amidase activity in CalB (v0.1)"

inferred← citeshttps://doi.org/10.7717/peerj.145openalex-snapshot

In silico screening of 393 mutants facilitates enzyme engineering of amidase activity in CalB

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