Mechanistic Insights into Substrate Positioning That Distinguish Non-heme Fe(II)/α-Ketoglutarate-Dependent Halogenases and Hydroxylases

Algorithm-aided engineering of aliphatic halogenase WelO5* for the asymmetric late-stage functionalization of soraphens

(2022) Johannes Büchler et al.   Nature Communications

Engineering Fe(II)/α-Ketoglutarate-Dependent Halogenases and Desaturases

(2022) Athena Papadopoulou et al.   BIOCHEMISTRY

Influence of the Greater Protein Environment on the Electrostatic Potential in Metalloenzyme Active Sites: The Case of Formate Dehydrogenase

(2022) Azadeh Nazemi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Probing the Mechanism of Isonitrile Formation by a Non-Heme Iron(II)-Dependent Oxidase/Decarboxylase

(2022) Antonio Del Rio Flores et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Are Vanadium Intermediates Suitable Mimics in Non-Heme Iron Enzymes? An Electronic Structure Analysis

(2022) Vyshnavi Vennelakanti et al.   ACS Catalysis

Status report on the quantum chemical cluster approach for modeling enzyme reactions

(2022) Fahmi Himo et al.   Communications Chemistry

Mechanism for the Halogenation and Azidation of Lysine Catalyzed by Non‐heme Iron BesD Enzyme

(2022) Rui‐Ning Li et al.   Chemistry-An Asian Journal

Using Computational Chemistry To Reveal Nature’s Blueprints for Single-Site Catalysis of C–H Activation

(2022) Aditya Nandy et al.   ACS Catalysis

Modulating Chemoselectivity in a Fe(II)/α-Ketoglutarate-Dependent Dioxygenase for the Oxidative Modification of a Nonproteinogenic Amino Acid

(2021) Fabian Meyer et al.   ACS Catalysis

Mechanisms of O2 Activation by Mononuclear Non-Heme Iron Enzymes

(2021) Edward I. Solomon et al.   BIOCHEMISTRY

Re‐Programming and Optimization of a L ‐Proline cis ‐4‐Hydroxylase for the cis ‐3‐Halogenation of its Native Substrate

(2021) Athena Papadopoulou et al.   ChemCatChem

Spectroscopically Guided Simulations Reveal Distinct Strategies for Positioning Substrates to Achieve Selectivity in Nonheme Fe(II)/α-Ketoglutarate-Dependent Halogenases

(2021) Rimsha Mehmood et al.   ACS Catalysis

Electrostatic Perturbations in the Substrate‐Binding Pocket of Taurine/α‐Ketoglutarate Dioxygenase Determine its Selectivity

(2021) Hafiz Saqib Ali et al.   CHEMISTRY-A EUROPEAN JOURNAL

Exploring the biocatalytic potential of Fe/α‐ketoglutarate dependent halogenases

(2020) Moritz Voss et al.   CHEMISTRY-A EUROPEAN JOURNAL

Determining the Inherent Selectivity for Carbon Radical Hydroxylation versus Halogenation with FeIII(OH)(X) Complexes: Relevance to the Rebound Step in Non-heme Iron Halogenases

(2020) Vishal Yadav et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

TeraChem : A graphical processing unit ‐accelerated electronic structure package for large‐scale ab initio molecular dynamics

(2020) Stefan Seritan et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Nuclear Resonance Vibrational Spectroscopic Definition of the Facial Triad FeIV═O Intermediate in Taurine Dioxygenase: Evaluation of Structural Contributions to Hydrogen Atom Abstraction

(2020) Martin Srnec et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Biochemical and crystallographic investigations into isonitrile formation by a non-heme iron-dependent oxidase/decarboxylase

(2020) Rohan Jonnalagadda et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Discovery of a pathway for terminal-alkyne amino acid biosynthesis

(2019) J. A. Marchand et al.   NATURE

Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis

(2019) Helena W. Qi et al.   Journal of Chemical Information and Modeling

The Protein’s Role in Substrate Positioning and Reactivity for Biosynthetic Enzyme Complexes: The Case of SyrB2/SyrB1

(2019) Rimsha Mehmood et al.   ACS Catalysis

A family of radical halogenases for the engineering of amino-acid-based products

(2019) Monica E. Neugebauer et al.   Nature Chemical Biology

Evolved Aliphatic Halogenases Enable Regiocomplementary C−H Functionalization of a Pharmaceutically Relevant Compound

(2019) Takahiro Hayashi et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Structure of a Ferryl Mimic in the Archetypal Iron(II)- and 2-(Oxo)-glutarate-Dependent Dioxygenase, TauD

(2019) Katherine M. Davis et al.   BIOCHEMISTRY

Isonitrile Formation by a Non-Heme Iron(II)-Dependent Oxidase/Decarboxylase

(2018) Nicholas C. Harris et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Chloride Supports O2 Activation in the D201G Facial Triad Variant of Factor-Inhibiting Hypoxia Inducible Factor, an α-Ketoglutarate Dependent Oxygenase

(2018) Vanessa D. Chaplin et al.   INORGANIC CHEMISTRY

Selective C–H halogenation over hydroxylation by non-heme iron(iv)-oxo

(2018) Sujoy Rana et al.   Chemical Science

A Comparative Review on the Catalytic Mechanism of Nonheme Iron Hydroxylases and Halogenases

(2018) Amy Timmins et al.   Catalysts

Does Substrate Positioning Affect the Selectivity and Reactivity in the Hectochlorin Biosynthesis Halogenase?

(2018) Amy Timmins et al.   Frontiers in Chemistry

Vanadyl as a Stable Structural Mimic of Reactive Ferryl Intermediates in Mononuclear Nonheme-Iron Enzymes

(2017) Ryan J. Martinie et al.   INORGANIC CHEMISTRY

Visualizing the Reaction Cycle in an Iron(II)- and 2-(Oxo)-glutarate-Dependent Hydroxylase

(2017) Andrew J. Mitchell et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Frontier Molecular Orbital Contributions to Chlorination versus Hydroxylation Selectivity in the Non-Heme Iron Halogenase SyrB2

(2017) Martin Srnec et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

O2 Activation by Non-Heme Iron Enzymes

(2016) Edward I. Solomon et al.   BIOCHEMISTRY

MCPB.py: A Python Based Metal Center Parameter Builder

(2016) Pengfei Li et al.   Journal of Chemical Information and Modeling

Electronic Structure of the Ferryl Intermediate in the α-Ketoglutarate Dependent Non-Heme Iron Halogenase SyrB2: Contributions to H Atom Abstraction Reactivity

(2016) Martin Srnec et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural basis for halogenation by iron- and 2-oxo-glutarate-dependent enzyme WelO5

(2016) Andrew J Mitchell et al.   Nature Chemical Biology

Selective Chlorination of Substrates by the Halogenase SyrB2 Is Controlled by the Protein According to a Combined Quantum Mechanics/Molecular Mechanics and Molecular Dynamics Study

(2016) Jing Huang et al.   ACS Catalysis

Structural analysis of a phosphonate hydroxylase with an access tunnel at the back of the active site

(2016) Changqing Li et al.   Acta Crystallographica Section F-Structural Biology Communications

Catalytic Mechanisms of Fe(II)- and 2-Oxoglutarate-dependent Oxygenases

(2015) Salette Martinez et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Experimental Correlation of Substrate Position with Reaction Outcome in the Aliphatic Halogenase, SyrB2

(2015) Ryan J. Martinie et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Identification and Characterization of a Welwitindolinone Alkaloid Biosynthetic Gene Cluster in the Stigonematalean CyanobacteriumHapalosiphon welwitschii

(2014) Matthew L. Hillwig et al.   CHEMBIOCHEM

A new family of iron-dependent halogenases acts on freestanding substrates

(2014) Matthew L Hillwig et al.   Nature Chemical Biology

Geometric and Electronic Structure Contributions to Function in Non-heme Iron Enzymes

(2013) Edward I. Solomon et al.   ACCOUNTS OF CHEMICAL RESEARCH

Substrate Placement Influences Reactivity in Non-heme Fe(II) Halogenases and Hydroxylases

(2013) Heather J. Kulik et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Measuring the Orientation of Taurine in the Active Site of the Non-Heme Fe(II)/α-Ketoglutarate-Dependent Taurine Hydroxylase (TauD) Using Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy

(2013) Thomas M. Casey et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Elucidation of the Fe(iv)=O intermediate in the catalytic cycle of the halogenase SyrB2

(2013) Shaun D. Wong et al.   NATURE

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

Ab Initio Quantum Chemistry for Protein Structures

(2012) Heather J. Kulik et al.   JOURNAL OF PHYSICAL CHEMISTRY B

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

 -Frontier molecular orbitals in S = 2 ferryl species and elucidation of their contributions to reactivity

(2012) M. Srnec et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiwfn: A multifunctional wavefunction analyzer

(2011) Tian Lu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

A smooth, nonsingular, and faithful discretization scheme for polarizable continuum models: The switching/Gaussian approach

(2010) Adrian W. Lange et al.   JOURNAL OF CHEMICAL PHYSICS

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

(2010) Stefan Grimme et al.   JOURNAL OF CHEMICAL PHYSICS

An Active-Site Phenylalanine Directs Substrate Binding and C−H Cleavage in the α-Ketoglutarate-Dependent Dioxygenase TauD

(2010) Kevin P. McCusker et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mechanism of Selective Halogenation by SyrB2: A Computational Study

(2010) Tomasz Borowski et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase

(2010) Chengqi Yi et al.   NATURE

Substrate-Triggered Formation and Remarkable Stability of the C−H Bond-Cleaving Chloroferryl Intermediate in the Aliphatic Halogenase, SyrB2

(2009) Megan L. Matthews et al.   BIOCHEMISTRY

Why does the enzyme SyrB2 chlorinate, but does not hydroxylate, saturated hydrocarbons? A density functional theory (DFT) study

(2009) Shanthi Pandian et al.   DALTON TRANSACTIONS

First-Principles Study of Non-heme Fe(II) Halogenase SyrB2 Reactivity

(2009) Heather J. Kulik et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Substrate positioning controls the partition between halogenation and hydroxylation in the aliphatic halogenase, SyrB2

(2009) M. L. Matthews et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation

(2008) Ivan S. Ufimtsev et al.   Journal of Chemical Theory and Computation

Comparative Quantum Mechanics/Molecular Mechanics (QM/MM) and Density Functional Theory Calculations on the Oxo−Iron Species of Taurine/α-Ketoglutarate Dioxygenase

(2008) Elizabeth Godfrey et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Carbon Dioxide: A Waste Product in the Catalytic Cycle of α-Ketoglutarate Dependent Halogenases Prevents the Formation of Hydroxylated By-Products

(2008) Sam P. de Visser et al.   JOURNAL OF PHYSICAL CHEMISTRY B