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Role of Structural Dynamics in Selectivity and Mechanism of Non-heme Fe(II) and 2-Oxoglutarate-Dependent Oxygenases Involved in DNA Repair

author

Christopher J. Schofield

1960 -

published in: ACS Central Science

date of publication: 2020-05-08

Cites articles 76

Date

Title

Authors

2019-12-11

Catalysis by the Non-Heme Iron(II) Histone Demethylase PHF8 Involves Iron Center Rearrangement and Conformational Modulation of Substrate Orientation

Christopher J. Schofield
2019-09-10

Structure-function relationships in KDM7 histone demethylases
2019-03-26

Conformational Dynamics Underlies Different Functions of Human KDM7 Histone Demethylases

Shobhit S Chaturvedi, Rajeev Ramanan, Sodiq O Waheed, Jon Ainsley, Martin Evison, Christopher J. Schofield, Tatyana G Karabencheva-Christova, Christo Z Christov
2019-02-01

Conformational flexibility influences structure-function relationships in nucleic acid N-methyl demethylases

Sodiq O Waheed, Rajeev Ramanan, Shobhit S Chaturvedi, Martin Evison, Christopher J. Schofield
2018-09-11

Insight into wild-type and T1372E TET2-mediated 5hmC oxidation using ab initio QM/MM calculations

Hedieh Torabifard, Gerardo Andrés Cisneros
2018-10-11

Active Site Breathing of Human Alkbh5 Revealed by Solution NMR and Accelerated Molecular Dynamics
2018-05-01

NMR analyses on N-hydroxymethylated nucleobases - implications for formaldehyde toxicity and nucleic acid demethylases

Tom Brown, Sr., Christopher J. Schofield, Richard J. Hopkinson, Shifali Shishodia, Afaf Helmy El-Sagheer, Tim Claridge
2017-09-11

Molecular and cellular mechanisms of HIF prolyl hydroxylase inhibitors in clinical trials.

Akane Kawamura, Peter J. Ratcliffe, Rasheduzzaman Chowdhury, Christopher J. Schofield, T-L Yeh, Martine I. Abboud, Cyrille C Thinnes, Onur Atasoylu, Christopher T Lohans, Ivanhoe K. H. Leung, Ian J Clifton, Emily Flashman, Xin Lu, Chris Pugh, Timothy D W Claridge, Anthony Tumber, James P Holt-Martyn, Kerstin Lippl
2017-07-05

Computational investigation of O2 diffusion through an intra-molecular tunnel in AlkB; influence of polarization on O2 transport

Gerardo Andrés Cisneros
2017-08-20

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

Carsten Krebs, Andrew J Mitchell, Ryan J Martinie, Christopher J Pollock, Wei-Chen Chang, Alexey Silakov, Amie K. Boal, J. Martin Bollinger Jr.
2017-07-20

Mechanistic insights into dioxygen activation, oxygen atom exchange and substrate epoxidation by AsqJ dioxygenase from quantum mechanical/molecular mechanical calculations
2017-05-22

Atom Tunneling in the Hydroxylation Process of Taurine/α-Ketoglutarate Dioxygenase Identified by Quantum Mechanics/Molecular Mechanics Simulations

Sonia Álvarez Barcia, Johannes Kästner
2017-03-24

Oncometabolites d- and l-2-Hydroxyglutarate Inhibit the AlkB Family DNA Repair Enzymes under Physiological Conditions

Bogdan Fedeles, Deyu Li, Ke Bian
2016-02-25

MCPB.py: A Python Based Metal Center Parameter Builder

Pengfei Li
2016-02-23

Mechanism of O2 Activation by α-Ketoglutarate Dependent Oxygenases Revisited. A Quantum Chemical Study

Mariusz Radoń
2015-11-18

Dioxygen Binding in the Active Site of Histone Demethylase JMJD2A and the Role of the Protein Environment.

Robert Paton
2015-07-23

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

Kevin E Hauser
2015-07-07

The AlkB Family of Fe(II)/α-Ketoglutarate-dependent Dioxygenases: Repairing Nucleic Acid Alkylation Damage and Beyond

Bogdan Fedeles
2015-04-01

New Langevin and gradient thermostats for rigid body dynamics

Thomas E. Ouldridge, Ruslan L. Davidchack, Michael V Tretyakov
2015-04-02

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

Samuel Genheden, Ulf Ryde
2014-10-27

Homology modeling, molecular dynamics, and site-directed mutagenesis study of AlkB human homolog 1 (ALKBH1)

Robert Hausinger, Gerardo Andrés Cisneros
2014-09-25

Alternative Pathway for the Reaction Catalyzed by DNA Dealkylase AlkB from Ab Initio QM/MM Calculations

Gerardo Andrés Cisneros
2014-09-22

Theory uncovers an unusual mechanism of DNA repair of a lesioned adenine by AlkB enzymes

Chunsen Li
2014-07-20

Protein dynamics control the progression and efficiency of the catalytic reaction cycle of the Escherichia coli DNA-repair enzyme AlkB

Michelle L Gill
2014-04-24

Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field

Anna Pabis, Inacrist Geronimo, Piotr Paneth, Darrin M York
2014-03-05

Switching demethylation activities between AlkB family RNA/DNA demethylases through exchange of active-site residues

Chenxu Zhu, Chengqi Yi
2014-02-28

Nucleic acid oxidation in DNA damage repair and epigenetics
2013-06-25

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

Thomas E. Cheatham, III
2013-12-11

Quantum mechanics/molecular mechanics study on the oxygen binding and substrate hydroxylation step in AlkB repair enzymes

Matthew Quesne, Reza Latifi
2013-09-26

Geometric and electronic structure contributions to function in non-heme iron enzymes

Edward I. Solomon
2013-05-13

A simple but effective modeling strategy for structural properties of non-heme Fe(II) sites in proteins: test of force field models and application to proteins in the AlkB family

Keli Han
2013-05-16

Ab initio QM/MM calculations show an intersystem crossing in the hydrogen abstraction step in dealkylation catalyzed by AlkB

Gerardo Andrés Cisneros, Richard L Lord

Article - wd:Q96110408

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