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

LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields

(2016) Eric G. Kratz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine

(2016) Monica Yun Liu et al.   Nature Chemical Biology

A computational investigation on the substrate preference of ten-eleven-translocation 2 (TET2)

(2016) Junyan Lu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Biochemical reconstitution of TET1–TDG–BER-dependent active DNA demethylation reveals a highly coordinated mechanism

(2016) Alain R. Weber et al.   Nature Communications

Computational Analysis of Ammonia Transfer Along Two Intramolecular Tunnels in Staphylococcus aureus Glutamine-Dependent Amidotransferase (GatCAB)

(2015) Sajeewa Walimuni Dewage et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural insight into substrate preference for TET-mediated oxidation

(2015) Lulu Hu et al.   NATURE

Charting oxidized methylcytosines at base resolution

(2015) Hao Wu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Charting oxidized methylcytosines at base resolution

(2015) Hao Wu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2014) Dong Fang et al.   Journal of Chemical Theory and Computation

5-Hydroxymethylcytosine is a predominantly stable DNA modification

(2014) Martin Bachman et al.   Nature Chemistry

Crystal Structure of TET2-DNA Complex: Insight into TET-Mediated 5mC Oxidation

(2013) Lulu Hu et al.   CELL

Toward a Deeper Understanding of Enzyme Reactions Using the Coupled ELF/NCI Analysis: Application to DNA Repair Enzymes

(2013) Dong Fang et al.   Journal of Chemical Theory and Computation

Ab Initio QM/MM Calculations Show an Intersystem Crossing in the Hydrogen Abstraction Step in Dealkylation Catalyzed by AlkB

(2013) Dong Fang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computational Prediction of Residues Involved in Fidelity Checking for DNA Synthesis in DNA Polymerase I

(2012) Sarah E. Graham et al.   BIOCHEMISTRY

Effects of Dispersion in Density Functional Based Quantum Mechanical/Molecular Mechanical Calculations on Cytochrome P450 Catalyzed Reactions

(2012) Richard Lonsdale et al.   Journal of Chemical Theory and Computation

Regulation and function of DNA methylation in plants and animals

(2011) Xin-Jian He et al.   CELL RESEARCH

Tet1 and Tet2 Regulate 5-Hydroxymethylcytosine Production and Cell Lineage Specification in Mouse Embryonic Stem Cells

(2011) Kian Peng Koh et al.   Cell Stem Cell

Advances in DNA methylation: 5-hydroxymethylcytosine revisited

(2011) Christina Dahl et al.   CLINICA CHIMICA ACTA

Thymine DNA Glycosylase Can Rapidly Excise 5-Formylcytosine and 5-Carboxylcytosine

(2011) Atanu Maiti et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

NCIPLOT: A Program for Plotting Noncovalent Interaction Regions

(2011) Julia Contreras-García et al.   Journal of Chemical Theory and Computation

Nonheme oxo-iron(IV) intermediates form an oxyl radical upon approaching the C-H bond activation transition state

(2011) S. Ye et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

(2011) Y.-F. He et al.   SCIENCE

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

(2011) S. Ito et al.   SCIENCE

TET Genes: new players in DNA demethylation and important determinants for stemness

(2010) Fabian Mohr et al.   EXPERIMENTAL HEMATOLOGY

Inclusion of Dispersion Effects Significantly Improves Accuracy of Calculated Reaction Barriers for Cytochrome P450 Catalyzed Reactions

(2010) Richard Lonsdale et al.   Journal of Physical Chemistry Letters

Revealing Noncovalent Interactions

(2010) Erin R. Johnson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification

(2010) Shinsuke Ito et al.   NATURE

Active DNA demethylation: many roads lead to Rome

(2010) Susan C. Wu et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Insight into the mechanism of an iron dioxygenase by resolution of steps following the FeIVboxHO species

(2010) P. K. Grzyska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reaction Mechanism of the ε Subunit ofE. coliDNA Polymerase III: Insights into Active Site Metal Coordination and Catalytically Significant Residues

(2009) G. Andrés Cisneros et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Reprogramming towards pluripotency requires AID-dependent DNA demethylation

(2009) Nidhi Bhutani et al.   NATURE

Cytosine-5-methyltransferases add aldehydes to DNA

(2009) Zita Liutkevičiūtė et al.   Nature Chemical Biology

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE

Catalytic mechanism of human DNA polymerase λ with Mg2+ and Mn2+ from ab initio quantum mechanical/molecular mechanical studies

(2008) G. Andrés Cisneros et al.   DNA REPAIR

What can be learnt on biologically relevant systems from the topological analysis of the electron localization function?

(2008) J.-P. Piquemal et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Systematic optimization of long-range corrected hybrid density functionals

(2008) Jeng-Da Chai et al.   JOURNAL OF CHEMICAL PHYSICS

A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes

(2008) Jerry M. Parks et al.   JOURNAL OF CHEMICAL PHYSICS

Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections

(2008) Jeng-Da Chai et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS