Metal ion modeling using classical mechanics
P Li, KM Merz Jr - Chemical reviews, 2017 - ACS Publications
Metal ions play significant roles in numerous fields including chemistry, geochemistry,
biochemistry, and materials science. With computational tools increasingly becoming …
biochemistry, and materials science. With computational tools increasingly becoming …
Nucleic acid oxidation in DNA damage repair and epigenetics
Methylation is a widely occurring chemical modification in nucleic acids and proteins.
Methylating agents, either extracellular or intracellular, can attack vulnerable sites in DNA …
Methylating agents, either extracellular or intracellular, can attack vulnerable sites in DNA …
Role of structural dynamics in selectivity and mechanism of non-heme Fe (II) and 2-oxoglutarate-dependent oxygenases involved in DNA repair
AlkB and its human homologue AlkBH2 are Fe (II)-and 2-oxoglutarate (2OG)-dependent
oxygenases that repair alkylated DNA bases occurring as a consequence of reactions with …
oxygenases that repair alkylated DNA bases occurring as a consequence of reactions with …
Molecular Dynamics Simulation of an Iron (III) Binding Site on the Fc Domain of IgG1 Relevant for Visible Light-Induced Protein Fragmentation
Molecular dynamics simulations were employed to investigate the interaction between Fe
(III) and an iron-binding site composed of THR259, ASP252, and GLU261 on the Fc domain …
(III) and an iron-binding site composed of THR259, ASP252, and GLU261 on the Fc domain …
Computational studies of DNA base repair mechanisms by nonheme iron dioxygenases: selective epoxidation and hydroxylation pathways
DNA base repair mechanisms of alkylated DNA bases is an important reaction in chemical
biology and particularly in the human body. It is typically catalyzed by an α-ketoglutarate …
biology and particularly in the human body. It is typically catalyzed by an α-ketoglutarate …
A computational investigation on the substrate preference of ten-eleven-translocation 2 (TET2)
TET proteins iteratively convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine
(5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) in a Fe (II)/α-ketoglutarate …
(5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) in a Fe (II)/α-ketoglutarate …
Conformational flexibility influences structure–function relationships in nucleic acid N-methyl demethylases
N-Methylation of DNA/RNA bases can be regulatory or damaging and is linked to diseases
including cancer and genetic disorders. Bacterial AlkB and human FTO are DNA/RNA …
including cancer and genetic disorders. Bacterial AlkB and human FTO are DNA/RNA …
Structural determinants of nucleobase modification recognition in the AlkB family of dioxygenases
V Van Deuren, S Plessers, J Robben - DNA repair, 2020 - Elsevier
Iron-dependent dioxygenases of the AlkB protein family found in most organisms throughout
the tree of life play a major role in oxidative dealkylation processes. Many of these enzymes …
the tree of life play a major role in oxidative dealkylation processes. Many of these enzymes …
Spectroscopic and computational studies of a bifunctional iron-and 2-oxoglutarate dependent enzyme, AsqJ
Iron and 2-oxoglutarate dependent (Fe/2OG) enzymes exhibit an exceedingly broad
reaction repertoire. The most prevalent reactivity is hydroxylation, but many other reactivities …
reaction repertoire. The most prevalent reactivity is hydroxylation, but many other reactivities …
Oxidative Demethylation of DNA and RNA Mediated by Non‐Heme Iron‐Dependent Dioxygenases
DNA/RNA methylation can be generated by methyltransferases and thus plays a critical role
in regulating cellular processes; alternatively, nucleic acid methylation can be produced by …
in regulating cellular processes; alternatively, nucleic acid methylation can be produced by …