Spectroscopic and in vitro Investigations of Fe 2+ /α-Ketoglutarate-Dependent Enzymes Involved in Nucleic Acid Repair and Modification.
David SchmidlNiko S W Lindlar Né JonassonAnnika MenkeSabine SchneiderLena J DaumannPublished in: Chembiochem : a European journal of chemical biology (2022)
The activation of molecular oxygen for the highly selective functionalization and repair of DNA and RNA nucleobases is achieved by α-ketoglutarate (α-KG)/iron-dependent dioxygenases. Of special interest are the human homologues AlkBH of Escherichia coli EcAlkB and ten-eleven translocation (TET) enzymes. These enzymes are involved in demethylation or dealkylation of DNA and RNA, although additional physiological functions are continuously being found. Given their importance, studying enzyme-substrate interactions, turnover and kinetic parameters is pivotal for the understanding of the mode of action of these enzymes. Diverse analytical methods, including X-ray crystallography, UV/Vis absorption, electron paramagnetic resonance (EPR), circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy have been employed to study the changes in the active site and the overall enzyme structure upon substrate, cofactor, and inhibitor addition. Several methods are now available to assess the activity of these enzymes. By discussing limitations and possibilities of these techniques for EcAlkB, AlkBH and TET we aim to give a comprehensive synopsis from a bioinorganic point-of-view, addressing researchers from different disciplines working in the highly interdisciplinary and rapidly evolving field of epigenetic processes and DNA/RNA repair and modification.
Keyphrases
- nucleic acid
- magnetic resonance
- escherichia coli
- circulating tumor
- single molecule
- cell free
- endothelial cells
- dna methylation
- gene expression
- high resolution
- magnetic resonance imaging
- pseudomonas aeruginosa
- computed tomography
- molecular docking
- staphylococcus aureus
- klebsiella pneumoniae
- bone mineral density
- cystic fibrosis
- amino acid
- candida albicans
- solar cells
- circulating tumor cells
- molecular dynamics simulations