Proteomics

Dataset Information

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The role and cooperation of AidB dehydrogenase and AlkB dioxygenase in repair of adducts to DNA and RNA bases

ABSTRACT: The aim of the project is to conduct in vivo, in vitro and in silico studies of the substrate specificity of AidB dehydrogenase against the by-products rising in AlkB dioxygenase repair reaction and AlkB and AidB cooperative interaction in the repair of adducts to DNA and RNA bases. AidB dehydrogenase and AlkB dioxygenase are induced in the E. coli adaptive response to alkylating agents. As a result of direct AlkB removal of base modifications, toxic and mutagenic by-products are formed: formaldehyde, glyoxal or malondialdehyde. Our studies indicate that AlkB is efficiently inhibited in vitro by the side products of the repair reaction. The biological role and substrates of AidB are unknown. It is known that AidB does not repair DNA lesions; its crystallographic structure points to small molecule substrates. This allowed me to formulate the hypothesis that AidB dehydrogenase may be involved in the detoxification of highly reactive by-products generated as a result of AlkB repair and that to prevent their release to the cell, these enzymes can interact directly in the cell homeostasis maintenance.

INSTRUMENT(S):

ORGANISM(S): Escherichia Coli

SUBMITTER: Ewa Sitkiewicz  

LAB HEAD: Michał Dadlez

PROVIDER: PXD057294 | Pride | 2025-05-07

REPOSITORIES: Pride

Json Xml

Dataset's files

Source:
Action DRS
AidB.DnX Other
AidBAlkB_exp_2.DnX Other
AidBAlkBwithIMStime.csv Csv
AidB_12_2023.raw.zip Raw
AidB_IMS.DnX Other
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Publications

HRaDeX: R Package and Web Server for Computing High-Resolution Deuterium Uptake Rates for HDX-MS Data.

Puchała Weronika W   Kistowski Michał M   Zhukova Liliya L   Burdukiewicz Michał M   Dadlez Michał M  

Journal of proteome research 20250319 4

Hydrogen-deuterium exchange monitored by mass spectrometry (HDX-MS) is a well-established and powerful technique used to study protein dynamics and stability by capturing local and global unfolding events in protein structures. However, in this technique, obtaining region-specific information requires proteolytic digestion that breaks the protein into peptide fragments, causing the HDX data to reflect averages over these fragments rather than individual amino acids. We propose a new computationa  ...[more]

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