Escherichia coli AlkB and single-stranded DNA binding protein SSB interaction explored by Molecular Dynamics Simulation

Mohan, Monisha and Pandya, Vishal and Roy, Anindya (2018) Escherichia coli AlkB and single-stranded DNA binding protein SSB interaction explored by Molecular Dynamics Simulation. Journal of Molecular Graphics and Modelling, 84. pp. 29-35. ISSN 1093-3263

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Abstract

Repair of alkylation damage in DNA is essential for maintaining genome integrity. Escherichia Coli (E.coli) DNA repair enzyme AlkB removes methyl adducts including 1-methyladenine and 3-methylcytosine present in DNA by oxidative demethylation from single-stranded DNA (ssDNA). E. coli single-stranded DNA binding protein (SSB) selectively binds ssDNA in a sequence-independent manner. We have recently shown that AlkB can repair methyl adduct present in SSB-coated ssDNA. In this study, we aimed to elucidate details of AlkB-mediated DNA repair of SSB-bound DNA substrate. Therefore, we generated a structural model of AlkB-SSB-ssDNA and using Molecular Dynamics simulation analysis we show that flexibility of SSB-bound DNA allows AlkB to bind in multiple ways. Our docking analysis of AlkB-SSB-ssDNA structure revealed that the Cyt109 base is present in the hydrophobic cavity of AlkB active site pocket. The characterization of AlkB-SSB interaction pattern would likely to help in understanding the mode of alkylated DNA adduct recognition

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IITH Creators:
IITH CreatorsORCiD
Roy, Anindyahttp://orcid.org/0000-0001-8561-907X
Item Type: Article
Uncontrolled Keywords: AlkB, Alkylation, DNA repair, Fe(II)/2-Oxoglutarate-dependent dioxygenase, SSB
Subjects: Others > Biotechnology
Depositing User: Team Library
Date Deposited: 04 Jun 2018 10:17
Last Modified: 04 Jun 2018 10:17
URI: http://raiith.iith.ac.in/id/eprint/3980
Publisher URL: http://doi.org/10.1016/j.jmgm.2018.05.007
OA policy: http://www.sherpa.ac.uk/romeo/issn/1093-3263/
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