Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Hyderabad, 502285, Telangana, India.
Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Hyderabad, 502285, Telangana, India.
J Mol Graph Model. 2018 Sep;84:29-35. doi: 10.1016/j.jmgm.2018.05.007. Epub 2018 May 18.
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 by AlkB.
DNA 中烷基化损伤的修复对于维持基因组完整性至关重要。大肠杆菌（E.coli）DNA 修复酶 AlkB 通过氧化脱甲基作用从单链 DNA（ssDNA）中去除 DNA 中存在的甲基加合物，包括 1-甲基腺嘌呤和 3-甲基胞嘧啶。大肠杆菌单链 DNA 结合蛋白（SSB）以序列非依赖性的方式选择性地结合 ssDNA。我们最近表明，AlkB 可以修复 SSB 覆盖的 ssDNA 中存在的甲基加合物。在这项研究中，我们旨在阐明 AlkB 介导的 SSB 结合 DNA 底物的 DNA 修复的细节。因此，我们生成了 AlkB-SSB-ssDNA 的结构模型，并通过分子动力学模拟分析表明，SSB 结合的 DNA 的灵活性允许 AlkB 以多种方式结合。我们对 AlkB-SSB-ssDNA 结构的对接分析表明，Cyt109 碱基存在于 AlkB 活性位点口袋的疏水性腔中。AlkB-SSB 相互作用模式的表征可能有助于理解 AlkB 对烷基化 DNA 加合物的识别模式。
