Role of Structural Dynamics in Selectivity and Mechanism of Non-heme Fe(II) and 2-Oxoglutarate-Dependent Oxygenases Involved in DNA Repair
Role of Structural Dynamics in Selectivity and Mechanism of Non-heme Fe(II) and 2-Oxoglutarate-Dependent Oxygenases Involved in DNA Repair
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DOI：
10.1021/acscentsci.0c00312
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发表时间：
2020-05-27
影响因子：
18.2
通讯作者：
Karabencheva-Christova, Tatyana G.
中科院分区：
文献类型：
--
作者：
Waheed, Sodiq O.;Ramanan, Rajeev;Karabencheva-Christova, Tatyana G.
AlkB及其人类同源物AlkBH2是铁(II)-和2-氧葡萄糖酸盐（20G）依赖的加氧酶，修复与诱变剂反应产生的烷基化DNA碱基。我们采用分子动力学（MD）和量子力学/分子力学（QM/MM）相结合的方法研究了结构动力学如何影响AlkB-和alkbh2催化的3-甲基胞嘧啶（m(3)C）在单链（ssDNA）和双链（dsDNA） DNA中的选择性和机制。动力学研究揭示了蛋白质和DNA组分的灵活性在决定AlkB对ssDNA的偏好和AlkBH2对dsDNA的偏好方面的重要性。相关运动，包括疏水β发夹，参与了AlkBH2-dsDNA的底物结合。计算结果表明，在双氧与活性位点Fe结合之前，2OG重排比铁基重排更有利于形成具有催化活性的Fe(IV)=O中间体。氢原子在AlkBH2-dsDNA和AlkB-dsDNA中通过sigma通道进行转移；在AlkB-ssDNA中，sigma-和pi-通道之间存在竞争，这意味着在底物氧化过程中，复杂DNA的性质有可能改变分子轨道相互作用。我们的结果揭示了整个蛋白质- dna复合物在决定选择性中的重要性，以及底物的性质如何影响其机制。
AlkB and its human homologue AlkBH2 are Fe(II)- and 2-oxoglutarate (20G)-dependent oxygenases that repair alkylated DNA bases occurring as a consequence of reactions with mutagenic agents. We used molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) methods to investigate how structural dynamics influences the selectivity and mechanisms of the AlkB- and AlkBH2-catalyzed demethylation of 3-methylcytosine (m(3)C) in single (ssDNA) and double (dsDNA) stranded DNA. Dynamics studies reveal the importance of the flexibility in both the protein and DNA components in determining the preferences of AlkB for ssDNA and of AlkBH2 for dsDNA. Correlated motions, including of a hydrophobic beta-hairpin, are involved in substrate binding in AlkBH2-dsDNA. The calculations reveal that 2OG rearrangement prior to binding of dioxygen to the active site Fe is preferred over a ferryl rearrangement to form a catalytically productive Fe(IV)=O intermediate. Hydrogen atom transfer proceeds via a sigma-channel in AlkBH2-dsDNA and AlkB-dsDNA; in AlkB-ssDNA, there is a competition between sigma- and pi-channels, implying that the nature of the complexed DNA has potential to alter molecular orbital interactions during the substrate oxidation. Our results reveal the importance of the overall protein-DNA complex in determining selectivity and how the nature of the substrate impacts the mechanism.