Similarities and Differences between Thymine(6?4)Thymine/Cytosine DNA Lesion Repairs by Photolyases
Similarities and Differences between Thymine(6?4)Thymine/Cytosine DNA Lesion Repairs by Photolyases
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光解酶修复胸腺嘧啶 (6?4) 胸腺嘧啶/胞嘧啶 DNA 损伤的异同
DOI：
10.1021/acs.jpcb.8b07048
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发表时间：
2018
期刊：
影响因子：
--
通讯作者：
Kitao Akio
中科院分区：
文献类型：
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作者：
Dokainish Hisham M.;Kitao Akio
光解酶是一种古老的酶，它收集阳光来修复DNA嘧啶损伤，如嘧啶（6-4）嘧啶酮和环丁烷二聚体。特别地，（6-4）光裂合酶（（6-4）PHR）通过修复胸腺嘧啶（6-4）胸腺嘧啶（T（6-4）T）和胸腺嘧啶（6-4）胞嘧啶（T（6-4）C）光损伤在维持遗传完整性中起重要作用。大多数（6-4）PHR研究都是基于前者的活性并假设两种修复机制的等效性进行的，尽管后者的活性研究仍然很少。在这里，我们描述的T（6-4）C二聚体的修复过程的调查使用几种计算方法，从分子动力学（MD）模拟大量子力学/分子力学方法。两种可能的机制，历史上提出的氮杂环丁烷四元环中间体和自由NH3的形成途径，被认为是。MD结果预测，用于修复T（6-4）C二聚体的重要活性位点组氨酸残基具有类似于（6-4）PHR/T（6-4）T复合物中所见的质子化状态。更重要的是，尽管两种底物之间存在化学差异，但确定了类似的修复机制：His 365质子化NH 2，导致游离NH3的形成/激活机制，诱导NH 2转移到5′碱基，最终导致嘧啶恢复。该反应在热力学上是有利的，其限速势垒为20.4 kcal mol-1。与此相反，氮杂环丁烷中间体是不可行的，拥有60千卡mol-1的能量障碍，这个障碍是类似的氧杂环丁烷中间体在T（6-4）T修复预测。虽然两种基质的修复具有相当的量子产率，但T（6-4）C中的反应性络合物被证明是3′碱基自由基，具有较低的背电子转移驱动力和较高的催化能垒。这些结果表明，在两种基板之间的一般修复机制的相似性，同时强调在修复周期中的电子动力学的差异。
Photolyases are ancient enzymes that harvest sunlight to repair DNA pyrimidine lesions such as pyrimidine(6–4)pyrimidone and cyclobutane dimers. Particularly, (6–4) photolyase ((6–4)PHR) plays an important role in maintaining genetic integrity by repairing thymine(6–4)thymine (T(6–4)T) and thymine(6–4)cytosine (T(6–4)C) photolesions. The majority of (6–4)PHR studies have been performed on the basis of the former’s activity and assuming the equivalence of the two repair mechanisms, although the latter’s activity remains poorly studied. Here, we describe investigations of the repair process of the T(6–4)C dimer using several computational methods from molecular dynamics (MD) simulations to large quantum mechanical/molecular mechanical approaches. Two possible mechanisms, the historically proposed azetidine four-member ring intermediate and the free NH3formation pathways, were considered. The MD results predicted that important active site histidine residues employed for the repair of the T(6–4)C dimer have protonation states similar to those seen in the (6–4)PHR/T(6–4)T complex. More importantly, despite chemical differences between the two substrates, a similar repair mechanism was identified: His365 protonates NH2, resulting in formation/activation mechanism of a free NH3, inducing NH2transfer to the 5′ base, and ultimately leading to pyrimidine restoration. This reaction is thermodynamically favorable with a rate-limiting barrier of 20.4 kcal mol–1. In contrast, the azetidine intermediate is unfeasible, possessing an energy barrier of 60 kcal mol–1; this barrier is similar to that predicted for the oxetane intermediate in T(6–4)T repair. Although both substrates are repaired with comparable quantum yields, the reactive complex in T(6–4)C was shown to be a 3′ base radical with a lower driving force for back electron transfer combined with higher energy barrier for catalysis. These results showed the similarity in the general repair mechanisms between the two substrates while emphasizing differences in the electron dynamics in the repair cycle.