Comparative Molecular Dynamics Studies of Human DNA Polymerase η.
Comparative Molecular Dynamics Studies of Human DNA Polymerase η.
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DOI：
10.1021/acs.jcim.5b00606
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发表时间：
2015-12-28
影响因子：
5.6
通讯作者：
Hammes-Schiffer S
中科院分区：
文献类型：
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作者：
Ucisik MN;Hammes-Schiffer S
高能紫外线辐射通过形成环丁烷嘧啶二聚体损伤DNA，从而阻碍复制。当损伤为胸腺嘧啶 - 胸腺嘧啶二聚体（TTD）时，人类DNA聚合酶η（Pol η）通过在损伤位点对面插入核苷酸来协助恢复复制过程。我们进行了广泛的分子动力学（MD）模拟，以研究四种不同的Pol η复合物在有或无TTD以及分别以dATP或dGTP作为进入碱基时的结构和动力学效应。在这四个系统中，未检测到整体结构和平衡动力学方面的重大差异，这表明该酶的特异性主要是由于结合区域局部相互作用的差异。对酶与DNA以及dNTP之间氢键相互作用的分析提供了分子层面的见解。具体而言，观察到TTD与酶之间的氢键相互作用比两个正常胸腺嘧啶未受损时更多。TTD由此产生的更大刚性和特定取向与在TTD位点比在具有两个正常胸腺嘧啶的类似位点具有更高的持续合成能力和整体效率的实验观察结果一致。含有dATP和dGTP的系统之间的相似性与关于进入碱基相对低保真度的实验观察结果一致。此外，发现Pol η家族中两个严格保守的氨基酸Q38和R61分别与TTD表现出持续的氢键相互作用以及与游离碱基的阳离子 - π相互作用。因此，这些模拟为该酶的选择性和效率的基础以及两个最严格保守残基的作用提供了分子层面的见解。
High-energy ultraviolet radiation damages DNA through the formation of cyclobutane pyrimidine dimers, which stall replication. When the lesion is a thymine–thymine dimer (TTD), human DNA polymerase η (Pol η) assists in resuming the replication process by inserting nucleotides opposite the damaged site. We performed extensive molecular dynamics (MD) simulations to investigate the structural and dynamical effects of four different Pol η complexes with or without a TTD and with either dATP or dGTP as the incoming base. No major differences in the overall structures and equilibrium dynamics were detected among the four systems, suggesting that the specificity of this enzyme is due predominantly to differences in local interactions in the binding regions. Analysis of the hydrogen-bonding interactions between the enzyme and the DNA and dNTP provided molecular-level insights. Specifically, the TTD was observed to engage in more hydrogen-bonding interactions with the enzyme than its undamaged counterpart of two normal thymines. The resulting greater rigidity and specific orientation of the TTD are consistent with the experimental observation of higher processivity and overall efficiency at TTD sites than at analogous sites with two normal thymines. The similarities between the systems containing dATP and dGTP are consistent with the experimental observation of relatively low fidelity with respect to the incoming base. Moreover, Q38 and R61, two strictly conserved amino acids across the Pol η family, were found to exhibit persistent hydrogen-bonding interactions with the TTD and cation-π interactions with the free base, respectively. Thus, these simulations provide molecular level insights into the basis for the selectivity and efficiency of this enzyme, as well as the roles of the two most strictly conserved residues.