Uncovering universal rules governing the selectivity of the archetypal DNA glycosylase TDG
Uncovering universal rules governing the selectivity of the archetypal DNA glycosylase TDG
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DOI：
10.1073/pnas.1803323115
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发表时间：
2018-06-05
影响因子：
11.1
通讯作者：
Ivanov, Ivaylo
中科院分区：
文献类型：
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作者：
Dodd, Thomas;Yan, Chunli;Ivanov, Ivaylo
胸腺嘧啶DNA糖基酶(TDG)是一种在基因组维持和表观遗传调控中具有双重作用的关键酶。TDG参与DNA中CpG位点的胞嘧啶去甲基化。在这里，我们使用分子建模来描述TDG的病变搜索和DNA碱基询问机制。首先，我们用经典分子动力学和加速分子动力学研究了TDG不仅能检测5-羧基胞嘧啶修饰的DNA底物，还能检测G：T错配和非错配(A：T)碱基对。为了确定动力学，我们构建了马尔可夫状态模型。碱基询问被发现是高度随机的，并通过在DNA小槽中插入含精氨酸环来瞬时扰乱Watson-Crick配对。接下来，我们使用复制链路径采样方法来计算TDG基挤出的最小自由能路径。我们确定了传递选择性的关键中间体，并确定了病变搜索和碱基挤出到TDG活性部位的有效自由能分布。我们的结果表明，DNA雕刻、动态糖基酶相互作用和稳定的接触共同为检测和区分DNA中的修饰碱基和表观遗传标记提供了强大的机制。
Thymine DNA glycosylase (TDG) is a pivotal enzyme with dual roles in both genome maintenance and epigenetic regulation. TDG is involved in cytosine demethylation at CpG sites in DNA. Here we have used molecular modeling to delineate the lesion search and DNA base interrogation mechanisms of TDG. First, we examined the capacity of TDG to interrogate not only DNA substrates with 5-carboxyl cytosine modifications but also G:T mismatches and nonmismatched (A:T) base pairs using classical and accelerated molecular dynamics. To determine the kinetics, we constructed Markov state models. Base interrogation was found to be highly stochastic and proceeded through insertion of an arginine-containing loop into the DNA minor groove to transiently disrupt Watson-Crick pairing. Next, we employed chain-of-replicas path-sampling methodologies to compute minimum free energy paths for TDG base extrusion. We identified the key intermediates imparting selectivity and determined effective free energy profiles for the lesion search and base extrusion into the TDG active site. Our results show that DNA sculpting, dynamic glycosylase interactions, and stabilizing contacts collectively provide a powerful mechanism for the detection and discrimination of modified bases and epigenetic marks in DNA.