Chemistry Department, Wesleyan University, Middletown, Connecticut.
Chemistry Department, Wesleyan University, Middletown, Connecticut.
Biophys J. 2023 Aug 8;122(15):3031-3043. doi: 10.1016/j.bpj.2023.06.006. Epub 2023 Jun 15.
The mismatch repair protein MutS safeguards genomic integrity by finding and initiating repair of basepairing errors in DNA. Single-molecule studies show MutS diffusing on DNA, presumably scanning for mispaired/unpaired bases, and crystal structures show a characteristic "mismatch-recognition" complex with DNA enclosed within MutS and kinked at the site of error. But how MutS goes from scanning thousands of Watson-Crick basepairs to recognizing rare mismatches remains unanswered, largely because atomic-resolution data on the search process are lacking. Here, 10 μs all-atom molecular dynamics simulations of Thermus aquaticus MutS bound to homoduplex DNA and T-bulge DNA illuminate the structural dynamics underlying the search mechanism. MutS-DNA interactions constitute a multistep mechanism to check DNA over two helical turns for its 1) shape, through contacts with the sugar-phosphate backbone, 2) conformational flexibility, through bending/unbending engineered by large-scale motions of the clamp domain, and 3) local deformability, through basepair destabilizing contacts. Thus, MutS can localize a potential target by indirect readout due to lower energetic costs of bending mismatched DNA and identify a site that distorts easily due to weaker base stacking and pairing as a mismatch. The MutS signature Phe-X-Glu motif can then lock in the mismatch-recognition complex to initiate repair.
错配修复蛋白 MutS 通过发现和启动 DNA 中碱基对错误的修复来保护基因组的完整性。单分子研究表明 MutS 在 DNA 上扩散，大概是在扫描错配/未配对的碱基，晶体结构显示出一种特征性的“错配识别”复合物，其中 DNA 被 MutS 包裹并在错误部位发生扭曲。但是 MutS 如何从扫描数千个沃森-克里克碱基对转变为识别罕见的错配仍然没有答案，主要是因为缺乏关于搜索过程的原子分辨率数据。在这里，10 μs 的全原子分子动力学模拟表明，水生栖热菌 MutS 与同源双链 DNA 和 T 型凸起 DNA 结合，阐明了搜索机制的结构动力学。MutS-DNA 相互作用构成了一个多步骤机制，通过与糖磷酸骨架的接触，检查 DNA 的形状；通过由夹钳结构域的大规模运动产生的弯曲/未弯曲，检查 DNA 的构象灵活性；通过碱基对破坏接触，检查 DNA 的局部可变形性。因此，MutS 可以通过间接读取来定位潜在的靶标，因为弯曲错配 DNA 的能量成本较低，并且可以识别由于较弱的碱基堆积和配对而容易变形的位点作为错配。然后，MutS 的特征性 Phe-X-Glu 基序可以锁定错配识别复合物以启动修复。
