人类DNA失配修复蛋白沿DNA的预识别扩散机制：Msh2-Msh3与Msh2-Msh6,Biochemistry

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人类DNA失配修复蛋白沿DNA的预识别扩散机制：Msh2-Msh3与Msh2-Msh6
Biochemistry ( IF 2.9 ) Pub Date : 2020-12-15 , DOI: 10.1021/acs.biochem.0c00669
Arumay Pal ₁ , Harry M. Greenblatt ₁ , Yaakov Levy ₁

Affiliation

DNA错配修复（MMR）是重要的复制后过程，可消除错配或未配对的核苷酸，以确保基因组复制保真度。在人类中，Msh2-Msh6和Msh2-Msh3是识别DNA损伤的两个错配修复起始因子。尽管这些蛋白质的X射线晶体结构与DNA损伤复合存在，但在沿非特异性双链DNA的初始搜索过程中对其结构了解甚少，因为它们寿命短且难以通过实验确定。在这项研究中，各种计算方法被用来规避这些困难。基于Msh2-Msh3和Msh2-Msh6晶体结构的全原子和粗粒度模拟显示沿DNA没有翻译，这表明初始搜索构象与病变结合的晶体结构不同。我们对MSH蛋白质的可能搜索模式结构进行了建模，并使用粗粒度分子动力学模拟显示了它们可以在DNA上进行旋转耦合扩散，这是一种对其功能适当且有效的搜索机制，并且通过荧光共振可以较早地预测出一种能量转移和荧光显微镜研究。这种搜索机制是通过错配结合结构域（MBD），钳位结构域和DNA主链之间的静电相互作用实现的。在模拟过程中，它们的扩散速率不会随盐浓度的增加而显着变化，这与来自实验研究的观察结果一致。当它们的DNA结合钳之间的间隙增加时，Msh2-Msh3主要通过钳域扩散，而Msh2-Msh6仍使用MBD扩散，再现实验测量的Msh2-Msh6较低的扩散系数。有趣的是，Msh2-Msh3能够从DNA解离，而Msh2-Msh6总是在DNA双链体上扩散。这与Msh2-Msh3与Msh2-Msh6不同，可以克服诸如核小体等障碍的实验观察结果一致。我们的模型提供了由Msh2-Msh6和Msh2-Msh3进行的不同错配搜索机制的分子图，尽管它们的结构相似。

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Prerecognition Diffusion Mechanism of Human DNA Mismatch Repair Proteins along DNA: Msh2-Msh3 versus Msh2-Msh6

DNA mismatch repair (MMR) is an important postreplication process that eliminates mispaired or unpaired nucleotides to ensure genomic replication fidelity. In humans, Msh2-Msh6 and Msh2-Msh3 are the two mismatch repair initiation factors that recognize DNA lesions. While X-ray crystal structures exist for these proteins in complex with DNA lesions, little is known about their structures during the initial search along nonspecific double-stranded DNA, because they are short-lived and difficult to determine experimentally. In this study, various computational approaches were used to sidestep these difficulties. All-atom and coarse-grained simulations based on the crystal structures of Msh2-Msh3 and Msh2-Msh6 showed no translation along the DNA, suggesting that the initial search conformation differs from the lesion-bound crystal structure. We modeled probable search-mode structures of MSH proteins and showed, using coarse-grained molecular dynamics simulations, that they can perform rotation-coupled diffusion on DNA, which is a suitable and efficient search mechanism for their function and one predicted earlier by fluorescence resonance energy transfer and fluorescence microscopy studies. This search mechanism is implemented by electrostatic interactions among the mismatch-binding domain (MBD), the clamp domains, and the DNA backbone. During simulations, their diffusion rate did not change significantly with an increasing salt concentration, which is consistent with observations from experimental studies. When the gap between their DNA-binding clamps was increased, Msh2-Msh3 diffused mostly via the clamp domains while Msh2-Msh6 still diffused using the MBD, reproducing the experimentally measured lower diffusion coefficient of Msh2-Msh6. Interestingly, Msh2-Msh3 was capable of dissociating from the DNA, whereas Msh2-Msh6 always diffused on the DNA duplex. This is consistent with the experimental observation that Msh2-Msh3, unlike Msh2-Msh6, can overcome obstacles such as nucleosomes. Our models provide a molecular picture of the different mismatch search mechanisms undertaken by Msh2-Msh6 and Msh2-Msh3, despite the similarity of their structures.

更新日期：2020-12-29

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