{"title":"Coarse-grained molecular dynamics simulations of base-pair mismatch recognition protein MutS sliding along DNA.","authors":"Keisuke Inoue, Shoji Takada, Tsuyoshi Terakawa","doi":"10.2142/biophysico.bppb-v19.0015","DOIUrl":null,"url":null,"abstract":"<p><p>DNA mismatches are frequently generated by various intrinsic and extrinsic factors including DNA replication errors, oxygen species, ultraviolet, and ionizing radiation. These mismatches should be corrected by the mismatches repair (MMR) pathway to maintain genome integrity. In the <i>Escherichia coli</i> (<i>E. coli</i>) MMR pathway, MutS searches and recognizes a base-pair mismatch from millions of base-pairs. Once recognized, ADP bound to MutS is exchanged with ATP, which induces a conformational change in MutS. Previous single-molecule fluorescence microscopy studies have suggested that ADP-bound MutS temporarily slides along double-stranded DNA in a rotation-coupled manner to search a base-pair mismatch and so does ATP-bound MutS in a rotation-uncoupled manner. However, the detailed structural dynamics of the sliding remains unclear. In this study, we performed coarse-grained molecular dynamics simulations of the <i>E. coli</i> MutS bound on DNA in three different conformations: ADP-bound (MutS<sup>ADP</sup>), ATP-bound open clamp ( <math> <msubsup><mrow><mi>M</mi> <mi>u</mi> <mi>t</mi> <mi>S</mi></mrow> <mrow><mi>O</mi> <mi>p</mi> <mi>e</mi> <mi>n</mi></mrow> <mrow><mi>A</mi> <mi>T</mi> <mi>P</mi></mrow> </msubsup> </math> ), and ATP-bound closed clamp ( <math> <msubsup><mrow><mi>M</mi> <mi>u</mi> <mi>t</mi> <mi>S</mi></mrow> <mrow><mi>C</mi> <mi>l</mi> <mi>o</mi> <mi>s</mi> <mi>e</mi> <mi>d</mi></mrow> <mrow><mi>A</mi> <mi>T</mi> <mi>P</mi></mrow> </msubsup> </math> ) conformations. In the simulations, we observed conformation-dependent diffusion of MutS along DNA. MutS<sup>ADP</sup> and <math> <msubsup><mrow><mi>M</mi> <mi>u</mi> <mi>t</mi> <mi>S</mi></mrow> <mrow><mi>C</mi> <mi>l</mi> <mi>o</mi> <mi>s</mi> <mi>e</mi> <mi>d</mi></mrow> <mrow><mi>A</mi> <mi>T</mi> <mi>P</mi></mrow> </msubsup> </math> diffused along DNA in a rotation-coupled manner with rare and frequent groove-crossing events, respectively. In the groove-crossing events, MutS overcame an edge of a groove and temporarily diffused in a rotation-uncoupled manner. It was also indicated that mismatch searches by <math> <msubsup><mrow><mi>M</mi> <mi>u</mi> <mi>t</mi> <mi>S</mi></mrow> <mrow><mi>O</mi> <mi>p</mi> <mi>e</mi> <mi>n</mi></mrow> <mrow><mi>A</mi> <mi>T</mi> <mi>P</mi></mrow> </msubsup> </math> is inefficient in terms of mismatch checking even though it diffuses along DNA and reaches unchecked regions more rapidly than MutS<sup>ADP</sup>.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2022-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/52/d6/19_e190015.PMC9173861.pdf","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Biophysics and Physicobiology","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.2142/biophysico.bppb-v19.0015","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2022/1/1 0:00:00","PubModel":"eCollection","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
Abstract
DNA mismatches are frequently generated by various intrinsic and extrinsic factors including DNA replication errors, oxygen species, ultraviolet, and ionizing radiation. These mismatches should be corrected by the mismatches repair (MMR) pathway to maintain genome integrity. In the Escherichia coli (E. coli) MMR pathway, MutS searches and recognizes a base-pair mismatch from millions of base-pairs. Once recognized, ADP bound to MutS is exchanged with ATP, which induces a conformational change in MutS. Previous single-molecule fluorescence microscopy studies have suggested that ADP-bound MutS temporarily slides along double-stranded DNA in a rotation-coupled manner to search a base-pair mismatch and so does ATP-bound MutS in a rotation-uncoupled manner. However, the detailed structural dynamics of the sliding remains unclear. In this study, we performed coarse-grained molecular dynamics simulations of the E. coli MutS bound on DNA in three different conformations: ADP-bound (MutSADP), ATP-bound open clamp ( ), and ATP-bound closed clamp ( ) conformations. In the simulations, we observed conformation-dependent diffusion of MutS along DNA. MutSADP and diffused along DNA in a rotation-coupled manner with rare and frequent groove-crossing events, respectively. In the groove-crossing events, MutS overcame an edge of a groove and temporarily diffused in a rotation-uncoupled manner. It was also indicated that mismatch searches by is inefficient in terms of mismatch checking even though it diffuses along DNA and reaches unchecked regions more rapidly than MutSADP.
DNA错配经常由各种内在和外在因素引起,包括DNA复制错误、氧气种类、紫外线和电离辐射。这些错配应该通过错配修复(MMR)途径来纠正,以维持基因组的完整性。在大肠杆菌(E. coli) MMR通路中,MutS从数百万个碱基对中搜索并识别碱基对不匹配。一旦被识别,结合在MutS上的ADP与ATP交换,引起MutS的构象变化。先前的单分子荧光显微镜研究表明,adp结合的MutS以旋转偶联的方式暂时沿着双链DNA滑动以搜索碱基对不匹配,atp结合的MutS也以旋转不偶联的方式滑动。然而,滑动的详细结构动力学仍然不清楚。在这项研究中,我们以三种不同的构象进行了大肠杆菌MutS结合DNA的粗颗粒分子动力学模拟:adp结合(MutSADP), atp结合的开放钳形(Mu到S O p和A t p)和atp结合的封闭钳形(Mu到S C l和A t p)。在模拟中,我们观察到MutS沿DNA的构象依赖扩散。MutSADP和M - t - S - C分别以旋转耦合的方式沿DNA扩散,具有罕见和频繁的凹槽交叉事件。在槽交叉事件中,MutS克服了槽的边缘,并以旋转不耦合的方式暂时扩散。研究还表明,尽管M - t - S - O - p - A - t - p沿着DNA扩散并比MutSADP更快地到达未检查区域,但在错配检查方面,M - t - S - O - p的错配搜索效率较低。