Department of Chemistry, Wesleyan University, Middletown, Connecticut, USA.
Biophys J. 2011 Oct 5;101(7):1730-9. doi: 10.1016/j.bpj.2011.08.039.
The multidomain protein Thermus aquaticus MutS and its prokaryotic and eukaryotic homologs recognize DNA replication errors and initiate mismatch repair. MutS actions are fueled by ATP binding and hydrolysis, which modulate its interactions with DNA and other proteins in the mismatch-repair pathway. The DNA binding and ATPase activities are allosterically coupled over a distance of ∼70 Å, and the molecular mechanism of coupling has not been clarified. To address this problem, all-atom molecular dynamics simulations of ∼150 ns including explicit solvent were performed on two key complexes--ATP-bound and ATP-free MutS⋅DNA(+T bulge). We used principal component analysis in fluctuation space to assess ATP ligand-induced changes in MutS structure and dynamics. The molecular dynamics-calculated ensembles of thermally accessible structures showed markedly small differences between the two complexes. However, analysis of the covariance of dynamical fluctuations revealed a number of potentially significant interresidue and interdomain couplings. Moreover, principal component analysis revealed clusters of correlated atomic fluctuations linking the DNA and nucleotide binding sites, especially in the ATP-bound MutS⋅DNA(+T) complex. These results support the idea that allosterism between the nucleotide and DNA binding sites in MutS can occur via ligand-induced changes in motion, i.e., dynamical allosterism.
水生栖热菌多结构域蛋白 MutS 及其原核和真核同源物可识别 DNA 复制错误并启动错配修复。MutS 的作用由 ATP 结合和水解提供动力，这调节了其与 DNA 以及错配修复途径中其他蛋白质的相互作用。DNA 结合和 ATP 酶活性在约 70 Å 的距离上呈变构偶联，但其偶联的分子机制尚未阐明。为了解决这个问题，我们对包括显式溶剂在内的约 150 ns 的两个关键复合物——ATP 结合态和无 ATP 态 MutS·DNA(+T 凸起)进行了全原子分子动力学模拟。我们使用波动空间中的主成分分析来评估 ATP 配体诱导的 MutS 结构和动力学变化。通过分子动力学计算得到的热可达结构集合显示，这两个复合物之间的差异非常小。然而，对动态波动协方差的分析揭示了许多潜在的重要残基间和域间偶联。此外，主成分分析揭示了连接 DNA 和核苷酸结合位点的相关原子波动簇，特别是在 ATP 结合态 MutS·DNA(+T)复合物中。这些结果支持这样一种观点，即 MutS 中核苷酸和 DNA 结合位点之间的变构作用可以通过配体诱导的运动变化发生，即动态变构作用。
