Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan, USA.
Biophys J. 2011 Nov 2;101(9):2223-31. doi: 10.1016/j.bpj.2011.09.045. Epub 2011 Nov 1.
DNA mismatch recognition and repair is vital for preserving the fidelity of the genome. Conserved across prokaryotes and eukaryotes, MutS is the primary protein that is responsible for recognizing a variety of DNA mismatches. From molecular dynamics simulations of the Escherichia coli MutS-DNA complex, we describe significant conformational dynamics in the DNA surrounding a G·T mismatch that involves weakening of the basepair hydrogen bonding in the basepair adjacent to the mismatch and, in one simulation, complete base opening via the major groove. The energetics of base flipping was further examined with Hamiltonian replica exchange free energy calculations revealing a stable flipped-out state with an initial barrier of ~2 kcal/mol. Furthermore, we observe changes in the local DNA structure as well as in the MutS structure that appear to be correlated with base flipping. Our results suggest a role of base flipping as part of the repair initiation mechanism most likely leading to sliding-clamp formation.
DNA 错配识别和修复对于保持基因组的忠实性至关重要。MutS 是一种在原核生物和真核生物中都保守的主要蛋白质，负责识别各种 DNA 错配。通过对大肠杆菌 MutS-DNA 复合物的分子动力学模拟，我们描述了围绕 G·T 错配的 DNA 的显著构象动力学，涉及到错配相邻碱基对的碱基氢键的弱化，并且在一次模拟中，通过主槽完全打开碱基。通过哈密顿复制交换自由能计算进一步研究了碱基翻转的能学，揭示了一个稳定的翻转出状态，初始势垒约为 2kcal/mol。此外，我们观察到局部 DNA 结构和 MutS 结构的变化，这些变化似乎与碱基翻转相关。我们的结果表明，碱基翻转可能是修复起始机制的一部分，最有可能导致滑动夹的形成。
