Teo Ruijie D, Migliore Agostino, Beratan David N
Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA . Email:
Department of Physics , Duke University , Durham , North Carolina 27708 , USA.
Chem Sci. 2020 Feb 21;11(27):7076-7085. doi: 10.1039/d0sc02245d. eCollection 2020 Jul 21.
Growing experimental evidence indicates that iron-sulfur proteins play key roles in DNA repair and replication. In particular, charge transport between [FeS] clusters, mediated by proteins and DNA, may convey signals to coordinate enzyme action. Human primase is a well studied [FeS] protein, and its p58c domain (which contains an [FeS] cluster) plays a role in the initiation of DNA replication. The Y345C mutation in p58c is linked to gastric tumors and may influence the protein-mediated charge transport. The complexity of protein-DNA systems, and the intricate electronic structure of [FeS] clusters, have impeded progress into understanding functional charge transport in these systems. In this study, we built force fields to describe the high potential [FeS] cluster in both oxidation states. The parameterization is compatible with AMBER force fields and enabled well-balanced molecular dynamics simulations of the p58c-RNA/DNA complex relevant to the initiation of DNA replication. Using the molecular mechanics Poisson-Boltzmann and surface area solvation method on the molecular dynamics trajectories, we find that the p58c mutation induces a modest change in the p58c-duplex binding free energy in agreement with recent experiments. Through kinetic modeling and analysis, we identify key features of the main charge transport pathways in p58c. In particular, we find that the Y345C mutation partially changes the composition and frequency of the most efficient (and potentially relevant to the biological function) charge transport pathways between the [FeS] cluster and the duplex. Moreover, our approach sets the stage for a deeper understanding of functional charge transfer in [FeS] protein-DNA complexes.
越来越多的实验证据表明，铁硫蛋白在DNA修复和复制中起关键作用。特别是，由蛋白质和DNA介导的[FeS]簇之间的电荷传输可能传递信号以协调酶的作用。人类引发酶是一种经过充分研究的[FeS]蛋白，其p58c结构域（包含一个[FeS]簇）在DNA复制起始中发挥作用。p58c中的Y345C突变与胃癌有关，可能会影响蛋白质介导的电荷传输。蛋白质-DNA系统的复杂性以及[FeS]簇复杂的电子结构阻碍了我们对这些系统中功能性电荷传输的理解。在本研究中，我们构建了力场来描述两种氧化态下的高电位[FeS]簇。该参数化与AMBER力场兼容，并能够对与DNA复制起始相关的p58c-RNA/DNA复合物进行平衡良好的分子动力学模拟。在分子动力学轨迹上使用分子力学泊松-玻尔兹曼和表面积溶剂化方法，我们发现p58c突变导致p58c-双链体结合自由能发生适度变化，这与最近的实验结果一致。通过动力学建模和分析，我们确定了p58c中主要电荷传输途径的关键特征。特别是，我们发现Y345C突变部分改变了[FeS]簇与双链体之间最有效的（且可能与生物学功能相关的）电荷传输途径的组成和频率。此外，我们的方法为更深入理解[FeS]蛋白-DNA复合物中的功能性电荷转移奠定了基础。
