Abstract：
In our recent publication, we have proposed a revised base excision repair pathway in which DNA polymerase β (Polβ) catalyzes Schiff base formation prior to the gap-filling DNA synthesis followed by β-elimination. In addition, the polymerase activity of Polβ employs the \"three-metal ion mechanism\" instead of the long-standing \"two-metal ion mechanism\" to catalyze phosphodiester bond formation based on the fact derived from time-resolved x-ray crystallography that a third Mg2+ was captured in the polymerase active site after the chemical reaction was initiated. In this study, we develop the models of the uncross-linked and cross-linked Polβ complexes and investigate the \"three-metal ion mechanism\" vs the \"two-metal ion mechanism\" by using the quantum mechanics/molecular mechanics molecular dynamics simulations. Our results suggest that the presence of the third Mg2+ ion stabilizes the reaction-state structures, strengthens correct nucleotide binding, and accelerates phosphodiester bond formation. The improved understanding of Polβ\'s catalytic mechanism provides valuable insights into DNA replication and damage repair.
摘要：
在我们最近的出版物中，我们提出了一种修订的碱基切除修复途径，其中DNA聚合酶β（Polβ）在填隙DNA合成之前催化席夫碱形成，然后进行β消除。此外,Polβ的聚合酶活性利用“三金属离子机制”而不是长期存在的“两金属离子机制”来催化磷酸二酯键的形成，这是基于时间分辨x射线晶体学得出的事实，即化学反应开始后，第三个Mg2+被捕获在聚合酶活性位点。在这项研究中,我们使用量子力学/分子力学分子动力学模拟，开发了未交联和交联的Polβ配合物的模型，并研究了“三金属离子机制”与“两金属离子机制”的关系。我们的结果表明，第三个Mg2+离子的存在稳定了反应态结构，加强正确的核苷酸结合，并加速磷酸二酯键的形成。对Polβ催化机制的进一步理解为DNA复制和损伤修复提供了有价值的见解。
