Optimizing DNA polymerases for a broad range of tasks requires an understanding of the factors influencing polymerase fidelity, but many details of polymerase behavior remain unknown, especially in the presence of mismatched nascent base pairs. Using molecular dynamics, the large fragment of Bacillus stearothermophilus DNA polymerase I is simulated in the presence of all 16 possible standard nucleoside triphosphate-template (dNTP-dN) pairs, including four Watson–Crick pairs and 12 mismatches. The precatalytic steps of nucleotide addition from nucleotide insertion to immediately preceding catalysis are explored using three starting structures representing different stages of nucleotide addition. From these simulations, interactions between dNTPs and the DNA–protein complex formed by the polymerase are elucidated. Patterns of large-scale conformational shifts, classification of nucleotide pairs based on composition, and investigation of the roles of residues interacting with dNTPs are completed on 50+ μs of simulation. The role of molecular dynamics in studies of polymerase behavior is discussed.

中文翻译：

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利用分子动力学研究DNA聚合酶I不匹配存在时的新生碱基对和聚合酶行为

优化DNA聚合酶以完成广泛的任务需要了解影响聚合酶保真度的因素，但是聚合酶行为的许多细节仍然未知，尤其是在新生碱基对不匹配的情况下。利用分子动力学，嗜热脂肪芽孢杆菌的大片段在所有16种可能的标准三磷酸核苷模板（dNTP-dN）对（包括4个Watson-Crick对和12个错配）的存在下模拟DNA聚合酶I。使用代表核苷酸添加不同阶段的三个起始结构，探索了从核苷酸插入到紧接在前的催化的核苷酸添加的预催化步骤。通过这些模拟，阐明了dNTP与聚合酶形成的DNA-蛋白质复合物之间的相互作用。在50+μs的仿真中完成了大规模构象变化的模式，基于组成的核苷酸对分类以及对与dNTPs相互作用的残基作用的研究。讨论了分子动力学在聚合酶行为研究中的作用。