Pistol ribozymes comprise a class of small, self‐cleaving RNAs discovered via comparative genomic analysis. Prior work in the field has probed the kinetics of the cleavage reaction, as well as the influence of various metal ion cofactors that accelerate the process. In the current study, we performed unbiased and unconstrained molecular dynamics simulations from two current high‐resolution pistol crystal structures, and we analyzed trajectory data within the context of the currently accepted ribozyme mechanistic framework. Root‐mean‐squared deviations, radial distribution functions, and distributions of nucleophilic angle‐of‐attack reveal insights into the potential roles of three magnesium ions with respect to catalysis and overall conformational stability of the molecule. A series of simulation trajectories containing in silico mutations reveal the relatively flexible and partially interchangeable roles of two particular magnesium ions within solvated hydrogen‐bonding distances from the catalytic center.

中文翻译：

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手枪核酶的 Mg 2+ 依赖性裂解的分子动力学分析揭示了用于催化的故障安全二次离子

手枪核酶包括通过比较基因组分析发现的一类小的、自切割的 RNA。该领域的先前工作已经探索了裂解反应的动力学，以及加速该过程的各种金属离子辅助因子的影响。在当前的研究中，我们从两种当前的高分辨率手枪晶体结构中进行了无偏和无约束的分子动力学模拟，并在当前公认的核酶机制框架的背景下分析了轨迹数据。均方根偏差、径向分布函数和亲核攻角分布揭示了三种镁离子在分子催化和整体构象稳定性方面的潜在作用。