Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation
Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation
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DOI：
10.1021/ja076529e
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发表时间：
2008-03-12
影响因子：
15
通讯作者：
York, Darrin M.
中科院分区：
文献类型：
--
作者：
Lee, Tai-Sung;Lopez, Carlos Silva;York, Darrin M.
采用分子动力学模拟方法研究了Mg ~（2+）在全长锤头状核酶切割反应中的作用。特别是，这项工作的目的是表征的结合模式和构象事件，产生催化活性的构象和稳定的过渡态。为此，一系列的8个12 ns的分子动力学模拟已经进行了不同的二价金属结合职业的反应物，早期和晚期的过渡态使用最近开发的力场参数的金属离子和活性中间体在RNA催化。此外，混合QM/MM计算的早期和晚期过渡态进行研究的质子转移步骤，在一般的酸催化，促进由催化Mg 2+离子。模拟表明，Mg 2+是深刻参与锤头状核酶机制在结构和催化水平。Mg 2+在活性位点的结合在茎I和II的稳定中起着关键的结构作用，并促进形成近攻击构象和亲核试剂与G12之间的相互作用，所涉及的一般碱催化剂。在过渡态中，Mg 2+结合在桥接位置，在那里它稳定离去基团的累积电荷，同时与G8的2 'OH（所涉及的通用酸催化剂）相互作用。QM/MM模拟提供了支持，在后期过渡态，G8的2 'OH可以转移质子到离去基团，同时直接配位桥接Mg 2+离子。本研究为Mg ~（2+）在锤头状核酶催化中的作用提供了证据。建议的模拟模型调和现有的实验结构和生化数据的解释，并提供了一个起点，结合QM/MM方法的化学反应路径的更详细的调查。
Molecular dynamics simulations have been performed to investig ate the role of Mg2+ in the full-length hammerhead ribozyme cleavage reaction. In particular, the aim of this work is to characterize the binding mode and conformational events that give rise to catalytically active conformations and stabilization of the transition state. Toward this end, a series of eight 12 ns molecular dynamics simulations have been performed with different divalent metal binding occupations for the reactant, early and late transition state using recently developed force field parameters for metal ions and reactive intermediates in RNA catalysis. In addition, hybrid QM/MM calculations of the early and late transition state were performed to study the proton-transfer step in general acid catalysis that is facilitated by the catalytic Mg2+ ion. The simulations suggest that Mg2+ is profoundly involved in the hammerhead ribozyme mechanism both at structural and catalytic levels. Binding of Mg2+ in the active site plays a key structural role in the stabilization of stem I and II and to facilitate formation of near attack conformations and interactions between the nucleophile and G12, the implicated general base catalyst. In the transition state, Mg2+ binds in a bridging position where it stabilizes the accumulated charge of the leaving group while interacting with the 2'OH of G8, the implicated general acid catalyst. The QM/MM simulations provide support that, in the late transition state, the 2'OH of G8 can transfer a proton to the leaving group while directly coordinating the bridging Mg2+ ion. The present study provides evidence for the role of Mg2+ in hammerhead ribozyme catalysis. The proposed simulation model reconciles the interpretation of available experimental structural and biochemical data, and provides a starting point for more detailed investigation of the chemical reaction path with combined QM/MM methods.