Role of Mg2+ in Hammerhead Ribozyme Catalysis from Molecular Simulation

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• 作者：Tai-Sung Lee ; Carlos Silva L&oacute ; pez ; George M. Giambamg src="http ; //pubs.acs.org/images/entities/scedil.gif" border="0">u ; Monika Martick ; William G. Scott ; Darrin M. York
• 刊名：Journal of the American Chemical Society
• 出版年：2008
• 出版时间：March 12, 2008
• 年：2008
• 卷：130
• 期：10
• 页码：3053 - 3064
• 全文大小：439K
• 年卷期：v.130,no.10(March 12, 2008)
• ISSN：1520-5126

文摘

Molecular dynamics simulations have been performed to investigate the role of Mg²⁺ in the full-length hammerhead ribozyme cleavage reaction. In particular, the aim of this work is to characterize thebinding mode and conformational events that give rise to catalytically active conformations and stabilizationof the transition state. Toward this end, a series of eight 12 ns molecular dynamics simulations have beenperformed with different divalent metal binding occupations for the reactant, early and late transition stateusing 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 theproton-transfer step in general acid catalysis that is facilitated by the catalytic Mg²⁺ ion. The simulationssuggest that Mg²⁺ is profoundly involved in the hammerhead ribozyme mechanism both at structural andcatalytic levels. Binding of Mg²⁺ in the active site plays a key structural role in the stabilization of stem Iand II and to facilitate formation of near attack conformations and interactions between the nucleophileand G12, the implicated general base catalyst. In the transition state, Mg²⁺ binds in a bridging positionwhere it stabilizes the accumulated charge of the leaving group while interacting with the 2'OH of G8, theimplicated 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 proposedsimulation 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 combinedQM/MM methods.