Lee Tai-Sung, López Carlos Silva, Martick Monika, Scott William G, York Darrin M
Consortium for Bioinformatics and Computational Biology, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, USA.
J Chem Theory Comput. 2007 Mar;3(2):325-327. doi: 10.1021/ct6003142.
Results of a series of 12 ns molecular dynamics (MD) simulations of the reactant state (with and without a Mg(2+) ion), early and late transition state mimics are presented based on a recently reported crystal structure of a full-length hammerhead RNA. The simulation results support a catalytically active conformation with a Mg(2+) ion bridging the A9 and scissile phosphates. In the reactant state, the Mg(2+) spends significant time closely associated with the 2'OH of G8, but remains fairly distant from the leaving group O(5') position. In the early TS mimic simulation, where the nucleophilic O(2') and leaving group O(5') are equidistant from the phosphorus, the Mg(2+) ion remains tightly coordinated to the 2'OH of G8, but is positioned closer to the O(5') leaving group, stabilizing the accumulating charge. In the late TS mimic simulation, the coordination around the bridging Mg(2+) ion undergoes a transition whereby the coordination with the 2'OH of G8 is replace by the leaving group O(5') that has developed significant charge. At the same time, the 2'OH of G8 forms a hydrogen bond with the leaving group O(5') and is positioned to act as a general acid catalyst. This work represents the first reported simulations of the full-length hammerhead structure and TS mimics, and provides direct evidence for the possible role of a bridging Mg(2+) ion in catalysis that is consistent with both crystallographic and biochemical data.
基于最近报道的全长锤头状核糖核酸（hammerhead RNA）晶体结构，展示了一系列针对反应物状态（有和没有Mg(2+)离子）、早期和晚期过渡态模拟物的12纳秒分子动力学（MD）模拟结果。模拟结果支持一种催化活性构象，其中Mg(2+)离子桥接A9和可裂解磷酸基团。在反应物状态下，Mg(2+)有相当长的时间与G8的2'OH紧密结合，但与离去基团O(5')位置仍相距较远。在早期过渡态模拟物模拟中，亲核的O(2')和离去基团O(5')与磷的距离相等，Mg(2+)离子仍与G8的2'OH紧密配位，但位置更靠近O(5')离去基团，从而稳定积累的电荷。在晚期过渡态模拟物模拟中，桥接Mg(2+)离子周围的配位发生转变，即与G8的2'OH的配位被已带显著电荷的离去基团O(5')取代。同时，G8的2'OH与离去基团O(5')形成氢键，并定位为充当广义酸催化剂。这项工作代表了首次报道的全长锤头状结构和过渡态模拟物的模拟，并为桥接Mg(2+)离子在催化中可能的作用提供了直接证据，这与晶体学和生化数据均一致。
