Intrinsic Base-Pair Rearrangement in the Hairpin Ribozyme Directs RNA Conformational Sampling and Tertiary Interface Formation
Intrinsic Base-Pair Rearrangement in the Hairpin Ribozyme Directs RNA Conformational Sampling and Tertiary Interface Formation
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发夹核酶中的内在碱基对重排指导 RNA 构象采样和三级界面形成
DOI：
10.1021/acs.jpcb.6b05606
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发表时间：
2016
期刊：
影响因子：
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通讯作者：
Hoogstraten, Charles G.
中科院分区：
文献类型：
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作者：
Ochieng, Patrick O.;White, Neil A.;Feig, Michael;Hoogstraten, Charles G.
RNA结构的动态波动使得催化和识别所需的构象变化成为可能。在发夹状核酶中，催化活性结构形成为两个RNA内环之间的复杂三级界面。在界面形成或对接时观察到每个环的结构的实质性改变。这种相对紧密的相互作用的非常慢的结合速率使我们假设RNA-RNA识别的双构象捕获机制。我们使用了广泛的分子动力学模拟，以评估构象采样的未对接形式的环域含有易裂的磷酸盐（环A）。我们观察到几个主要的可访问的构象与独特的模式的氢键和基地堆积的相互作用在活性位点的内部循环。几个重要的构象特征的对接状态中观察到人口稠密的子状态，与动力学采样的对接主管状态隔离环A。我们的观察结果表明，一个混合或多级结合机制，其中初始构象选择的对接能力的状态，然后诱导适合调整到一个在线的，化学反应状态，只有在形成的初始复合物与环B。
Dynamic fluctuations in RNA structure enable conformational changes that are required for catalysis and recognition. In the hairpin ribozyme, the catalytically active structure is formed as an intricate tertiary interface between two RNA internal loops. Substantial alterations in the structure of each loop are observed upon interface formation, or docking. The very slow on-rate for this relatively tight interaction has led us to hypothesize a double conformational capture mechanism for RNA–RNA recognition. We used extensive molecular dynamics simulations to assess conformational sampling in the undocked form of the loop domain containing the scissile phosphate (loop A). We observed several major accessible conformations with distinctive patterns of hydrogen bonding and base stacking interactions in the active-site internal loop. Several important conformational features characteristic of the docked state were observed in well-populated substates, consistent with the kinetic sampling of docking-competent states by isolated loop A. Our observations suggest a hybrid or multistage binding mechanism, in which initial conformational selection of a docking-competent state is followed by induced-fit adjustment to an in-line, chemically reactive state only after formation of the initial complex with loop B.