Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
J Chem Phys. 2013 Jun 7;138(21):215103. doi: 10.1063/1.4804301.
We describe a method of determining the conformational fluctuations of RNA based on the incorporation of nuclear magnetic resonance (NMR) residual dipolar couplings (RDCs) as replica-averaged structural restraints in molecular dynamics simulations. In this approach, the alignment tensor required to calculate the RDCs corresponding to a given conformation is estimated from its shape, and multiple replicas of the RNA molecule are simulated simultaneously to reproduce in silico the ensemble-averaging procedure performed in the NMR measurements. We provide initial evidence that with this approach it is possible to determine accurately structural ensembles representing the conformational fluctuations of RNA by applying the reference ensemble test to the trans-activation response element of the human immunodeficiency virus type 1.
我们描述了一种基于将核磁共振（NMR）残差偶极耦合（RDC）作为分子动力学模拟的复制品平均结构约束纳入其中来确定 RNA 构象波动的方法。在这种方法中，通过其形状来估计计算给定构象的 RDC 所需的对准张量，并同时模拟 RNA 分子的多个副本，以在计算机中重现 NMR 测量中执行的集合平均过程。我们提供了初步证据，表明通过将参考集合测试应用于人免疫缺陷病毒 1 的转录激活反应元件，可以通过应用参考集合测试来准确确定代表 RNA 构象波动的结构集合。
