Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
Phys Rev E. 2019 Jan;99(1-1):012420. doi: 10.1103/PhysRevE.99.012420.
Noncoding RNA molecules take part in many biological processes, while metal ions play crucial roles in helping RNAs to perform their functions. However, the statics and dynamics of these metal ions around RNA molecules are still not well understood. In this work, we report a detailed molecular dynamics study of the type-I preQ_{1}-bound riboswitch aptamer domain (PRAD) at different ionic conditions (K^{+}, Na^{+}, and Mg^{2+}). The results show that the structural properties and flexibility of the PRAD molecule greatly influence the distributions and dynamics of metal ions around it. Simultaneously, Na^{+} ions show a stronger competitiveness with Mg^{2+} ions than K^{+} ions, and the three types of metal ions have different modes of interaction with the RNA molecule. Furthermore, we have also investigated specific binding sites of metal ions on the PRAD molecule and found that the dynamics and hydration structures of metal ions located at the ion-binding sites were obviously affected by the RNA structure near these ion-binding sites. These results may be useful to understand the role of the metal ions in noncoding RNA functions.
非编码 RNA 分子参与许多生物过程，而金属离子在帮助 RNA 发挥其功能方面起着至关重要的作用。然而，这些金属离子在 RNA 分子周围的静态和动态特性仍未得到很好的理解。在这项工作中，我们报告了在不同离子条件（K+、Na+和 Mg2+）下，I 型 preQ1-结合核糖开关适体结构域（PRAD）的详细分子动力学研究。结果表明，PRAD 分子的结构特性和柔韧性极大地影响了其周围金属离子的分布和动力学。同时，Na+离子与 Mg2+离子的竞争能力强于 K+离子，三种类型的金属离子与 RNA 分子的相互作用模式不同。此外，我们还研究了 PRAD 分子上金属离子的特定结合位点，发现位于离子结合位点的金属离子的动力学和水合结构明显受到附近 RNA 结构的影响。这些结果可能有助于理解金属离子在非编码 RNA 功能中的作用。
