Perdomo Valentina Abondano, Kim Taejin
Physical Sciences Department, West Virginia University Institute of Technology, Beckley, WV, USA.
Methods Mol Biol. 2023;2709:3-29. doi: 10.1007/978-1-0716-3417-2_1.
Molecular dynamics (MD) simulations can be used to investigate the stability and conformational characteristics of RNA nanostructures. However, MD simulations of an RNA nanostructure is computationally expensive due to the size of nanostructure and the number of atoms. Alternatively, MD simulations of RNA motifs can be used to estimate the conformational stability of constructed RNA nanostructure due to their small sizes. In this chapter, we introduce the preparation and MD simulations of two RNA kissing loop (KL) motifs, a linear KL complex and a bent KL complex, and an RNA nanoring. The initial solvated system and topology files of each system will be prepared by two major force fields, AMBER and CHARMM force fields. MD simulations will be performed by NAMD simulation package, which can accept both force fields. In addition, we will introduce the use of the AMBER cpptraj program and visual molecular dynamics (VMD) for data analysis. We will also discuss how MD simulations of two KL motifs can be used to estimate the conformation and stability of RNA nanoring as well as to explain the vibrational characteristics of RNA nanoring.
分子动力学（MD）模拟可用于研究RNA纳米结构的稳定性和构象特征。然而，由于纳米结构的大小和原子数量，对RNA纳米结构进行MD模拟在计算上成本很高。另外，由于RNA基序尺寸较小，可利用对RNA基序的MD模拟来估计所构建RNA纳米结构的构象稳定性。在本章中，我们介绍了两种RNA亲吻环（KL）基序（一种线性KL复合物和一种弯曲KL复合物）以及一种RNA纳米环的制备和MD模拟。每个系统的初始溶剂化体系和拓扑文件将由两个主要的力场（AMBER和CHARMM力场）来制备。MD模拟将通过NAMD模拟软件包进行，该软件包可接受这两种力场。此外，我们将介绍如何使用AMBER cpptraj程序和可视化分子动力学（VMD）进行数据分析。我们还将讨论如何利用对两种KL基序的MD模拟来估计RNA纳米环的构象和稳定性，以及解释RNA纳米环的振动特征。
