RNA纳米结构的分子动力学模拟方案
Protocols for Molecular Dynamics Simulations of RNA Nanostructures.
作者信息
Kim Taejin, Kasprzak Wojciech K, Shapiro Bruce A
机构信息
Department of Chemistry, New York University, 10th Floor Silver Center, 100 Washington Square East, New York, NY, 10003, USA.
Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
出版信息
Methods Mol Biol. 2017;1632:33-64. doi: 10.1007/978-1-4939-7138-1_3.
Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package. We also show examples of post-simulation analysis steps and briefly mention selected tools beyond the Amber package. Limitations of the methods, tools, and protocols are also discussed. Most of the examples are illustrated for a small RNA duplex (helix), but the protocols are applicable to any nucleic acid structure, subject only to the computational speed and memory limitations of the hardware available to the user.
分子动力学（MD）模拟已成为研究广泛生物系统的主要研究工具之一，并弥合了X射线晶体学或核磁共振结构与生物学机制之间的差距。在RNA纳米结构领域，MD模拟已用于修复计算设计的RNA纳米结构中的空间冲突、表征动力学，并研究RNA与其他生物分子（如递送剂和膜）之间的相互作用。在本章中，我们展示了使用Amber分子动力学软件包在显式和隐式溶剂中进行分子动力学模拟的计算协议示例。我们还展示了模拟后分析步骤的示例，并简要提及了Amber软件包之外的选定工具。还讨论了方法、工具和协议的局限性。大多数示例是针对小RNA双链体（螺旋）进行说明的，但这些协议适用于任何核酸结构，仅受用户可用硬件的计算速度和内存限制。
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