On the Power and Challenges of Atomistic Molecular Dynamics to Investigate RNA Molecules,Journal of Chemical Theory and Computation

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On the Power and Challenges of Atomistic Molecular Dynamics to Investigate RNA Molecules
Journal of Chemical Theory and Computation ( IF 5.7 ) Pub Date : 2024-08-16 , DOI: 10.1021/acs.jctc.4c00773
Stefano Muscat ₁ , Gianfranco Martino ₁ , Jacopo Manigrasso ₂ , Marco Marcia _{3,

4,

5} , Marco De Vivo ₁

Affiliation

RNA molecules play a vital role in biological processes within the cell, with significant implications for science and medicine. Notably, the biological functions exerted by specific RNA molecules are often linked to the RNA conformational ensemble. However, the experimental characterization of such three-dimensional RNA structures is challenged by the structural heterogeneity of RNA and by its multiple dynamic interactions with binding partners such as small molecules, proteins, and metal ions. Consequently, our current understanding of the structure–function relationship of RNA molecules is still limited. In this context, we highlight molecular dynamics (MD) simulations as a powerful tool to complement experimental efforts on RNAs. Despite the recognized limitations of current force fields for RNA MD simulations, examining the dynamics of selected RNAs has provided valuable functional insights into their structures.

中文翻译：

论原子分子动力学研究 RNA 分子的力量和挑战

RNA 分子在细胞内的生物过程中发挥着至关重要的作用，对科学和医学具有重大影响。值得注意的是，特定 RNA 分子发挥的生物学功能通常与 RNA 构象整体相关。然而，这种三维RNA结构的实验表征受到RNA结构异质性及其与小分子、蛋白质和金属离子等结合伴侣的多重动态相互作用的挑战。因此，我们目前对 RNA 分子结构与功能关系的理解仍然有限。在这种背景下，我们强调分子动力学 (MD) 模拟是补充 RNA 实验工作的强大工具。尽管目前 RNA MD 模拟的力场存在公认的局限性，但检查选定 RNA 的动力学为其结构提供了有价值的功能见解。

更新日期：2024-08-16

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