Theoretical studies of nucleic acids folding
Theoretical studies of nucleic acids folding
复制标题
核酸折叠的理论研究
DOI：
10.1002/wcms.1146
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发表时间：
2014
期刊：
影响因子：
--
通讯作者：
Zacharias
中科院分区：
文献类型：
--
作者：
Zacharias
RNA和DNA分子如何折叠成定义的三维（3D）结构的机制仍然没有得到很好的理解。分子模拟方法越来越多地被用于研究核酸的结构形成过程和理解折叠的驱动力。可以使用基于经典力场的分子动力学（MD）模拟来以原子分辨率和高时间分辨率跟踪核酸的动力学，并且明确地包括周围的溶剂分子和离子。最近的研究表明，它是可能的，研究折叠的小图案，如发夹结构，使用MD模拟。然而，这种方法仍然受到当前可获得的时间尺度和力场精度的限制。先进的采样方法，如复制交换MD（REMD）方法，可以显着增强核酸的构象采样，并有助于系统地研究结构形成过程和完善力场。在大RNA或含有大分子结构的RNA的情况下，粗粒度表示可以帮助克服当前的计算限制。结合实验推导的约束和预测的二级结构，已经开发了几种方法来将RNA分子折叠成可能的3D结构。这样的结构模型通常可以帮助设计实验或解释实验结果。这篇文章被分类在：电子结构理论>密度泛函理论
The mechanism of how RNA and DNA molecules fold into defined three‐dimensional (3D) structures is still not well understood. Molecular simulation approaches are increasingly being used to study structure formation processes of nucleic acids and to understand the driving forces for folding. It is possible to use molecular dynamics (MD) simulations based on a classical force field to follow the dynamics of nucleic acids at atomic resolution and high time resolution and including surrounding solvent molecules and ions explicitly. Recent studies indicate that it is possible to investigate folding of small motifs such as hairpin structures using MD simulations. However, this approach is still limited by the currently accessible time scales and force field accuracy. Advanced sampling methods such as the replica‐exchange MD (REMD) approach allow significant enhancement of conformational sampling of nucleic acids and could help to systematically study structure formation processes and to refine force fields. In case of large RNAs or RNA containing macromolecular structures, coarse‐grained representations can help to overcome current computational limitations. In combination with experimentally derived constraints and predicted secondary structure, several approaches have been developed to fold RNA molecules into possible 3D structures. Such structural model can often be helpful to plan experiments or to interpret experimental results.This article is categorized under:Electronic Structure Theory > Density Functional Theory
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DOI：
--
发表时间：
2003
期刊：
影响因子：
--
作者：
M. Zacharias
通讯作者：
M. Zacharias