Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation.
Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation.
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DOI：
10.1016/j.sbi.2011.03.009
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发表时间：
2011-06
影响因子：
6.8
通讯作者：
Al-Hashimi, Hashim M.
中科院分区：
文献类型：
--
作者：
Bailor, Maximillian H.;Mustoe, Anthony M.;Brooks, Charles L., III;Al-Hashimi, Hashim M.
伴随着确定RNA二级结构的最新进展，人们越来越认识到在二级结构水平编码的相对简单的拓扑约束在定义RNA的整体结构、折叠途径和动态适应性方面的重要性。一种新的观点正在出现，其中三级相互作用不定义RNA 3D结构，而是帮助从已经狭窄的拓扑预定义的构象分布中选择特定的构象。这些研究提供了对这些拓扑约束的性质的基本见解，它们如何由RNA二级结构编码，以及它们如何与其他相互作用相互作用，为RNA二级结构注入新的意义。已经开发了新的方法，其利用拓扑约束在基于二级结构和有限的一组其他容易获得的约束来确定RNA骨架构象。拓扑约束也为合理化和描述RNA动力学和结构适应提供了一个急需的框架。最后，研究表明，拓扑约束可能在引导RNA折叠途径中发挥重要作用。在这里，我们回顾了最近的进展，我们的理解拓扑约束编码的RNA二级结构。
Accompanying recent advances in determining RNA secondary structure is the growing appreciation for the importance of relatively simple topological constraints, encoded at the secondary structure level, in defining the overall architecture, folding pathways, and dynamic adaptability of RNA. A new view is emerging in which tertiary interactions do not define RNA 3D structure, but rather, help select specific conformers from an already narrow, topologically pre-defined conformational distribution. Studies are providing fundamental insights into the nature of these topological constraints, how they are encoded by the RNA secondary structure, and how they interplay with other interactions, breathing new meaning to RNA secondary structure. New approaches have been developed that take advantage of topological constraints in determining RNA backbone conformation based on secondary structure, and a limited set of other, easily accessible constraints. Topological constraints are also providing a much-needed framework for rationalizing and describing RNA dynamics and structural adaptation. Finally, studies suggest that topological constraints may play important roles steering RNA folding pathways. Here, we review recent advances in our understanding of topological constraints encoded by the RNA secondary structure.
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