Predicting structure and stability for RNA complexes with intermolecular loop-loop base-pairing.
Predicting structure and stability for RNA complexes with intermolecular loop-loop base-pairing.
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DOI：
10.1261/rna.043976.113
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发表时间：
2014-06
期刊：
影响因子：
--
通讯作者：
Chen SJ
中科院分区：
文献类型：
--
作者：
Cao S;Xu X;Chen SJ
描述了一种基于统计力学的计算方法，用于预测具有环-环接吻相互作用的RNA复合物的结构和热力学稳定性。该方法不仅可以预测RNA/RNA复合物的天然结构，而且还可以预测替代的亚稳结构。RNA环-环相互作用对于基因组RNA二聚化和基因表达调控是必不可少的。在这篇文章中，一个基于统计力学的计算方法，预测的结构和热力学稳定性的RNA复合物与环-环接吻相互作用的描述。该方法考虑了环-环相互作用形成的熵变化，这是其他计算模型忽略的一个显著进步。几个实验验证的系统的基准测试表明，熵参数的列入确实可以提高RNA复合物的预测。此外，该方法不仅可以预测RNA/RNA复合物的天然结构，还可以预测替代的亚稳态结构。例如，该模型预测HIV-1 RNA的SL 1结构域可以形成具有相似稳定性的两种不同的二聚体结构。预测结果与实验观察相一致。此外，该模型预测了两个不同的结合位点的hTR二聚化：一个结合位点已被实验提出，另一种结构，具有较高的稳定性，是结构上可行的，需要进一步的实验验证。
A statistical mechanics-based computational method for the prediction of the structures and thermodynamic stabilities of RNA complexes with loop–loop kissing interactions is described. The method can predict not only the native structures of RNA/RNA complexes but also alternative metastable structures. RNA loop–loop interactions are essential for genomic RNA dimerization and regulation of gene expression. In this article, a statistical mechanics-based computational method that predicts the structures and thermodynamic stabilities of RNA complexes with loop–loop kissing interactions is described. The method accounts for the entropy changes for the formation of loop–loop interactions, which is a notable advancement that other computational models have neglected. Benchmark tests with several experimentally validated systems show that the inclusion of the entropy parameters can indeed improve predictions for RNA complexes. Furthermore, the method can predict not only the native structures of RNA/RNA complexes but also alternative metastable structures. For instance, the model predicts that the SL1 domain of HIV-1 RNA can form two different dimer structures with similar stabilities. The prediction is consistent with experimental observation. In addition, the model predicts two different binding sites for hTR dimerization: One binding site has been experimentally proposed, and the other structure, which has a higher stability, is structurally feasible and needs further experimental validation.
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