Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions.
Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions.
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预测单价和二价离子溶液中 RNA 假结的 3D 结构和稳定性
DOI：
10.1371/journal.pcbi.1006222
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发表时间：
2018-06
影响因子：
4.3
通讯作者：
Tan ZJ
中科院分区：
文献类型：
--
作者：
Shi YZ;Jin L;Feng CJ;Tan YL;Tan ZJ
RNA假结是一类最小的RNA三级结构模体，其三维结构和稳定性对多种生物学功能起着至关重要的作用。因此，预测RNA假结的三维结构和稳定性对于理解其功能至关重要。在这项工作中，我们采用我们以前开发的隐式盐的粗粒度模型，对一价/二价离子溶液中RNA伪结的3D结构和稳定性进行了广泛的预测和全面的分析。与已有实验数据的比较表明，我们的模型可以成功地预测的3D结构的RNA伪结从他们的序列，也可以作出可靠的预测的稳定性的RNA伪结的长度和序列在很宽的范围内的单价/二价离子浓度。此外，我们对各种RNA假结在离子溶液中的解折叠途径进行了全面的分析。我们的分析广泛的pseudokonts和广泛的一价/二价离子浓度验证了RNA pseudokonts的解折叠途径主要取决于未折叠的中间状态的相对稳定性，并表明RNA pseudokonts的解折叠途径可以显着调制其序列和溶液离子条件。
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of RNA pseudoknots is essential for understanding their functions. In the work, we employed our previously developed coarse-grained model with implicit salt to make extensive predictions and comprehensive analyses on the 3D structures and stability for RNA pseudoknots in monovalent/divalent ion solutions. The comparisons with available experimental data show that our model can successfully predict the 3D structures of RNA pseudoknots from their sequences, and can also make reliable predictions for the stability of RNA pseudoknots with different lengths and sequences over a wide range of monovalent/divalent ion concentrations. Furthermore, we made comprehensive analyses on the unfolding pathway for various RNA pseudoknots in ion solutions. Our analyses for extensive pseudokonts and the wide range of monovalent/divalent ion concentrations verify that the unfolding pathway of RNA pseudoknots is mainly dependent on the relative stability of unfolded intermediate states, and show that the unfolding pathway of RNA pseudoknots can be significantly modulated by their sequences and solution ion conditions.
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