Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan, China.
Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
PLoS Comput Biol. 2018 Jun 7;14(6):e1006222. doi: 10.1371/journal.pcbi.1006222. eCollection 2018 Jun.
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.
RNA 假结是一种最小的 RNA 三级结构基序，其三维（3D）结构和稳定性在多种生物功能中起着至关重要的作用。因此，预测 RNA 假结的 3D 结构和稳定性对于理解其功能至关重要。在这项工作中，我们使用了之前开发的具有隐盐的粗粒模型，对单价/二价离子溶液中 RNA 假结的 3D 结构和稳定性进行了广泛的预测和综合分析。与现有实验数据的比较表明，我们的模型可以成功地从 RNA 假结的序列预测其 3D 结构，并且可以在广泛的单价/二价离子浓度范围内对不同长度和序列的 RNA 假结的稳定性进行可靠的预测。此外，我们还对各种 RNA 假结在离子溶液中的展开途径进行了全面分析。我们对广泛的假结和广泛的单价/二价离子浓度的分析验证了 RNA 假结的展开途径主要取决于展开中间态的相对稳定性，并表明 RNA 假结的展开途径可以通过其序列和溶液离子条件得到显著调节。
