Thermodynamics of unfolding mechanisms of mouse mammary tumor virus pseudoknot from a coarse-grained loop-entropy model
Thermodynamics of unfolding mechanisms of mouse mammary tumor virus pseudoknot from a coarse-grained loop-entropy model
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DOI：
10.1007/s10867-022-09602-2
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发表时间：
2022-04-20
影响因子：
1.8
通讯作者：
Liang，Jie
中科院分区：
文献类型：
--
作者：
Tang，Ke;Roca，Jorjethe;Liang，Jie
假结RNA分子发挥着重要的生物学作用，这取决于它们的折叠结构。为了理解决定其热力学和折叠/展开机制的基本原理，我们对小鼠乳腺肿瘤病毒假结RNA（VPK）的变体进行了研究，VPK是一种广泛研究的RNA假结模型系统。我们的方法是基于一个粗粒度的离散状态模型和PK 3D（三维空间中的伪结结构预测器）的算法，明确构建RNA环和它们的构象熵效应。我们的循环熵计算验证了准确地捕捉先前测得的不同环长度的RNA发夹的熔化温度。对于构成VPK的每个发夹，我们确定了在低温下比发夹结构更稳定的替代构象，并预测了它们在不同温度下的种群。我们的预测验证了这些发夹的热力学实验。我们进一步计算了VPK的热容分布，这与现有的实验数据非常吻合。值得注意的是，我们的模型提供了关于假结RNA的展开机制的详细信息。VPK的碱基配对概率分布的分析揭示了一个合作的展开机制，而不是一个简单的顺序展开的第一个茎，然后其他。具体来说，我们发现一个同时“松动”的两个茎的温度升高，从而两个茎成为部分熔化，并在展开过程中共存。
Pseudoknotted RNA molecules play important biological roles that depend on their folded structure. To understand the underlying principles that determine their thermodynamics and folding/unfolding mechanisms, we carried out a study on a variant of the mouse mammary tumor virus pseudoknotted RNA (VPK), a widely studied model system for RNA pseudoknots. Our method is based on a coarse-grained discrete-state model and the algorithm of PK3D (pseudoknot structure predictor in three-dimensional space), with RNA loops explicitly constructed and their conformational entropic effects incorporated. Our loop entropy calculations are validated by accurately capturing previously measured melting temperatures of RNA hairpins with varying loop lengths. For each of the hairpins that constitutes the VPK, we identified alternative conformations that are more stable than the hairpin structures at low temperatures and predicted their populations at different temperatures. Our predictions were validated by thermodynamic experiments on these hairpins. We further computed the heat capacity profiles of VPK, which are in excellent agreement with available experimental data. Notably, our model provides detailed information on the unfolding mechanisms of pseudoknotted RNA. Analysis of the distribution of base-pairing probability of VPK reveals a cooperative unfolding mechanism instead of a simple sequential unfolding of first one stem and then the other. Specifically, we find a simultaneous “loosening” of both stems as the temperature is raised, whereby both stems become partially melted and co-exist during the unfolding process.