Computing the conformational entropy for RNA folds
Computing the conformational entropy for RNA folds
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DOI：
10.1063/1.3447385
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发表时间：
2010-06-21
影响因子：
4.4
通讯作者：
Chen, Shi-Jie
中科院分区：
文献类型：
--
作者：
Liu, Liang;Chen, Shi-Jie
我们开发了一种基于聚合物物理学的方法来计算 RNA 三级折叠的构象熵，即由通过（交联）环连接的多个螺旋组成的构象。该理论基于核苷酸链的虚拟键构象模型。熵计算的一个关键问题是如何处理排除的体积相互作用。不同环之间的弱排除体积干扰导致整个结构分解为许多三体构建块，每个三体构建块由一个环和连接到环两端的两个螺旋组成。三体系统的简单构造允许准确计算每个构建块的构象熵。构建块的组装给出了整个结构的熵。这种方法能够处理 RNA 的熔球状折叠（部分展开的三级结构）。大量的实验测试和精确的计算机计算表明该方法可以给出准确的熵结果。这里开发的方法为系统地发展 RNA 和蛋白质复杂三级折叠的熵和自由能景观理论迈出了坚实的第一步。 (c) 2010 年美国物理研究所。 [号码：10.1063/1.3447385]
We develop a polymer physics-based method to compute the conformational entropy for RNA tertiary folds, namely, conformations consisting of multiple helices connected through (cross-linked) loops. The theory is based on a virtual bond conformational model for the nucleotide chain. A key issue in the calculation of the entropy is how to treat the excluded volume interactions. The weak excluded volume interference between the different loops leads to the decomposition of the whole structure into a number of three-body building blocks, each consisting of a loop and two helices connected to the two ends of the loop. The simple construct of the three-body system allows an accurate computation for the conformational entropy for each building block. The assembly of the building blocks gives the entropy of the whole structure. This approach enables treatment of molten globule-like folds (partially unfolded tertiary structures) for RNAs. Extensive tests against experiments and exact computer enumerations indicate that the method can give accurate results for the entropy. The method developed here provides a solid first step toward a systematic development of a theory for the entropy and free energy landscape for complex tertiary folds for RNAs and proteins. (c) 2010 American Institute of Physics. [doi: 10.1063/1.3447385]