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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Clustering to identify RNA conformations constrained by secondary structure
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Clustering to identify RNA conformations constrained by secondary structure

机译：聚类以鉴定受二级结构限制的RNA构象

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摘要

RNA often folds hierarchically, so that its sequence defines its secondary structure (helical base-paired regions connected by single-stranded junctions), which subsequently defines its tertiary fold. To preserve base-pairing and chain connectivity, the three-dimensional conformations that RNA can explore are strongly confined compared to when secondary structure constraints are not enforced. Using three examples, we studied how secondary structure confines and dictates an RNA's preferred conformations. We made use of Macromolecular Conformations by SYMbolic programming (MC-Sym) fragment assembly to generate RNA conformations constrained by secondary structure. Then, to understand the correlations between different helix placements and orientations, we robustly clustered all RNA conformations by employing unique methods to remove outliers and estimate the best number of conformational clusters. We observed that the preferred conformation (as judged by largest cluster size) for each type of RNA junction molecule tested is consistent with its biological function. Further, the improved quality of models in our pruned datasets facilitates subsequent discrimination using scoring functions based either on statistical analysis (knowledge based) or experimental data.
机译：RNA通常会按层次折叠，因此其序列定义了其二级结构（通过单链连接连接的螺旋碱基配对区域），随后又定义了其三级折叠。为了保留碱基配对和链连接性，与不强制二级结构约束的情况相比，RNA可以探索的三维构象受到严格限制。使用三个示例，我们研究了二级结构如何限制和指示RNA的优选构象。我们通过SYMbolic编程（MC-Sym）片段组装利用大分子构象来生成受二级结构约束的RNA构象。然后，为了了解不同螺旋位置和方向之间的相关性，我们通过采用独特的方法去除异常值并估计最佳构象簇数，来稳健地对所有RNA构象进行聚类。我们观察到，所测试的每种类型的RNA连接分子的优选构象（通过最大簇大小判断）与其生物学功能一致。此外，修剪后的数据集中模型质量的提高有利于使用基于统计分析（基于知识）或实验数据的评分函数进行后续区分。

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