Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions
Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions
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DOI：
10.1093/bioinformatics/btt453
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发表时间：
2013-10-15
期刊：
影响因子：
5.8
通讯作者：
Hamada, Michiaki
中科院分区：
文献类型：
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作者：
Iwakiri, Junichi;Kameda, Tomoshi;Hamada, Michiaki
动机：了解蛋白质 - RNA相互作用的细节对于揭示RNA和蛋白质的功能都很重要。在这些相互作用中，RNA的二级结构起着重要作用。由于蛋白质 - RNA复合物中的RNA二级结构是可变的，考虑RNA二级结构的集合是一种有用的方法。特别是，最近的研究支持这样一种观点，即在RNA二级结构分析中，RNA的碱基配对概率（BPPs）（即RNA二级结构集合中形成碱基对的概率）比单一的RNA二级结构（例如最小自由能结构或蛋白质数据库中的结构快照）提供了更丰富、更可靠的结构信息。然而，尚未有对蛋白质 - RNA相互作用中BPPs的研究。
结果：在这项研究中，我们分析了蛋白质数据库中已知蛋白质 - RNA复合物中所涉及的RNA分子的BPPs。我们的分析表明，在三级结构中，与氨基酸有分子间氢键（hbonds）的未配对核苷酸的BPPs（仅使用序列信息计算）显著低于没有氢键的未配对核苷酸的BPPs。另一方面，有和没有分子间氢键的配对核苷酸的BPPs之间没有发现差异。这些发现得到了三个概率模型的普遍支持，这些模型提供了RNA二级结构的集合，包括基于特纳二级结构自由能的麦卡斯基尔模型。
Motivation: Understanding the details of protein-RNA interactions is important to reveal the functions of both the RNAs and the proteins. In these interactions, the secondary structures of the RNAs play an important role. Because RNA secondary structures in protein-RNA complexes are variable, considering the ensemble of RNA secondary structures is a useful approach. In particular, recent studies have supported the idea that, in the analysis of RNA secondary structures, the base-pairing probabilities (BPPs) of RNAs (i.e. the probabilities of forming a base pair in the ensemble of RNA secondary structures) provide richer and more robust information about the structures than a single RNA secondary structure, for example, the minimum free energy structure or a snapshot of structures in the Protein Data Bank. However, there has been no investigation of the BPPs in protein-RNA interactions.Results: In this study, we analyzed BPPs of RNA molecules involved in known protein-RNA complexes in the Protein Data Bank. Our analysis suggests that, in the tertiary structures, the BPPs (which are computed using only sequence information) for unpaired nucleotides with intermolecular hydrogen bonds (hbonds) to amino acids were significantly lower than those for unpaired nucleotides without hbonds. On the other hand, no difference was found between the BPPs for paired nucleotides with and without intermolecular hbonds. Those findings were commonly supported by three probabilistic models, which provide the ensemble of RNA secondary structures, including the McCaskill model based on Turner's free energy of secondary structures.