Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures
Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures
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DOI：
10.1093/nar/gkg288
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发表时间：
2003-04-01
影响因子：
14.9
通讯作者：
Yamamoto, K
中科院分区：
文献类型：
--
作者：
Kitagawa, J;Futamura, Y;Yamamoto, K
阐明RNA序列与其结构和生物学功能的关系是一个亟待解决的问题。我们提出了一种简化的RNA二级结构树表示的度量定义，并分析了人类剪接体SnRNAs的构象能量景观。通过计算次优结构集合中各对之间的结构距离来计算构象能景观，从而讨论了生物序列的结构特性。引入了新的指标值来估计构象能量景观中分布格局的形状。我们将我们的方法应用于五个人类SnRNA，表明U1 SnRNA具有多山谷的景观轮廓，而其他四个SnRNA的景观具有一个陡峭的山谷。这一结果反映了这些SnRNAs在前mRNA剪接过程中的不同生物学功能。对tRNAs和rRNAs的分析结果表明，这些层序的构象能量景观具有多谷剖面。
It is an outstanding problem to clarify how the RNA sequence is related to its structure and biological functions. We developed a simplified definition of a metric for tree representation of RNA secondary structures and analyzed the conformational energy landscapes of human spliceosomal snRNAs. We discuss the structural properties of the biological sequence by calculating the conformational energy landscapes based on the structural distance between each of the pairs in the set of suboptimal structures. The new index value is introduced for estimating the shapes of distribution patterns in conformational energy landscapes. We apply our method to the five human snRNAs and show that U1 snRNA has a multi-valley profile of the landscape, whereas the landscapes of the other four snRNAs have one steep valley. This result reflects different biological functions of these snRNAs in the pre-mRNA splicing process. The results of analyzing tRNAs and rRNAs show that the conformational energy landscapes of these sequences have multi-valley profiles.