Structural Genomics Unit, Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain.
BMC Bioinformatics. 2010 Jun 15;11:322. doi: 10.1186/1471-2105-11-322.
In recent years, the number of available RNA structures has rapidly grown reflecting the increased interest on RNA biology. Similarly to the studies carried out two decades ago for proteins, which gave the fundamental grounds for developing comparative protein structure prediction methods, we are now able to quantify the relationship between sequence and structure conservation in RNA.
Here we introduce an all-against-all sequence- and three-dimensional (3D) structure-based comparison of a representative set of RNA structures, which have allowed us to quantitatively confirm that: (i) there is a measurable relationship between sequence and structure conservation that weakens for alignments resulting in below 60% sequence identity, (ii) evolution tends to conserve more RNA structure than sequence, and (iii) there is a twilight zone for RNA homology detection.
The computational analysis here presented quantitatively describes the relationship between sequence and structure for RNA molecules and defines a twilight zone region for detecting RNA homology. Our work could represent the theoretical basis and limitations for future developments in comparative RNA 3D structure prediction.
近年来，随着人们对 RNA 生物学兴趣的增加，可用的 RNA 结构数量迅速增加。与二十年前针对蛋白质进行的研究类似，这些研究为开发比较蛋白质结构预测方法奠定了基础，我们现在能够量化 RNA 序列和结构保守性之间的关系。
在这里，我们引入了一组代表性 RNA 结构的全对全序列和三维 (3D) 结构比较，这使我们能够定量证实：（i）序列和结构保守性之间存在可衡量的关系，这种关系在导致序列同一性低于 60%的比对中减弱，（ii）进化倾向于比序列更保守 RNA 结构，以及（iii）存在 RNA 同源性检测的暮光区。
这里提出的计算分析定量描述了 RNA 分子中序列和结构之间的关系，并定义了检测 RNA 同源性的暮光区。我们的工作可以为未来的比较 RNA 3D 结构预测的发展提供理论基础和限制。
