Bottaro Sandro, Lindorff-Larsen Kresten
Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Biophys J. 2017 Jul 25;113(2):257-267. doi: 10.1016/j.bpj.2017.06.011. Epub 2017 Jun 30.
We report a map of RNA tetraloop conformations constructed by calculating pairwise distances among all experimentally determined four-nucleotide hairpin loops. Tetraloops with similar structures are clustered together and, as expected, the two largest clusters are the canonical GNRA and UNCG folds. We identify clusters corresponding to known tetraloop folds such as GGUG, RNYA, AGNN, and CUUG. These clusters are represented in a simple two-dimensional projection that recapitulates the relationship among the different folds. The cluster analysis also identifies 20 novel tetraloop folds that are peculiar to specific positions in ribosomal RNAs and that are stabilized by tertiary interactions. In our RNA tetraloop database we find a significant number of non-GNRA and non-UNCG sequences adopting the canonical GNRA and UNCG folds. Conversely, we find a significant number of GNRA and UNCG sequences adopting non-GNRA and non-UNCG folds. Our analysis demonstrates that there is not a simple one-to-one, but rather a many-to-many mapping between tetraloop sequence and tetraloop fold.
我们报道了一张RNA四环构象图谱，该图谱通过计算所有实验测定的四核苷酸发夹环之间的成对距离构建而成。结构相似的四环聚集在一起，不出所料，两个最大的簇是典型的GNRA和UNCG折叠。我们识别出了与已知四环折叠相对应的簇，如GGUG、RNYA、AGNN和CUUG。这些簇呈现在一个简单的二维投影中，概括了不同折叠之间的关系。聚类分析还识别出20种新的四环折叠，它们在核糖体RNA的特定位置具有独特性，并通过三级相互作用得以稳定。在我们的RNA四环数据库中，我们发现大量非GNRA和非UNCG序列采用典型的GNRA和UNCG折叠。相反，我们发现大量GNRA和UNCG序列采用非GNRA和非UNCG折叠。我们的分析表明，四环序列与四环折叠之间不是简单的一对一映射，而是多对多映射。
