Visualizing the ai5γ group IIB intron
Visualizing the ai5γ group IIB intron
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DOI：
10.1093/nar/gkt1051
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发表时间：
2014-02-01
影响因子：
14.9
通讯作者：
Pyle, Anna Marie
中科院分区：
文献类型：
--
作者：
Somarowthu, Srinivas;Legiewicz, Michal;Pyle, Anna Marie
很明显，许多细胞代谢是由大的折叠良好的非编码RNA分子控制的。除了晶体学方法外，还需要计算方法来可视化大rna的3D结构。在这里，我们用细菌IIC族同源物的晶体结构模拟了酵母ai5 γ族IIB内含子的分子结构。这是通过适应同源性和从头建模的策略，以及为RNA精化创建新的计算工具来完成的。利用结构导向诱变和RNA结构探测相结合的方法，实验验证了所得到的模型。该模型为剪接的机制和调控提供了重要的见解，例如剪接第二步前后分支位点的位置，以及控制靶特异性的子结构域的位置，强调了建模大功能RNA分子的可行性。
It has become apparent that much of cellular metabolism is controlled by large well-folded noncoding RNA molecules. In addition to crystallographic approaches, computational methods are needed for visualizing the 3D structure of large RNAs. Here, we modeled the molecular structure of the ai5 gamma group IIB intron from yeast using the crystal structure of a bacterial group IIC homolog. This was accomplished by adapting strategies for homology and de novo modeling, and creating a new computational tool for RNA refinement. The resulting model was validated experimentally using a combination of structure-guided mutagenesis and RNA structure probing. The model provides major insights into the mechanism and regulation of splicing, such as the position of the branch-site before and after the second step of splicing, and the location of subdomains that control target specificity, underscoring the feasibility of modeling large functional RNA molecules.