Computational Biophysics Group, Department of Biological Sciences, CENUR Litoral Norte, Universidad de la República, 50000 Salto, Uruguay.
Bioinformatics Unit, Institute Pasteur of Montevideo, 11400 Montevideo, Uruguay.
RNA. 2023 Dec;29(12):1896-1909. doi: 10.1261/rna.079821.123. Epub 2023 Oct 4.
The characterization of the conformational landscape of the RNA backbone is rather complex due to the ability of RNA to assume a large variety of conformations. These backbone conformations can be depicted by pseudotorsional angles linking RNA backbone atoms, from which Ramachandran-like plots can be built. We explore here different definitions of these pseudotorsional angles, finding that the most accurate ones are the traditional (eta) and (theta) angles, which represent the relative position of RNA backbone atoms P and C4'. We explore the distribution of - in known experimental structures, comparing the pseudotorsional space generated with structures determined exclusively by one experimental technique. We found that the complete picture only appears when combining data from different sources. The maps provide a quite comprehensive representation of the RNA accessible space, which can be used in RNA-structural predictions. Finally, our results highlight that protein interactions lead to significant changes in the population of the - space, pointing toward the role of induced-fit mechanisms in protein-RNA recognition.
由于 RNA 能够采取多种构象，因此对 RNA 骨架构象景观的描述相当复杂。这些骨架构象可以通过连接 RNA 骨架原子的伪扭转角来描绘，从中可以构建类似于 Ramachandran 的图谱。我们在这里探索了这些伪扭转角的不同定义，发现最准确的是传统的 (eta) 和 (theta) 角，它们代表 RNA 骨架原子 P 和 C4'的相对位置。我们探索了已知实验结构中 - 的分布，比较了仅由一种实验技术确定的结构产生的伪扭转空间。我们发现，只有当结合来自不同来源的数据时，才会出现完整的图谱。这些图谱提供了 RNA 可及空间的相当全面的表示，可用于 RNA 结构预测。最后，我们的结果表明，蛋白质相互作用导致 - 空间的种群发生显著变化，这表明诱导契合机制在蛋白质-RNA 识别中起作用。
