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首页> 外文期刊>Journal of Molecular Biology >The ligand-free state of the TPP riboswitch: a partially folded RNA structure.
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The ligand-free state of the TPP riboswitch: a partially folded RNA structure.

机译：TPP核糖开关的无配体状态：部分折叠的RNA结构。

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Riboswitches are elements of mRNA that regulate gene expression by undergoing structural changes upon binding of small ligands. Although the structures of several riboswitches have been solved with their ligands bound, the ligand-free states of only a few riboswitches have been characterized. The ligand-free state is as important for the functionality of the riboswitch as the ligand-bound form, but the ligand-free state is often a partially folded structure of the RNA, with conformational heterogeneity that makes it particularly challenging to study. Here, we present models of the ligand-free state of a thiamine pyrophosphate riboswitch that are derived from a combination of complementary experimental and computational modeling approaches. We obtain a global picture of the molecule using small-angle X-ray scattering data and use an RNA structure modeling software, MC-Sym, to fit local structural details to these data on an atomic scale. We have used two different approaches to obtaining these models. Our first approach develops a model of the RNA from the structures of its constituent junction fragments in isolation. The second approach treats the RNA as a single entity, without bias from the structure of its individual constituents. We find that both approaches give similar models for the ligand-free form, but the ligand-bound models differ for the two approaches, and only the models from the second approach agree with the ligand-bound structure known previously from X-ray crystallography. Our models provide a picture of the conformational changes that may occur in the riboswitch upon binding of its ligand. Our results also demonstrate the power of combining experimental small-angle X-ray scattering data with theoretical structure prediction tools in the determination of RNA structures beyond riboswitches.
机译：核糖开关是通过与小配体结合而经历结构变化来调节基因表达的mRNA元件。尽管几个核糖开关的结构已通过结合其配体的方法解决，但仅表征了几个核糖开关的无配体状态。无配体状态对于核糖开关的功能与与配体结合的形式一样重要，但是无配体状态通常是RNA的部分折叠结构，具有构象异质性，这使得研究特别具有挑战性。在这里，我们介绍了硫胺素焦磷酸核糖开关的无配体状态模型，这些模型是从互补的实验和计算建模方法的组合中得出的。我们使用小角度X射线散射数据获取分子的全局图片，并使用RNA结构建模软件MC-Sym在原子尺度上将局部结构细节拟合到这些数据。我们使用两种不同的方法来获得这些模型。我们的第一种方法是通过分离其组成连接片段的结构来开发RNA模型。第二种方法将RNA视为单个实体，而不会因其单个成分的结构而产生偏差。我们发现两种方法都为无配体形式提供了相似的模型，但两种方法的配体结合模型不同，只有第二种方法的模型与以前从X射线晶体学已知的配体结合结构相符。我们的模型提供了核糖开关在其配体结合后可能发生的构象变化的图片。我们的结果还证明了将小角度X射线散射实验数据与理论结构预测工具相结合可以确定核糖开关以外的RNA结构的能力。

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