Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer
Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer
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DOI：
10.1073/pnas.1115045109
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发表时间：
2012-01-31
影响因子：
11.1
通讯作者：
Block, Steven M.
中科院分区：
文献类型：
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作者：
Anthony, Peter C.;Perez, Christian F.;Block, Steven M.
核糖开关是RNA转录物的非翻译区（UTR）中的基序，其感测代谢物水平并调节代谢物输入、输出、合成或降解的相应基因的表达。所有的核糖开关都含有一个适体：一种RNA结构，在结合配体时，折叠以暴露或通过替代核苷酸配对隔离相邻序列中的调节元件。配体结合和适体折叠之间的耦合是焦磷酸硫胺素（TPP）核糖开关的调节机制的核心，尚未得到充分表征。在这里，我们表明，TPP适体折叠可以分解成配体独立的和依赖的步骤，分别对应于二级和三级结构的形成。我们重建了野生型（WT）适体折叠的全能量景观，并测量了突变或配体结合引起的扰动。我们表明，TPP的绑定收益在两个步骤中，从弱到强绑定状态。我们的数据意味着一个分层折叠序列，并提供了一个框架，了解整个TPP核糖开关家族的分子机制。
Riboswitches are motifs in the untranslated regions (UTRs) of RNA transcripts that sense metabolite levels and modulate the expression of the corresponding genes for metabolite import, export, synthesis, or degradation. All riboswitches contain an aptamer: an RNA structure that, upon binding ligand, folds to expose or sequester regulatory elements in the adjacent sequence through alternative nucleotide pairing. The coupling between ligand binding and aptamer folding is central to the regulatory mechanisms of thiamine pyrophosphate (TPP) riboswitches and has not been fully characterized. Here, we show that TPP aptamer folding can be decomposed into ligand-independent and -dependent steps that correspond to the formation of secondary and tertiary structures, respectively. We reconstructed the full energy landscape for folding of the wild-type (WT) aptamer and measured perturbations of this landscape arising from mutations or ligand binding. We show that TPP binding proceeds in two steps, from a weakly to a strongly bound state. Our data imply a hierarchical folding sequence, and provide a framework for understanding molecular mechanism throughout the TPP riboswitch family.