Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function

Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way in which sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we compute energy landscapes, which describe the accessible secondary structures for a range of sequence lengths, to analyze the transcriptional process as a given sequence elongates to full length. In line with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: low-barrier landscape with an ensemble of different conformations in equilibrium before encountering a substrate; barrier-free landscape in which a direct, dominant “downhill” pathway to the minimum free energy structure is apparent; and a barrier-dominated landscape with two isolated conformational states, each associated with a different biological function. Sharing concepts with the “new view” of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved in various riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design.

核糖开关（riboswitch）是一类通过配体诱导的构象变化来调控基因表达的核糖核酸（RNA）分子。然而，序列如何决定基因调控的可变折叠通路，这一问题仍未得到阐明。本研究通过构建能量景观（energy landscape）——该景观可描述不同序列长度下的可及二级结构——来分析当序列逐步延伸至全长时的转录过程。本研究发现，多数核糖开关的能量景观可依据构象簇的分布与势垒类型，按序列长度划分为三大类，且与实验证据一致：低势垒景观：在结合底物前，体系处于多种构象的平衡集合状态；无势垒景观：存在一条直接且占主导的“下坡”通路，可直达最低自由能结构；势垒主导景观：存在两个孤立的构象状态，各自对应不同的生物学功能。借鉴蛋白质折叠能量景观的“新视角”研究思路，我们将上述三类序列区间分别命名为感知窗口、下坡折叠窗口与功能窗口。研究发现，尽管三类窗口的顺序可能因核糖开关种类不同而存在差异，但上述能量景观模式在多种核糖开关类群中均保守存在。事实上，三类窗口的排布顺序可反映配体结合是受动力学还是热力学调控。本研究结果有助于阐明核糖开关的结构与功能之间的关联，并为核糖开关的设计开辟了全新路径。