Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function.

ABSTRACT: 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 dire

SUBMITTER: Quarta G 

PROVIDER: S-EPMC3280964 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature