ArticlePLoS computational biology2012
Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Riboswitch Distribution in the Human Gut Microbiome Reveals Common Metabolite Pathways.The journal of physical chemistry. B · 2024Article
- Translation regulation by a guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity.RNA (New York, N.Y.) · 2023Article
- Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches.The journal of physical chemistry. B · 2021Article
- Beyond Plug and Pray: Context Sensitivity andRNA biology · 2021Article
- RNA Modeling with the Computational Energy Landscape Framework.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Towards an understanding of RNA structural modalities: a riboswitch case study.Computational and mathematical biophysics · 2019Article
- Article
- Development of an inducible anti-VEGF rAAV gene therapy strategy for the treatment of wet AMD.Scientific reports · 2018Article
- Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch.PloS one · 2017Article
- Predicting Large RNA-Like Topologies by a Knowledge-Based Clustering Approach.Journal of molecular biology · 2016Article
- Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression.Nucleic acids research · 2015Article
- Secondary structural entropy in RNA switch (Riboswitch) identification.BMC bioinformatics · 2015Article
- Mn(2+)-sensing mechanisms of yybP-ykoY orphan riboswitches.Molecular cell · 2015Article
- Using simulations and kinetic network models to reveal the dynamics and functions of riboswitches.Methods in enzymology · 2015Article
- Single-molecule studies of riboswitch folding.Biochimica et biophysica acta · 2014Review
- A family of synthetic riboswitches adopts a kinetic trapping mechanism.Nucleic acids research · 2014Article
- Differences between cotranscriptional and free riboswitch folding.Nucleic acids research · 2014Article
- RNA graph partitioning for the discovery of RNA modularity: a novel application of graph partition algorithm to biology.PloS one · 2014Article
- Kinetics of allosteric transitions in S-adenosylmethionine riboswitch are accurately predicted from the folding landscape.Journal of the American Chemical Society · 2013Article
- Network Theory Tools for RNA Modeling.WSEAS transactions on mathematics · 2013Article
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3 authors.
Funding
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 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.
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