ArticlePhysical chemistry chemical physics : PCCP2014
Sequence-dependent folding landscapes of adenine riboswitch aptamers.
Article in Physical chemistry chemical physics : PCCP, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 17 citations in OpenAlex.
- Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements.RNA (New York, N.Y.) · 2024Article
- Article
- Exploring the free-energy landscape of GPCR activation.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Molecular Modeling Applied to Nucleic Acid-Based Molecule Development.Biomolecules · 2018Review
- Predicting Cotranscriptional Folding Kinetics For Riboswitch.The journal of physical chemistry. B · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Computational Methods for Modeling Aptamers and Designing Riboswitches.International journal of molecular sciences · 2017Review
- Co-Transcriptional Folding and Regulation Mechanisms of Riboswitches.Molecules (Basel, Switzerland) · 2017Review
- Using simulations and kinetic network models to reveal the dynamics and functions of riboswitches.Methods in enzymology · 2015Article
- Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations.BMC bioinformatics · 2015Article
- Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design.Wiley interdisciplinary reviews. RNAReview
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Expression of a large fraction of genes in bacteria is controlled by riboswitches, which are found in the untranslated region of mRNA. Structurally riboswitches have a conserved aptamer domain to which a metabolite binds, resulting in a conformational change in the downstream expression platform. Prediction of the functions of riboswitches requires a quantitative description of the folding landscape so that the barriers and time scales for the conformational change in the switching region in the aptamer can be estimated. Using a combination of all atom molecular dynamics (MD) and coarse-grained model simulations we studied the response of adenine (A) binding add and pbuE A-riboswitches to mechanical force. The two riboswitches contain a structurally similar three-way junction formed by three paired helices, P1, P2, and P3, but carry out different functions. Using pulling simulations, with structures generated in MD simulations, we show that after P1 rips the dominant unfolding pathway in the add A-riboswitch is the rupture of P2 followed by unraveling of P3. In the pbuE A-riboswitch, after P1 unfolds P3 ruptures ahead of P2. The order of unfolding of the helices, which is in accord with single molecule pulling experiments, is determined by the relative stabilities of the individual helices. Our results show that the stability of isolated helices determines the order of assembly and response to force in these non-coding regions. We use the simulated free energy profile for the pbuE A-riboswitch to estimate the time scale for allosteric switching, which shows that this riboswitch is under kinetic control lending additional support to the conclusion based on single molecule pulling experiments. A consequence of the stability hypothesis is that a single point mutation (U28C) in the P2 helix of the add A-riboswitch, which increases the stability of P2, would make the folding landscapes of the two riboswitches similar. This prediction can be tested in single molecule pulling experiments.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.