ArticleNucleic acids research2014
Differences between cotranscriptional and free riboswitch folding.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- An RNA structural switch controlling bacterial toxin translation.Nucleic acids research · 2026Article
- Influence of contact map topology on RNA structure prediction.Nucleic acids research · 2025Article
- Transcription reshapes RNA hairpin folding pathways revealed by all-atom molecular dynamics simulations.PLoS computational biology · 2025Article
- CAG-Repeat RNA Hairpin Folding and Recruitment to Nuclear Speckles with a Pivotal Role of ATP as a Cosolute.Journal of the American Chemical Society · 2023Article
- Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding.Journal of chemical theory and computation · 2022Article
- Beyond Plug and Pray: Context Sensitivity andRNA biology · 2021Article
- Transcriptional and translational S-box riboswitches differ in ligand-binding properties.The Journal of biological chemistry · 2020Article
- Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch.Nucleic acids research · 2019Article
- Rapid interpretation of small-angle X-ray scattering data.PLoS computational biology · 2019Article
- Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing.Molecular cell · 2018Article
- Life times of metastable states guide regulatory signaling in transcriptional riboswitches.Nature communications · 2018Article
- Computational Methods for Modeling Aptamers and Designing Riboswitches.International journal of molecular sciences · 2017Review
- Cooperation between Magnesium and Metabolite Controls Collapse of the SAM-I Riboswitch.Biophysical journal · 2017Article
- Co-Transcriptional Folding and Regulation Mechanisms of Riboswitches.Molecules (Basel, Switzerland) · 2017Review
- Contact Statistics Highlight Distinct Organizing Principles of Proteins and RNA.Biophysical journal · 2016Article
- Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction.Nucleic acids research · 2015Article
- A Highly Coupled Network of Tertiary Interactions in the SAM-I Riboswitch and Their Role in Regulatory Tuning.Journal of molecular biology · 2015Article
- Generalized Manning Condensation Model Captures the RNA Ion Atmosphere.Physical review letters · 2015Article
- Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.Methods in enzymology · 2015Article
- Dynamics of riboswitches: Molecular simulations.Biochimica et biophysica acta · 2014Review
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Riboswitches are part of noncoding regions of messenger RNA (mRNA) that act as RNA sensors regulating gene expression of the downstream gene. Typically, one out of two distinct conformations is formed depending on ligand binding when the transcript leaves RNA polymerase (RNAP). Elongation of the RNA chain by RNAP, folding and binding all occurs simultaneously and interdependently on the seconds' timescale. To investigate the effect of transcript elongation velocity on folding for the S-adenosylmethionine (SAM)-I and adenine riboswitches we employ two complementary coarse-grained in silico techniques. Native structure-based molecular dynamics simulations provide a 3D, atomically resolved model of folding with homogenous energetics. Energetically more detailed kinetic Monte Carlo simulations give access to longer timescale by describing folding on the secondary structure level and feature the incorporation of competing aptamer conformations and a ligand-binding model. Depending on the extrusion scenarios, we observe and quantify different pathways in structure formation with robust agreements between the two techniques. In these scenarios, free-folding riboswitches exhibit different folding characteristics compared with transcription-rate limited folding. The critical transcription rate distinguishing these cases is higher than physiologically relevant rates. This result suggests that in vivo folding of the analyzed SAM-I and adenine riboswitches is transcription-rate limited.
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