ArticleRNA (New York, N.Y.)2013
Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch.
Article in RNA (New York, N.Y.), 2013. 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.
- Recovering Small Molecule Ligand-RNA Binding Pocket Binding Modes and Exploring Potential Binding Pathways Using Metadynamics.Molecules (Basel, Switzerland) · 2026Article
- Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements.RNA (New York, N.Y.) · 2024Article
- Potential effects of metal ion induced two-state allostery on the regulatory mechanism of add adenine riboswitch.Communications biology · 2022Article
- A single change in the aptamer of the Lactiplantibacillus plantarum rib operon riboswitch severely impairs its regulatory activity and leads to a vitamin BMicrobial biotechnology · 2022Article
- Article
- Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides.Biophysical journal · 2021Article
- Binding free energy decomposition and multiple unbinding paths of buried ligands in a PreQ1 riboswitch.PLoS computational biology · 2021Article
- Ligand Binding Mechanism and Its Relationship with Conformational Changes in Adenine Riboswitch.International journal of molecular sciences · 2020Article
- Common Secondary and Tertiary Structural Features of Aptamer-Ligand Interaction Shared by RNA Aptamers with Different Primary Sequences.Molecules (Basel, Switzerland) · 2019Article
- Conformational flexibility of adenine riboswitch aptamer in apo and bound states using NMR and an X-ray free electron laser.Journal of biomolecular NMR · 2019Article
- Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations.Nucleic acids research · 2019Article
- Optimal Coarse-Grained Site Selection in Elastic Network Models of Biomolecules.Journal of chemical theory and computation · 2019Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Real-time crystallographic studies of the adenine riboswitch using an X-ray free-electron laser.The FEBS journal · 2017Review
- Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography.Nature · 2017Article
- Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch.PloS one · 2017Article
- Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.Nucleic acids research · 2015Article
- Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations.BMC bioinformatics · 2015Article
- The role of nucleobase interactions in RNA structure and dynamics.Nucleic acids research · 2014Article
- An RNA aptamer possessing a novel monovalent cation-mediated fold inhibits lysozyme catalysis by inhibiting the binding of long natural substrates.RNA (New York, N.Y.) · 2014Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Riboswitches are structured mRNA elements that modulate gene expression. They undergo conformational changes triggered by highly specific interactions with sensed metabolites. Among the structural rearrangements engaged by riboswitches, the forming and melting of the aptamer terminal helix, the so-called P1 stem, is essential for genetic control. The structural mechanisms by which this conformational change is modulated upon ligand binding mostly remain to be elucidated. Here, we used pulling molecular dynamics simulations to study the thermodynamics of the P1 stem in the add adenine riboswitch. The P1 ligand-dependent stabilization was quantified in terms of free energy and compared with thermodynamic data. This comparison suggests a model for the aptamer folding in which direct P1-ligand interactions play a minor role on the conformational switch when compared with those related to the ligand-induced aptamer preorganization.
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