ArticleRNA (New York, N.Y.)2013
Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study.
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 24 papers.
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Who cites it
24 citing papers in PubMed.
- Potential effects of metal ion induced two-state allostery on the regulatory mechanism of add adenine riboswitch.Communications biology · 2022Article
- Binding free energy decomposition and multiple unbinding paths of buried ligands in a PreQ1 riboswitch.PLoS computational biology · 2021Article
- Conformational Ensemble ofThe journal of physical chemistry. B · 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
- Intrinsic structural variability in GNRA-like tetraloops: insight from molecular dynamics simulation.Journal of molecular modeling · 2017Article
- MgBiophysical journal · 2017Article
- Co-Transcriptional Folding and Regulation Mechanisms of Riboswitches.Molecules (Basel, Switzerland) · 2017Review
- Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch.PloS one · 2017Article
- Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model.The Journal of chemical physics · 2016Article
- A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers.Nucleic acids research · 2016Article
- Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.Nucleic acids research · 2015Article
- Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics.Journal of chemical theory and computation · 2015Article
- Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations.BMC bioinformatics · 2015Article
- Using simulations and kinetic network models to reveal the dynamics and functions of riboswitches.Methods in enzymology · 2015Article
- DFT and MD study of the divalent-cation-mediated interaction of ochratoxin A with DNA nucleosides.Journal of molecular modeling · 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 mRNA-based molecules capable of controlling the expression of genes. They undergo conformational changes upon ligand binding, and as a result, they inhibit or promote the expression of the associated gene. The close connection between structural rearrangement and function makes a detailed knowledge of the molecular interactions an important step to understand the riboswitch mechanism and efficiency. We have performed all-atom molecular dynamics simulations of the adenine-sensing add A-riboswitch to study the breaking of the kissing loop, one key tertiary element in the aptamer structure. We investigated the aptamer domain of the add A-riboswitch in complex with its cognate ligand and in the absence of the ligand. The opening of the hairpins was simulated using umbrella sampling using the distance between two loops as the reaction coordinate. A two-step process was observed in all the simulated systems. First, a general loss of stacking and hydrogen bond interactions is seen. The last interactions that break are the two base pairs G37-C61 and G38-C60, but the break does not affect the energy profile, indicating their pivotal role in the tertiary structure formation but not in the structure stabilization. The junction area is partially organized before the kissing loop formation and residue A24 anchors together the loop helices. Moreover, when the distance between the loops is increased, one of the hairpins showed more flexibility by changing its orientation in the structure, while the other conserved its coaxial arrangement with the rest of the structure.
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