ArticleRNA (New York, N.Y.)2009
MD simulations of ligand-bound and ligand-free aptamer: molecular level insights into the binding and switching mechanism of the add A-riboswitch.
Article in RNA (New York, N.Y.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 35 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
35 citing papers in PubMed, 70 citations in OpenAlex.
- Recovering Small Molecule Ligand-RNA Binding Pocket Binding Modes and Exploring Potential Binding Pathways Using Metadynamics.Molecules (Basel, Switzerland) · 2026Article
- Potential effects of metal ion induced two-state allostery on the regulatory mechanism of add adenine riboswitch.Communications biology · 2022Article
- Contact networks in RNA: a structural bioinformatics study with a new tool.Journal of computer-aided molecular design · 2022Article
- High Affinity Binding of N2-Modified Guanine Derivatives Significantly Disrupts the Ligand Binding Pocket of the Guanine Riboswitch.Molecules (Basel, Switzerland) · 2020Article
- Ligand Binding Mechanism and Its Relationship with Conformational Changes in Adenine Riboswitch.International journal of molecular sciences · 2020Article
- Pairing interactions between nucleobases and ligands in aptamer:ligand complexes of riboswitches: crystal structure analysis, classification, optimal structures, and accurate interaction energies.RNA (New York, N.Y.) · 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
- Going beyond base-pairs: topology-based characterization of base-multiplets in RNA.RNA (New York, N.Y.) · 2019Article
- 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
- 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
- Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics.RNA (New York, N.Y.) · 2015Article
- RNABP COGEST: a resource for investigating functional RNAs.Database : the journal of biological databases and curation · 2015Article
- Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations.BMC bioinformatics · 2015Article
- The purine riboswitch as a model system for exploring RNA biology and chemistry.Biochimica et biophysica acta · 2014Review
- Dynamics of riboswitches: Molecular simulations.Biochimica et biophysica acta · 2014Review
- DFT and MD study of the divalent-cation-mediated interaction of ochratoxin A with DNA nucleosides.Journal of molecular modeling · 2014Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Riboswitches are structural cis-acting genetic regulatory elements in 5' UTRs of mRNAs, consisting of an aptamer domain that regulates the behavior of an expression platform in response to its recognition of, and binding to, specific ligands. While our understanding of the ligand-bound structure of the aptamer domain of the adenine riboswitches is based on crystal structure data and is well characterized, understanding of the structure and dynamics of the ligand-free aptamer is limited to indirect inferences from physicochemical probing experiments. Here we report the results of 15-nsec-long explicit-solvent molecular dynamics simulations of the add A-riboswitch crystal structure (1Y26), both in the adenine-bound (CLOSED) state and in the adenine-free (OPEN) state. Root-mean-square deviation, root-mean-square fluctuation, dynamic cross-correlation, and backbone torsion angle analyses are carried out on the two trajectories. These, along with solvent accessible surface area analysis of the two average structures, are benchmarked against available experimental data and are shown to constitute the basis for obtaining reliable insights into the molecular level details of the binding and switching mechanism. Our analysis reveals the interaction network responsible for, and conformational changes associated with, the communication between the binding pocket and the expression platform. It further highlights the significance of a, hitherto unreported, noncanonical W:H trans base pairing between A73 and A24, in the OPEN state, and also helps us to propose a possibly crucial role of U51 in the context of ligand binding and ligand discrimination.
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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.