ArticleNucleic acids research2009
Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Assessing Molecular Dynamics in Predicting Aptamer-Ligand Binding Thermodynamics: Insights from the OTA Binding Aptamers.Journal of chemical information and modeling · 2026Article
- Beyond the niche - unlocking the full potential of synthetic riboswitches.Nature communications · 2025Review
- A DNA Aptamer for 2-Aminopurine: Binding-Induced Fluorescence Quenching.Chemistry, an Asian journal · 2024Article
- Systematic bio-fabrication of aptamers and their applications in engineering biology.Systems microbiology and biomanufacturing · 2023Review
- Potential effects of metal ion induced two-state allostery on the regulatory mechanism of add adenine riboswitch.Communications biology · 2022Article
- Insights into the aggregation mechanism of RNA recognition motif domains in TDP-43: a theoretical exploration.Royal Society open science · 2021Article
- Ligand Binding Mechanism and Its Relationship with Conformational Changes in Adenine Riboswitch.International journal of molecular sciences · 2020Article
- Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations.Nucleic acids research · 2019Article
- Structural Studies of the 3',3'-cGAMP Riboswitch Induced by Cognate and Noncognate Ligands Using Molecular Dynamics Simulation.International journal of molecular sciences · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- The conformational feasibility for the formation of reaching dimer in ASV and HIV integrase: a molecular dynamics study.Journal of biomolecular structure & dynamics · 2017Article
- Effect of single-residue bulges on RNA double-helical structures: crystallographic database analysis and molecular dynamics simulation studies.Journal of molecular modeling · 2017Article
- A magnesium-induced triplex pre-organizes the SAM-II riboswitch.PLoS computational biology · 2017Article
- Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch.PloS one · 2017Article
- Dynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch.Scientific reports · 2016Article
- Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics.RNA (New York, N.Y.) · 2015Article
- Dynamics of riboswitches: Molecular simulations.Biochimica et biophysica acta · 2014Review
- The purine riboswitch as a model system for exploring RNA biology and chemistry.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
- Methods to enable the design of bioactive small molecules targeting RNA.Organic & biomolecular chemistry · 2014Review
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3 authors.
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Abstract
Riboswitches are a novel class of genetic control elements that function through the direct interaction of small metabolite molecules with structured RNA elements. The ligand is bound with high specificity and affinity to its RNA target and induces conformational changes of the RNA's secondary and tertiary structure upon binding. To elucidate the molecular basis of the remarkable ligand selectivity and affinity of one of these riboswitches, extensive all-atom molecular dynamics simulations in explicit solvent (approximately 1 micros total simulation length) of the aptamer domain of the guanine sensing riboswitch are performed. The conformational dynamics is studied when the system is bound to its cognate ligand guanine as well as bound to the non-cognate ligand adenine and in its free form. The simulations indicate that residue U51 in the aptamer domain functions as a general docking platform for purine bases, whereas the interactions between C74 and the ligand are crucial for ligand selectivity. These findings either suggest a two-step ligand recognition process, including a general purine binding step and a subsequent selection of the cognate ligand, or hint at different initial interactions of cognate and noncognate ligands with residues of the ligand binding pocket. To explore possible pathways of complex dissociation, various nonequilibrium simulations are performed which account for the first steps of ligand unbinding. The results delineate the minimal set of conformational changes needed for ligand release, suggest two possible pathways for the dissociation reaction, and underline the importance of long-range tertiary contacts for locking the ligand in the complex.
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