ArticlePLoS computational biology2021
Binding free energy decomposition and multiple unbinding paths of buried ligands in a PreQ1 riboswitch.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 11 citations in OpenAlex.
- A cooperative effect of ligands, MgThe Journal of biological chemistry · 2026Article
- Predicting an intrinsic conformational twist in Card1: an in silico study.Journal of molecular modeling · 2026Article
- Binding Mechanism of Inhibitors to CDK6 Deciphered by Multiple Independent Molecular Dynamics Simulations and Free Energy Predictions.Molecules (Basel, Switzerland) · 2025Article
- Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages.Microbiology and molecular biology reviews : MMBR · 2024Review
- How Robust Is the Ligand Binding Transition State?Journal of the American Chemical Society · 2023Article
- Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch.Communications biology · 2023Article
- Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch.bioRxiv : the preprint server for biology · 2023Article
- Potential effects of metal ion induced two-state allostery on the regulatory mechanism of add adenine riboswitch.Communications biology · 2022Article
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
Abstract
Riboswitches are naturally occurring RNA elements that control bacterial gene expression by binding to specific small molecules. They serve as important models for RNA-small molecule recognition and have also become a novel class of targets for developing antibiotics. Here, we carried out conventional and enhanced-sampling molecular dynamics (MD) simulations, totaling 153.5 μs, to characterize the determinants of binding free energies and unbinding paths for the cognate and synthetic ligands of a PreQ1 riboswitch. Binding free energy analysis showed that two triplets of nucleotides, U6-C15-A29 and G5-G11-C16, contribute the most to the binding of the cognate ligands, by hydrogen bonding and by base stacking, respectively. Mg2+ ions are essential in stabilizing the binding pocket. For the synthetic ligands, the hydrogen-bonding contributions of the U6-C15-A29 triplet are significantly compromised, and the bound state resembles the apo state in several respects, including the disengagement of the C15-A14-A13 and A32-G33 base stacks. The bulkier synthetic ligands lead to significantly loosening of the binding pocket, including extrusion of the C15 nucleobase and a widening of the C15-C30 groove. Enhanced-sampling simulations further revealed that the cognate and synthetic ligands unbind in almost opposite directions. Our work offers new insight for designing riboswitch ligands.
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