ArticleNucleic acids research2018
Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 16 citations in OpenAlex.
- Destabilization of Structured RNAs by OPC and TIP4PD Water Models.Journal of chemical theory and computation · 2026Article
- Fluorescent Dyes for Differential Scanning Fluorimetry of RNA.Chembiochem : a European journal of chemical biology · 2025Article
- The caspase-inhibitor Emricasan efficiently counteracts cisplatin- and neomycin-induced cytotoxicity in cochlear cells.Journal of molecular medicine (Berlin, Germany) · 2024Article
- Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Multi-Site Conformational Exchange in the Synthetic Neomycin-Sensing Riboswitch Studied byAngewandte Chemie (International ed. in English) · 2023Article
- Article
- Drug synergy discovery of tavaborole and aminoglycosides against Escherichia coli using high throughput screening.AMB Express · 2022Article
- RNA Chemical Labeling with Site-Specific, Relative Quantification by Mass Spectrometry for the Structural Study of a Neomycin-Sensing Riboswitch Aptamer Domain.ChemPlusChem · 2022Article
- Aptamers, Riboswitches, and Ribozymes inLife (Basel, Switzerland) · 2021Review
- Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection.Frontiers in molecular biosciences · 2021Article
- From Petri Dish to Patient: Bioavailability Estimation and Mechanism of Action for Antimicrobial and Immunomodulatory Natural Products.Frontiers in microbiology · 2019Review
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A synthetic riboswitch N1, inserted into the 5'-untranslated mRNA region of yeast, regulates gene expression upon binding ribostamycin and neomycin. Interestingly, a similar aminoglycoside, paromomycin, differing from neomycin by only one substituent (amino versus hydroxyl), also binds to the N1 riboswitch, but without affecting gene expression, despite NMR evidence that the N1 riboswitch binds all aminoglycosides in a similar way. Here, to explore the details of structural dynamics of the aminoglycoside-N1 riboswitch complexes, we applied all-atom molecular dynamics (MD) and temperature replica-exchange MD simulations in explicit solvent. Indeed, we found that ribostamycin and neomycin affect riboswitch dynamics similarly but paromomycin allows for more flexibility because its complex lacks the contact between the distinctive 6' hydroxyl group and the G9 phosphate. Instead, a transient hydrogen bond of 6'-OH with A17 is formed, which partially diminishes interactions between the bulge and apical loop of the riboswitch, likely contributing to riboswitch inactivity. In many ways, the paromomycin complex mimics the conformations, interactions, and Na+ distribution of the free riboswitch. The MD-derived interaction network helps understand why riboswitch activity depends on aminoglycoside type, whereas for another aminoglycoside-binding site, aminoacyl-tRNA site in 16S rRNA, activity is not discriminatory.
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