A magnesium-induced triplex pre-organizes the SAM-II riboswitch

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dc.citation.articleNumbere1005406en_US
dc.citation.issueNumber3en_US
dc.citation.journalTitlePLoS Computational Biologyen_US
dc.citation.volumeNumber13en_US
dc.contributor.authorRoy, Susmitaen_US
dc.contributor.authorLammert, Heikoen_US
dc.contributor.authorHayes, Ryan L.en_US
dc.contributor.authorChen, Binen_US
dc.contributor.authorLeBlanc, Reganen_US
dc.contributor.authorDayie, T.Kwakuen_US
dc.contributor.authorOnuchic, José Nelsonen_US
dc.contributor.authorSanbonmatsu, Karissa Y.en_US
dc.contributor.orgCenter for Theoretical Biological Physicsen_US
dc.date.accessioned2017-05-05T19:00:53Zen_US
dc.date.available2017-05-05T19:00:53Zen_US
dc.date.issued2017en_US
dc.description.abstractOur 13C- and 1H-chemical exchange saturation transfer (CEST) experiments previously revealed a dynamic exchange between partially closed and open conformations of the SAM-II riboswitch in the absence of ligand. Here, all-atom structure-based molecular simulations, with the electrostatic effects of Manning counter-ion condensation and explicit magnesium ions are employed to calculate the folding free energy landscape of the SAM-II riboswitch. We use this analysis to predict that magnesium ions remodel the landscape, shifting the equilibrium away from the extended, partially unfolded state towards a compact, pre-organized conformation that resembles the ligand-bound state. Our CEST and SAXS experiments, at different magnesium ion concentrations, quantitatively confirm our simulation results, demonstrating that magnesium ions induce collapse and pre-organization. Agreement between theory and experiment bolsters microscopic interpretation of our simulations, which shows that triplex formation between helix P2b and loop L1 is highly sensitive to magnesium and plays a key role in pre-organization. Pre-organization of the SAM-II riboswitch allows rapid detection of ligand with high selectivity, which is important for biological function.en_US
dc.identifier.citationRoy, Susmita, Lammert, Heiko, Hayes, Ryan L., et al.. "A magnesium-induced triplex pre-organizes the SAM-II riboswitch." <i>PLoS Computational Biology,</i> 13, no. 3 (2017) Public Library of Science: https://doi.org/10.1371/journal.pcbi.1005406.en_US
dc.identifier.doihttps://doi.org/10.1371/journal.pcbi.1005406en_US
dc.identifier.urihttps://hdl.handle.net/1911/94189en_US
dc.language.isoengen_US
dc.publisherPublic Library of Scienceen_US
dc.rightsThis is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.en_US
dc.rights.urihttps://creativecommons.org/publicdomain/zero/1.0/en_US
dc.titleA magnesium-induced triplex pre-organizes the SAM-II riboswitchen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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