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

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dc.citation.articleNumbere1005406
dc.citation.issueNumber3
dc.citation.journalTitlePLoS Computational Biology
dc.citation.volumeNumber13
dc.contributor.authorRoy, Susmita
dc.contributor.authorLammert, Heiko
dc.contributor.authorHayes, Ryan L.
dc.contributor.authorChen, Bin
dc.contributor.authorLeBlanc, Regan
dc.contributor.authorDayie, T.Kwaku
dc.contributor.authorOnuchic, José Nelson
dc.contributor.authorSanbonmatsu, Karissa Y.
dc.contributor.orgCenter for Theoretical Biological Physics
dc.date.accessioned2017-05-05T19:00:53Z
dc.date.available2017-05-05T19:00:53Z
dc.date.issued2017
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.
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.
dc.identifier.doihttps://doi.org/10.1371/journal.pcbi.1005406
dc.identifier.urihttps://hdl.handle.net/1911/94189
dc.language.isoeng
dc.publisherPublic Library of Science
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.
dc.rights.urihttps://creativecommons.org/publicdomain/zero/1.0/
dc.titleA magnesium-induced triplex pre-organizes the SAM-II riboswitch
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpublisher version
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