Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch
dc.citation.firstpage | 12043 | en_US |
dc.citation.issueNumber | 29 | en_US |
dc.citation.journalTitle | Journal of the American Chemical Society | en_US |
dc.citation.lastpage | 12053 | en_US |
dc.citation.volumeNumber | 134 | en_US |
dc.contributor.author | Hayes, Ryan L. | en_US |
dc.contributor.author | Noel, Jeffrey K. | en_US |
dc.contributor.author | Mohanty, Udayan | en_US |
dc.contributor.author | Whitford, Paul C. | en_US |
dc.contributor.author | Hennelly, Scott P. | en_US |
dc.contributor.author | Onuchic, José N. | en_US |
dc.contributor.author | Sanbonmatsu, Karissa Y. | en_US |
dc.contributor.org | Center for Theoretical Biological Physics | en_US |
dc.date.accessioned | 2014-12-15T20:35:08Z | en_US |
dc.date.available | 2014-12-15T20:35:08Z | en_US |
dc.date.issued | 2012 | en_US |
dc.description.abstract | Experiments demonstrate that Mg2+ is crucial for structure and function of RNA systems, yet the detailed molecular mechanism of Mg2+ action on RNA is not well understood. We investigate the interplay between RNA and Mg2+ at atomic resolution through ten 2-μs explicit solvent molecular dynamics simulations of the SAM-I riboswitch with varying ion concentrations. The structure, including three stemloops, is very stable on this time scale. Simulations reveal that outer-sphere coordinated Mg2+ ions fluctuate on the same time scale as the RNA, and that their dynamics couple. Locally, Mg2+ association affects RNA conformation through tertiary bridging interactions; globally, increasing Mg2+ concentration slows RNA fluctuations. Outer-sphere Mg2+ ions responsible for these effects account for 80% of Mg2+ in our simulations. These ions are transiently bound to the RNA, maintaining interactions, but shuttled from site to site. Outer-sphere Mg2+ are separated from the RNA by a single hydration shell, occupying a thin layer 3–5 Å from the RNA. Distribution functions reveal that outer-sphere Mg2+ are positioned by electronegative atoms, hydration layers, and a preference for the major groove. Diffusion analysis suggests transient outer-sphere Mg2+ dynamics are glassy. Since outer-sphere Mg2+ ions account for most of the Mg2+ in our simulations, these ions may change the paradigm of Mg2+–RNA interactions. Rather than a few inner-sphere ions anchoring the RNA structure surrounded by a continuum of diffuse ions, we observe a layer of outer-sphere coordinated Mg2+ that is transiently bound but strongly coupled to the RNA. | en_US |
dc.identifier.citation | Hayes, Ryan L., Noel, Jeffrey K., Mohanty, Udayan, et al.. "Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch." <i>Journal of the American Chemical Society,</i> 134, no. 29 (2012) American Chemical Society: 12043-12053. http://dx.doi.org/10.1021/ja301454u. | en_US |
dc.identifier.doi | http://dx.doi.org/10.1021/ja301454u | en_US |
dc.identifier.uri | https://hdl.handle.net/1911/78752 | en_US |
dc.language.iso | eng | en_US |
dc.publisher | American Chemical Society | en_US |
dc.rights | This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the American Chemical Society. | en_US |
dc.title | Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch | en_US |
dc.type | Journal article | en_US |
dc.type.dcmi | Text | en_US |
dc.type.publication | post-print | en_US |
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