Browsing by Author "Hennelly, Scott P."

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    Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch
    (Oxford University Press, 2019) Roy, Susmita; Hennelly, Scott P.; Lammert, Heiko; Onuchic, José Nelson; Sanbonmatsu, Karissa Y.
    Investigations of most riboswitches remain confined to the ligand-binding aptamer domain. However, during the riboswitch mediated transcription regulation process, the aptamer domain and the expression platform compete for a shared strand. If the expression platform dominates, an anti-terminator helix is formed, and the transcription process is active (ON state). When the aptamer dominates, transcription is terminated (OFF state). Here, we use an expression platform switching experimental assay and structure-based electrostatic simulations to investigate this ON-OFF transition of the full length SAM-I riboswitch and its magnesium concentration dependence. Interestingly, we find the ratio of the OFF population to the ON population to vary non-monotonically as magnesium concentration increases. Upon addition of magnesium, the aptamer domain pre-organizes, populating the OFF state, but only up to an intermediate magnesium concentration level. Higher magnesium concentration preferentially stabilizes the anti-terminator helix, populating the ON state, relatively destabilizing the OFF state. Magnesium mediated aptamer-expression platform domain closure explains this relative destabilization of the OFF state at higher magnesium concentration. Our study reveals the functional potential of magnesium in controlling transcription of its downstream genes and underscores the importance of a narrow concentration regime near the physiological magnesium concentration ranges, striking a balance between the OFF and ON states in bacterial gene regulation.
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    Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch
    (American Chemical Society, 2012) Hayes, Ryan L.; Noel, Jeffrey K.; Mohanty, Udayan; Whitford, Paul C.; Hennelly, Scott P.; Onuchic, José N.; Sanbonmatsu, Karissa Y.; Center for Theoretical Biological Physics
    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.