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• W1971218796 startingPage "1393" @default.
• W1971218796 abstract "Riboswitches are complex folded RNA domains found in noncoding regions of mRNA that regulate gene expression upon small molecule binding. Recently, Breaker and coworkers reported a tandem aptamer riboswitch (VCI-II) that binds glycine cooperatively. Here, we use hydroxyl radical footprinting and small-angle X-ray scattering (SAXS) to study the conformations of this tandem aptamer as a function of Mg(2+) and glycine concentration. We fit a simple three-state thermodynamic model that describes the energetic coupling between magnesium-induced folding and glycine binding. Furthermore, we characterize the structural conformations of each of the three states: In low salt with no magnesium present, the VCI-II construct has an extended overall conformation, presumably representing unfolded structures. Addition of millimolar concentrations of Mg(2+) in the absence of glycine leads to a significant compaction and partial folding as judged by hydroxyl radical protections. In the presence of millimolar Mg(2+) concentrations, the tandem aptamer binds glycine cooperatively. The glycine binding transition involves a further compaction, additional tertiary packing interactions and further uptake of magnesium ions relative to the state in high Mg(2+) but no glycine. Employing density reconstruction algorithms, we obtain low resolution 3-D structures for all three states from the SAXS measurements. These data provide a first glimpse into the structural conformations of the VCI-II aptamer, establish rigorous constraints for further modeling, and provide a framework for future mechanistic studies." @default.
• W1971218796 created "2016-06-24" @default.
• W1971218796 creator A5010576393 @default.
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• W1971218796 date "2007-02-01" @default.
• W1971218796 modified "2023-10-17" @default.
• W1971218796 title "Structural Transitions and Thermodynamics of a Glycine-Dependent Riboswitch from Vibrio cholerae" @default.
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• W1971218796 doi "https://doi.org/10.1016/j.jmb.2006.10.022" @default.
• W1971218796 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/1941672" @default.
• W1971218796 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/17118400" @default.
• W1971218796 hasPublicationYear "2007" @default.
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