1. Structural Transitions and Thermodynamics of a Glycine-Dependent Riboswitch from Vibrio cholerae
- Author
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Lipfert, Jan, Das, Rhiju, Chu, Vincent B., Kudaravalli, Madhuri, Boyd, Nathan, Herschlag, Daniel, and Doniach, Sebastian
- Subjects
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AMINO acid neurotransmitters , *AMINO acids , *RNA , *MESSENGER RNA , *GENE expression , *MAGNESIUM ions - Abstract
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 Mg2+ 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 Mg2+ in the absence of glycine leads to a significant compaction and partial folding as judged by hydroxyl radical protections. In the presence of millimolar Mg2+ 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 Mg2+ 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. [Copyright &y& Elsevier]
- Published
- 2007
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