title: Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy.
abstract: Riboswitches are a newly discovered large family of structured functional RNA elements that specifically bind small molecule targets out of a myriad of cellular metabolites to modulate gene expression. Structural studies of ligand-bound riboswitches by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy have provided insights into detailed RNA-ligand recognition and interactions. However, the structures of ligand-free riboswitches remain poorly characterized. In this study, we have used a variety of biochemical, biophysical and computational techniques including small-angle X-ray scattering and NMR spectroscopy to characterize the ligand-free and ligand-bound forms of SAM-II riboswitch. Our data demonstrate that the RNA adopts multiple conformations along its folding pathway and suggest that the RNA undergoes marked conformational changes upon Mg(2+) compaction and S-adenosylmethionine (SAM) metabolite binding. Further studies indicated that Mg(2+) ion is not essential for the ligand binding but can stabilize the complex by facilitating loop/stem interactions. In the presence of millimolar concentration of Mg(2+) ion, the RNA samples a more compact conformation. This conformation is near to, but distinct from, the native fold and competent to bind the metabolite. We conclude that the formation of various secondary and tertiary structural elements, including a pseudoknot, occur to sequester the putative Shine-Dalgarno sequence of the RNA only after metabolite binding.
authors.affiliation: Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
authors.forename: Bin
authors.initials: B
authors.lastname: Chen
authors.forename: Xiaobing
authors.initials: X
authors.lastname: Zuo
authors.forename: Yun-Xing
authors.initials: YX
authors.lastname: Wang
authors.forename: T Kwaku
authors.initials: TK
authors.lastname: Dayie
mesh_terms: D018360:Crystallography, X-Ray; D024202:Electrophoretic Mobility Shift Assay; D008274:Magnesium / Q000737:chemistry; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry; D058928:Riboswitch; D012436:S-Adenosylmethionine / Q000378:metabolism*; D053838:Scattering, Small Angle; D014961:X-Ray Diffraction
chemical_list: D058928:Riboswitch; D012313:RNA; D012436:S-Adenosylmethionine; D008274:Magnesium