title: SAM-II Riboswitch Samples at least Two Conformations in Solution in the Absence of Ligand: Implications for Recognition.
abstract: Conformational equilibria are increasingly recognized as pivotal for biological function. Traditional structural analyses provide a static image of conformers in solution that sometimes present conflicting views. From (13) C and (1) H chemical exchange saturation transfer experiments, in concert with ligation and selective labeling strategies, we show that in the absence of metabolite, a Mg(2+) (0-0.5 mm)-bound apo SAM-II riboswitch RNA exists in a minor (≈10 %) partially closed state that rapidly exchanges with a predominantly (≈90 %) open form with a lifetime of ≈32 ms. The base and sugar (H6,C6, H1',C1') chemical shifts of C43 for the dominant conformer are similar to those of a free CMP, but those of the minor apo species are comparable to shifts of CMPs in helical RNA regions. Our results suggest that these transient, low populated states stabilized by Mg(2+) will likely enhance rapid ligand recognition and, we anticipate, will play potentially ubiquitous roles in RNA signaling.
authors.affiliation: Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sciences Building (296), 8314 Paint Branch Dr., College Park, MD, 20782, USA.
authors.forename: Bin
authors.identifier: http://orcid.org/0000-0001-7501-4229
authors.initials: B
authors.lastname: Chen
authors.affiliation: Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sciences Building (296), 8314 Paint Branch Dr., College Park, MD, 20782, USA.
authors.forename: Regan
authors.identifier: http://orcid.org/0000-0001-9685-3689
authors.initials: R
authors.lastname: LeBlanc
authors.affiliation: Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sciences Building (296), 8314 Paint Branch Dr., College Park, MD, 20782, USA. Dayie@umd.edu.
authors.forename: T Kwaku
authors.identifier: http://orcid.org/0000-0002-7119-4362
authors.initials: TK
authors.lastname: Dayie
mesh_terms: D066241:Carbon-13 Magnetic Resonance Spectroscopy; D008024:Ligands; D009690:Nucleic Acid Conformation; D066244:Proton Magnetic Resonance Spectroscopy; D058928:Riboswitch
chemical_list: D008024:Ligands; D058928:Riboswitch
keywords: NMR spectroscopy; RNA; RNA dynamics; conformational dynamics; riboswitches