title: A magnesium-induced triplex pre-organizes the SAM-II riboswitch.
abstract: Our 13C- and 1H-chemical exchange saturation transfer (CEST) experiments previously revealed a dynamic exchange between partially closed and open conformations of the SAM-II riboswitch in the absence of ligand. Here, all-atom structure-based molecular simulations, with the electrostatic effects of Manning counter-ion condensation and explicit magnesium ions are employed to calculate the folding free energy landscape of the SAM-II riboswitch. We use this analysis to predict that magnesium ions remodel the landscape, shifting the equilibrium away from the extended, partially unfolded state towards a compact, pre-organized conformation that resembles the ligand-bound state. Our CEST and SAXS experiments, at different magnesium ion concentrations, quantitatively confirm our simulation results, demonstrating that magnesium ions induce collapse and pre-organization. Agreement between theory and experiment bolsters microscopic interpretation of our simulations, which shows that triplex formation between helix P2b and loop L1 is highly sensitive to magnesium and plays a key role in pre-organization. Pre-organization of the SAM-II riboswitch allows rapid detection of ligand with high selectivity, which is important for biological function.
authors.affiliation: Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America.
authors.forename: Susmita
authors.initials: S
authors.lastname: Roy
authors.affiliation: Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America.
authors.forename: Heiko
authors.initials: H
authors.lastname: Lammert
authors.affiliation: Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America.
authors.forename: Ryan L
authors.identifier: 0000-0003-1052-6391
authors.initials: RL
authors.lastname: Hayes
authors.affiliation: Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America.
authors.forename: Bin
authors.identifier: 0000-0001-7501-4229
authors.initials: B
authors.lastname: Chen
authors.affiliation: Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America.
authors.forename: Regan
authors.identifier: 0000-0001-9685-3689
authors.initials: R
authors.lastname: LeBlanc
authors.affiliation: Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America.
authors.forename: T Kwaku
authors.initials: TK
authors.lastname: Dayie
authors.affiliation: Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America.|Departments of Physics and Astronomy, Chemistry, and Biosciences, Rice University, Houston, Texas, United States of America.
authors.forename: José N
authors.identifier: 0000-0002-9448-0388
authors.initials: JN
authors.lastname: Onuchic
authors.affiliation: Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America.|New Mexico Consortium, Los Alamos, New Mexico, United States of America.
authors.forename: Karissa Y
authors.initials: KY
authors.lastname: Sanbonmatsu
mesh_terms: D001665:Binding Sites; D008274:Magnesium / Q000737:chemistry*; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012333:RNA, Messenger / Q000737:chemistry* / Q000648:ultrastructure*; D058928:Riboswitch
chemical_list: D012333:RNA, Messenger; D058928:Riboswitch; D008274:Magnesium