title: Modulation of Conformational Equilibria in the S-Adenosylmethionine (SAM) II Riboswitch by SAM, Mg(2+), and Trimethylamine N-Oxide.
abstract: The dependence of the conformation of the S-adenosylmethionine (SAM) II riboswitch on the concentration of added Mg(2+) ions and SAM, individually and in mixtures, was monitored by circular dichroism (CD) spectroscopy and by measurement of the diffusion coefficient. The results are analyzed in the context of two complementary quantitative models, both of which are consistent with a single underlying physical model. Magnesium binding sites in the open state have an affinity on average higher than the affinity of those in the compact state, but formation of the compact state is accompanied by an increase in the number of binding sites. Consequently, at low Mg(2+) concentrations, Mg(2+) binds preferentially to the open state, favoring its formation, but at high concentrations, Mg(2+) binds preferentially to the compact state. The affinity of the riboswitch for SAM increases drastically with an increased level of binding of Mg(2+) to the compact pseudoknot conformation. The effect of increasing concentrations of trimethylamine N-oxide (TMAO), a well-studied molecular crowding agent, on the conformation of the riboswitch and its affinity for SAM were also monitored by CD spectroscopy and measurement of diffusion. In the absence of added Mg(2+), high concentrations of TMAO were found to induce a conformational change compatible with the formation of the pseudoknot form but have only a small effect on the affinity of the RNA for SAM.
authors.affiliation: Section on Physical Biochemistry, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States.
authors.forename: Peter
authors.initials: P
authors.lastname: McPhie
authors.affiliation: Section on Dynamics of Macromolecular of Assembly, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health , Bethesda, Maryland 20892, United States.
authors.forename: Patrick
authors.initials: P
authors.lastname: Brown
authors.affiliation: Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States.
authors.forename: Bin
authors.initials: B
authors.lastname: Chen
authors.affiliation: Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States.
authors.forename: Theodore K
authors.initials: TK
authors.lastname: Dayie
authors.affiliation: Section on Physical Biochemistry, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States.
authors.forename: Allen P
authors.initials: AP
authors.lastname: Minton
mesh_terms: D002614:Chelating Agents / Q000737:chemistry; D002942:Circular Dichroism; D008274:Magnesium / Q000737:chemistry*; D008744:Methylamines / Q000737:chemistry*; D011487:Protein Conformation; D058928:Riboswitch; D012436:S-Adenosylmethionine / Q000737:chemistry*
chemical_list: D002614:Chelating Agents; D008744:Methylamines; D058928:Riboswitch; D012436:S-Adenosylmethionine; C005855:trimethyloxamine; D008274:Magnesium