Modelling the impact of magnesium ions concentration on the folding of the SAM-II riboswitch

Riboswitches are regulatory elements present in bacterial messenger RNA acting as sensors of small molecules and consequently playing a vital role in bacterial gene regulation. The SAM-II riboswitch is a class of riboswitches, that recognizes S-adenosyl methionine. It has been previously illustrated that the presence of Mg2+ ions stabilizes the pre-existing minor state of the riboswitch, which is structurally characterised by having a nucleated pseudoknot, leading to the increase of its probability. In this study, an analytical equilibrium model is developed to describe the impact of Mg2+ ions concentration on the folding of the SAM-II riboswitch, linking RNA folding and tertiary interactions energetics to ligand binding, and, hence enabling quantitative predictions. The method was used to study the role of the P1 helix sequence in determining the fraction of binding competent conformers of the SAM-II riboswitch, by simulating the Mg2+ titration curves of various mutants. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/439486v2_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@19367ecorg.highwire.dtl.DTLVardef@8be5ecorg.highwire.dtl.DTLVardef@a3fec6org.highwire.dtl.DTLVardef@ab9d65_HPS_FORMAT_FIGEXP M_FIG C_FIG