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Riboswitches are structured mRNA elements that modulate gene expression. Theyundergo conformational changes triggered by highly specific interactions withsensed metabolites. Among the structural rearrangements engaged byriboswitches, the forming and melting of the aptamer terminal helix, theso-called P1 stem, is essential for genetic control. The structural mechanismsby which this conformational change is modulated upon ligand binding mostlyremain to be elucidated. Here, we used pulling molecular dynamics simulationsto study the thermodynamics of the P1 stem in the add adenine riboswitch. TheP1 ligand-dependent stabilization was quantified in terms of free energy andcompared with thermodynamic data. This comparison suggests a model for theaptamer folding in which direct P1-ligand interactions play a minor role on theconformational switch when compared with those related to the ligand-inducedaptamer preorganization.

Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch