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