Riboswitches are cis-acting genetic control elements that have been found in the un- traslated region of some mRNAs in bacteria and plants. Riboswitches are known to regulate the genetic expression by means of conformational changes triggered by highly specific interactions of the aptamer with the sensed metabolite. The non-coding sequence in the mRNA of add gene from V. vulnificus contains an adenine responsive riboswitch. Classical molecular dynamics simulations of its aptamer have been performed, both in presence and absence of its physiological ligand starting from the experimental crystal structure. We first use steered MD to induce the opening of the P1 stem and investigate its stability. Our results show that the ligand directly stabilizes the P1 stem by means of stacking interactions quantitatively consistent with thermodynamic data. Then, using both umbrella sampling and a combination of metadynamics and hamiltonian replica exchange, we show that the formation of L2-L3 kissing complex cooperates with ligand binding and we quantify the ligand-induced stabilization. In this context also the influ- ence given by either the monovalent cations or divalent cations was evaluated. Confor- mational changes at pairings detailed level are characterized using a recently introduced technique that is able to distinguish and classify each interaction (i.e. Watson-Crick base pair, non-canonical bp, stacking). Results are compatible with known experimental measurements and shed a new light on the ligand-dependent folding mechanism of the adenine riboswitch.
