Modeling Riboswitches: The impact of SAM concentration on the folding of the SAM-II riboswitch

ABSTRACT Several mechanistic (thermodynamic) models have been developed for the folding of SAM-II riboswitch as a function of SAM and magnesium ions concentrations. For each model, the parameters have been determined from experimental (apparent) binding data, based on the underlying assumptions of the model. The predicted titration curves computed from the different models were calculated and compared with actual experimental observation of the fraction of the RNA forming a pseudoknot at specific concentrations of the ligands. Strikingly, only one of the six models correctly predicts the experimental findings, unveiling the dominant mechanism of the riboswitch function. More interestingly, the latter mechanism is found to be the most efficient compared to the other possible mechanisms. The study sheds light on the cognate ligand conformational capture mechanism of the SAM-II riboswitch in the presence of specific concentrations of magnesium ions. The presented mathematical and thermodynamic framework, as well as the inferred equilibrium constants, provide foundations for making accurate quantitative prediction of the SAM-II riboswitch ensemble populations as a function of SAM and magnesium concentrations. The mechanistic linked equilibria model can be generalized to describe other thermodynamically driven riboswitches and hence facilitate identifying RNA intermediates that can be leveraged for small molecule drug design. Graphical Abstract