Atomistic Simulations Reveal Crucial Role of Metal Ions for Ligand Binding in Gd-I Riboswitch

Riboswitches are structured RNA segments that act as specific sensors for small molecules in bacterial metabolism. Due to the flexi- ble nature of these highly charged macromolecules, molecular dynamics simulations are instrumental to investigating the mechanistic details of their regulatory function. In the present study, a guanidinium sensing riboswitch (the Gd-I riboswitch) serves as example how atomistic simulations can shed light on the role of ions on structure and dynamics of the RNA and on ligand binding. Rely- ing on two crystal structures from orthologous forms from different bacterial species, it is demonstrated how the ion setup crucially determines whether the simulation yields meaningful insights into the conformational stability of the RNA, functionally relevant residues and RNA-ligand interactions. Ion setup in this context includes the free ions in solution and ions associated directly with the RNA, in particular a triad of 2 Mg2+ ions and a K+ ion in close proximity to the guanidinium binding site. A detailed investi- gation of the binding pocket reveals that K+ from the ion triad plays a decisive role in stabilizing the ligand binding by stabilizing important localized interactions which in turn contribute to the overall shape of the folded state of the RNA.