Conformational Switching between ON and OFF States Proceeds through Multiple Pathways in the SAM-III Translational Riboswitch

Gene regulation via translational riboswitches is characterized by repeated and reversible conformational switching between ON (apo) and OFF (holo) states. The mechanism often entails substantial structural rearrangement, and the role of metal ions in this process remains unclear. Researchers employed molecular dynamics simulations to investigate the switching transition of a riboswitch controlling S-adenosyl methionine (SAM) levels, a universal methyl donor.

They discovered that Mg2+ ions are crucial for maintaining the ON-state, and the three-way junction undergoes a dynamic "breathing-like" interconversion between open and closed modes.

The riboswitch exhibits a low population of a holo-like READY (R) state, featuring a partially organized SAM-binding pocket even before ligand binding. Numerous intermediates are identified in the switching landscape, facilitating a gradual, stepwise structural transition between the ON and R states. These intermediates traverse multiple competing pathways, with Mg2+ ions influencing the dominant pathway for the ON-to-R transition. Conversely, the reverse transition displays only a weak dependence on metal ions.

The findings offer valuable insights into the function of translational riboswitches, which rapidly respond to alterations in metabolite concentrations, unlike their transcriptional counterparts.