Figure 7.

Proposed mechanism of ligand binding to the Gd-II riboswitch. Insights originating from this work are shown in blue boxes. (A) In absence of guanidinium, the two stem–loops are split apart. (B) In presence of guanidinium, the two stem–loops bind a guanidinium each and dimerize by a loop-loop interaction along a stable dimerization interface (green). Our work shows, that the apo-state of the riboswitch is characterized by two alternating conformations of the binding pocket: a collapsed state (C), where the binding interface (red) is substantially deformed and an open state (D), where the binding interface is recovered (green), and guanidinium can be bound. (E) Our results indicate that the aptamer with bound guanidinium is also stable as a monomer. This suggests that ligand binding in the Gd-II stem–loop does not require a pairing of the two stem loops prior to the binding, but rather functions as the initiation event for subsequent dimerization of the stem–loops.