Molecular mechanism for preQ₁-II riboswitch function revealed by molecular dynamics

The structure of the binding pocket with ligand-bound (left panel) and in apo simulations (right panel). The apo structure (right panel) was the consensus for three of four of the apo simulations. Nucleotides A29 and A43 formed a trans-Hoogsteen/sugar-edge A29•A43 pair. At the top, a noncanonical, Watson–Crick face U31•U41 base pair (Leontis et al. 2002) and, in the middle, a C30-G42 Watson–Crick base pair formed. This structure was taken from simulation number 3 at 560 nsec. For comparison, the ligand-bound binding pocket is in the left panel with the ligand drawn in green from simulation number 3 at 730 nsec.