Fig. 5.

Model for ligand recognition and folding of the preQ₁-II riboswitch. For direct comparison, lifetimes of closed pseudoknot conformations τ(P3) in the absence and presence of ligands (Mg²⁺, preQ₁) are depicted (in red) next to each structure cartoon. Lifetimes of compacted P4/J2–3 conformations τ(P4) are indicated in green. The pseudoknot becomes prefolded in the presence of Mg²⁺ ions and further stabilized in the presence of preQ_1. The extra stem–loop P4 behaves rather uncoupled from pseudoknot formation and retains higher dynamics throughout all three conditions (no ligands; Mg²⁺; Mg²⁺ and preQ₁) investigated here, even in the fully folded, preQ₁-bound state.