Figure 6.

Model of Hfq RNA chaperone function. The sRNA displayed by the full-atom model with atoms colour-coded is shown bound to the proximal face of Hfq_Ec (green, solvent accessible surface). Through conformational fluctuations, the sRNA can cover a larger conformational space (nine representative DsrA₃₄ models are displayed with their solvent accessible surface coloured as in Figure 5). The mRNA is bound on the distal side (polyA₉ orange flat cartoon representation) to one of the six tripartite binding motifs as shown in the crystal structure pdb3GIB (11). The model of a hypothetical mRNA chain is displayed in orange oval cartoon. Hfq_Ec acts by restructuring the mRNA (6), which may be accomplished by the conformationally flexible C-termini (29). The structural variability of both RNAs in a transient ternary 1:1:1 complex (18) would allow to sample large spaces. In this way, Hfq_Ec would not only act as a platform for binding and by increasing the local concentration of both ligands but would also serve to promote their flexibility and consequently successful annealing in a stochastic manner.