Figure 3. A/P–P/E to P/P–E/E transition involves large-scale rotation and tilting of the 30S head.

Probability distributions calculated from 250 unrestrained (unguided) simulations highlight the relationship between tRNA and 30S head motions. (a) For the transition from the A/P–P/E to the P/P–E/E ensemble, the probability P(R_P−ASL,φ_head) indicates the presence of two intermediate ensembles: a chimeric ap/P–pe/E ensemble and a head-tilted (HT) ensemble. The ap/P–pe/E ensemble includes highly rotated head configurations (φ_head≈14–20°). Adopting the HT ensemble is associated with nearly complete back rotation of the head (Δφ_head ≈−13°). (b) P(R_P−ASL,θ_head) shows that there is a large degree of head tilting (θ_head≈10°) in the HT ensemble. (c) Representative directions (parallel or perpendicular to the mRNA) of the tilt axis of the 30S head are shown. The direction of the tilt axis is measured by χ_head (see Supplementary Information for details). By construction, χ_head=0° corresponds to tilting about an axis that is parallel to the mRNA, where the head is displaced away from the 30S–50S interface. Similarly, χ_head=180° corresponds to tilting towards the 30S–50S interface. In contrast, χ_head=±90° corresponds to tilting that is perpendicular to the mRNA. (d) P(χ_head) shows that head tilting in the HT ensemble occurs predominantly along the χ_head=0° direction (that is, about the mRNA axis), with a full-width at half-maximum (FWHM; red bar) of 24°. As a technical note, simulations were initiated from an A/A–P/E conformation. Initial relaxation into the A/P–P/E ensemble was allowed before data was included for analysis. Accordingly, probability distributions were calculated for R_A−ELB<4 Å.