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Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome

Figure 3

Reaction coordinates for 30S rotation and tRNA movement.

A) rmsf, by residue, for the 23S (left) and 16S (right) rRNA. rmsf measures (See Text S1) were used to define the core residues (shown with side chains) of the: B) 23S rRNA (gray) and C) 16S body (cyan) and 16S head (blue). Core residue groups were used to define the planes of rotation for D) body rotation (, positive in the counter-clockwise direction) and E) head swivel (). The vectors that define the rotation planes are depicted by orange arrows. The angle between the vectors is . In (D) and (E), the classical and rotated configurations are shown in cyan and white. tRNA position is measured by , as defined previously [49], [50] and is shown for F) the classical A/A-P/P tRNA configuration.

doi: https://doi.org/10.1371/journal.pcbi.1003003.g003