Alternate conformational trajectories in ribosome translocation
Fig 3
Variant helical axis and hinge motions.
(a) Calculated helical axis (red) for the structural core of the 30S head in 16S rRNA. The head (domain III) is shown in cyan, and the body (domains I, II and IV) is shown in green (PDB ID 4V7B, Reference 9). (b) Displacement at each position along the calculated helical axis from the classical PRE state to the simulated conformation at 16° swivel for wild type and top selected hinge 1 variants. (c) Same as (b) for wild type and top selected hinge 2 variants. (d) Hinge 1 motion in the wild type ribosome. Hinge 1 is positioned in a weak point in h28 and its motion results from the kinked helix h28 being straightened during swivel. Cylinders show helical axes in the 16S rRNA core for the classical PRE (tan) and swiveled INT2 (magenta) conformations. (e) Root-mean-square-fluctuations (RMSF) of hinge 1 during forward swivel for wild type and top selected hinge 1 variants. (f) Same as (e) for wild type and top selected hinge 2 variants. Symbol keys are ordered according to their RISE selection enrichment.