Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome
Figure 4
Estimating diffusion coefficients for subunit rotation and tRNA movement.
A) Rotation coordinates and
as functions of time for a simulation about the pre-translocation (A/A-P/P) configuration (every 1 ns shown). B) Effective diffusion coefficients
and
were obtained from the displacement squared in the angles
.
is linear for
30 ns, which is characteristic of diffusive dynamics. Linear fits are depicted with gray dashed lines. C)
over the course of the simulation. D) Displacement squared of
is linear for
10 ns, allowing the tRNA effective diffusion coefficient
to be measured.