Molecular Dynamics Simulations of the Ribosome - Biophysical Approaches to Translational Control of Gene Expression - page 56

rRNA elements at the PTC. In addition, two distinguishable hybrid configurations
arising from motions of each tRNA end were observed. Both hybrid configurations
result from the motion of the deacylated P-site tRNA towards the E site, where it
adopts a P/E configuration (Munro et al. 2007 ) . Hybrid tRNA con fi gurations, fi rst
demonstrated by Noller and coworkers using chemical footprinting methods
(Moazed and Noller 1989 ), are key intermediates in the translocation process, low-
ering the activation barrier for translocation. Analytic treatment of the smFRET data
revealed that A- and P-site tRNA motions can occur through independent or coupled
processes. The rates of motions observed suggest that A- and P-site tRNA motions
entailed large-scale conformational events in the ribosome.

3.3 Overall Dynamics of the Ribosome

In addition to the tRNA, the ribosome itself has been shown to have several dynamic
regions. We refer to motion of a region of a subunit with respect to the same subunit
as intrasubunit motion. We refer to the motion of the two subunits with respect to
each other as intersubunit motion (Frank and Agrawal 2000 ) . The most obvious
motion performed by the ribosome is the so-called ratchet-like pivoting of the 30S
subunit with respect to the 50S subunit (Fig. 3.6 ) (Frank and Agrawal 2000 ) . Cryo-EM

Fig. 3.6 Dynamic regions of the ribosome: pivoting of the 30S with respect to the 50S