Molecular Dynamics Simulations of the Ribosome - Biophysical Approaches to Translational Control of Gene Expression - page 52

Fig. 3.2 30S small ribosomal subunit

The precise alignment of tRNA in each state presents a paradox: how can the tRNA
be surrounded by many specific ribosome interactions, yet move to two other com-
pletely different states with equally complex interactions? The solution to this para-
dox is that both the ribosome and the tRNA are extremely dynamic, as evidenced by
single-molecule FRET (smFRET), cryo electron microscopy (cryo-EM), and X-ray
crystallography data (Munro et al. 2007 ; Blanchard et al. 2004 ; Blanchard 2009 ;
Zhang et al. 2008, 2009 ; Schuwirth et al. 2005 ; Fischer et al. 2010 ) . While smFRET
provides excellent information on the dynamics of the ribosome, it has low spatial
resolution. Cryo-EM and crystallographic studies provide higher resolution spatial
information but provide little information about dynamics. Molecular dynamics
simulations help to bridge the gap between single molecule dynamics experiments
and structural biology studies.