Molecular Dynamics Simulations of the Ribosome - Biophysical Approaches to Translational Control of Gene Expression - page 57

Fig. 3.7 Dynamics of the 30S head swivel in all-atom structure-based simulations
reconstructions of the 70S ribosome in the presence of EF-G showed a substantial
rotation of the 30S relative to its initiator configuration upon EF-G binding (Frank
and Agrawal 2000 ). It was previously thought that this motion causes translocation
of the tRNA and mRNA through the ribosome. Recent FRET experiments have
shown that ratchet-like fluctuations occur at equilibrium in absence of EF-G
(Ermolenko et al. 2007 ). EF-G acts to trap the ribosome in the ratcheted position.
Several intrasubunit motions have been observed within the small subunit. The
decoding center of the small subunit contains two universally conserved nucleotides:
A1492 and A1493. These have been shown to be dynamic in NMR studies (Fourmy
et al. 1998 ), fluorescence studies (Kaul and Pilch 2002 ) and are observed to be dis-
ordered in X-ray crystallography systems (Ogle et al. 2001 ; Berk et al. 2006 ) .
The head domain of the small subunit has been shown to exist in multiple con-
formations (Schuwirth et al. 2005 ; Ratje et al. 2010 ) and also to be dynamic (Fig. 3.7 )
(Schuwirth et al. 2005 ; Ermolenko et al. 2007 ; Majumdar et al. 2005 ) . Cate and
coworkers first observed in alternative crystal forms that the head of the small sub-
unit was rotated around a neck region with respect to its body. Spahn and coworkers
have shown that this rotation is critical for translocation (Ratje et al. 2010 ) . In par-
ticular, cryo-EM reconstructions of EF-G bound ribosomes have recently shown