text: Average structures of the three most numerous populatio | Open-i
  Fig4: Average structures of the three most numerous populations of EF-G (left) and EF-Tu:tRNA (right) derived on the basis of clustering of their RMSD matrices presented in Fig. 3
  Mentions: To discern the conformational movements in EF-G and EF-Tu:tRNA, we quantified the changes in RMSD between each trajectory frame. The RMSD-matrices and the cluster analysis are presented in Fig. 3. We observed several clusters with a time-span between 1.5 and 6 ns; 16 groups of different configurations for EF-G (Fig. 3), 22 groups for EF-G:GDP (data not shown), and 11 groups for EF-Tu:tRNA (Fig. 3). The average structures of the most numerous populations of EF-G and EF-Tu:tRNA are shown in Fig. 4. The average RMSD between the structures within each cluster is about 1 Å. The RMSD between structures from different clusters ranges from 2 to 3 Å. In both cases the most important structural differences between the generated clusters are in the elongated parts, i.e. domains III, IV, and V of EF-G and tRNA of the EF-Tu:tRNA complex. The changes are in agreement with studies showing that the mobility of these fragments is important for the binding of the factors to the ribosome (Agrawal et al. 1998; Valle et al. 2003; Tama et al. 2004; Wriggers et al. 2000). Specifically, when tRNA is delivered by EF-Tu to the ribosome, the tRNA anticodon arm is distorted (Valle et al. 2002; Schuette et al. 2009).Fig. 3