Fig. 7.
Conserved dynamics of the RdRps from PV, CVB3, HRV16 and FMDV. (a) The relative displacements of Cα atoms observed in the sum of the first six PCs (modes) are plotted for each residue. Peaks correspond to regions contributing to the major motions observed during the MD simulations. The structure has been divided into seven segments (S1–S7). The fingers subdomain is shaded purple, the palm subdomain is shaded light gray and the thumb subdomain is shaded orange. The conserved motifs A–G are indicated. Other regions of PV RdRp known to have functional significance have been labeled I–III. Dynamic regions under the peaks across the different polymerases show a striking similarity; the observed dynamic patterns are largely conserved. The major peaks in the different segments (S1–S7) observed in PV are also observed at equivalent positions for the other three RdRps. Nonetheless, differences in relative displacements of motifs A and E as well as of the region spanning residues 43–55 in the fingers are noted. Local sequence and structural variations might account for the differences in the observed dynamics. The plot of PV RdRp, shown previously in Fig. 4, is included for comparison with the other RdRps. (b) The average relative displacement calculated for the conserved motifs A–G and functional regions I–III of each RdRp is shown. The average was calculated by using the relative displacement of all residues constituting the motif as defined in Table S1.