Figure 5.

The effect of tilting of the end subunit on the loops at the pointed end. (A) The same energy minimization and MD simulation described in the main text were performed on a putative model in which no tilting is assumed for the subunit P. The calculation was independently performed four times and the resultant model with the lowest energy is presented. The subunits P and P-1 are coloured in magenta and cyan, respectively. (B) Our final pointed end model, as presented in Figure 4C, with the subunits P and P-1 in red and blue, respectively. (C) Superposition of (A) and (B). The regions indicated by the thick tubes are the same as in Figure 4. The residues in the space-filling model in (A) and (B) are those involved at the interface between the DNase I binding loop and the hydrophobic plug in each model. The interface in (A) is largely limited, indicating that the tilting of P observed by the fitting is associated with the tighter loop-to-loop interactions at the pointed end.