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. 2005 Oct 7;90(1):42–56. doi: 10.1529/biophysj.105.071944

FIGURE 3.

FIGURE 3

RMSD plots for helix E of the free pol X structures obtained by superimposing the palm (residues 1–105) for simulations performed at physiological, 150 mM (a and b) (simulations 1 and 2), and high salt concentration, 500 mM (c and d) (simulations 3 and 4). (a) Time evolution plots of the RMSD values for both structure A (initially closed) and structure B (initially open) with respect to initial conformation at physiological conditions. (b) RMSD values obtained by superimposing the palm of structure A in the trajectory with initial structure A and initial structure B. This plot clearly shows that final structure A (at the 10 ns) superimposes better with structure B (average RMSD for the final 2 ns ∼3.5 Å) than with the initial structure A (average RMSD for the final 2 ns ∼5.5 Å). (c) Time evolution plots of the RMSD values for both structure A (initially closed) and structure B (initially open) with respect to initial conformation at high salt. (d) RMSD of structure B plotted with respect to its starting conformation and with respect to structure A. RMSD with respect to structure A is corrected for translational motion following earlier works (see Arora and Schlick (61)) and shows that the final structure B superimposes better with structure A than with initial structure B.