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Effects of Ligand Binding on the Mechanical Properties of Ankyrin Repeat Protein Gankyrin

Figure 9

Time dependence of the binding contacts between Gank and S6-C at 0.01 Å/ps pulling speed.

A. Lifetime of binding contacts with S6-C for the residues of Gank (red error bars represent 1 standard error around average). Black and blue boxes represent 1 standard error around the average unfolding time of the corresponding repeats in Gank-S6-C complex and isolated Gank simulations, respectively, as measured using RMSD. Grey and green shadowed regions indicate the beta-turn and N-terminal helix regions, respectively. (B)–(C). Front and upper views of Gank (cartoon representation), colored according to the average time each residue took to lose contact with S6-C (glass surface representation, displayed to mark the position of the binding site in the native conformation). The residues that form long-lasting contacts with S6-C are shown in licorice. The figure was prepared using VMD [38].

Figure 9

doi: https://doi.org/10.1371/journal.pcbi.1002864.g009