Figure 5.

D-loop fluctuations. (A) First two principal components from dPCA analysis reveal three states, folded, unfolded and cofilin-like. (B) DM analysis confirms existence of same three states. Results for filament with coordinated Mg²⁺ are restricted to a subset of unfolded structures. (C) Typical snapshots taken from the different states identified in (A). All are oriented from N-term to C-term going from left to right. Unfolded conformations have PC1 > −1 and PC2 < 2, folded conformations have PC > 2.5, and cofilin-like structures have PC1 < −1. (D,E) Interface between segments with and without coordinated stiffness ion. Twenty snapshots for D-loop and adjacent residues (40–62) are shown every 2.5 ps from a representative molecular dynamics trajectory. The D-loop conformations in the ion-bound system are more tightly bound to the adjacent subdomain 3 (Figure 4).