Figure 2. Mobility and conformational change of loop-containing regions.

A) Sausage representation of the wt-PAH initial structure, in which the thickness of the sausage is proportional to the root mean square fluctuation of C^α atoms from their average positions. Average positions are calculated after least-squares fit superimposition of the trajectory structures onto the starting structure used as reference. B) Porcupine representation of the first PC (accounting for 78% of the overall fluctuation of C^α atoms) extracted from the simulation of the wt-hPAH. The orange cones, attached to the average positions of each C^α atom, point in the direction of motion described by PC1. Blue arrows highlight the motion corresponding to the transition of L2 to β-strand. C) Initial (light green) and final (light pink) wt-hPAH structures with the L2 and L4 regions drawn in green and magenta.