Figure 5
Low frequency – large amplitude motions in active PAI-1. The per-residue, per-frame Cα-RMSD values relative to the average structure was calculated once every 200 ps for the four simulations on active PAI-1 (total of 20000 frames). (a) For each residue, the frames used for calculations were grouped in Cα-RMSD value bins of 0.1 Å size and the %-fraction of frames in each bin was plotted as histograms according to the indicated color scale. (b) Data for S37, L69 and M83 in active PAI-1 are shown as examples. The histograms were then collapsed to a 1-dimensional representation and rotated 90° counter clockwise to facilitate the construction of a density plot of the binned Cα-RMSD data as a function of PAI-1 residue number in (b). The per-residue average Cα-RMSD values are indicated by the black line.
