Skip to main content
. 2020 Jun 17;119(2):360–374. doi: 10.1016/j.bpj.2020.06.010

Figure 5.

Figure 5

Insights from all-atom MD simulations with collagen backbone restrained (A and B) and unrestrained (C and D). Three-dimensional scatter plots of S142–S366 distance (represents interdomain dynamics), N171–T230 distance (represents the opening of the MMP1 catalytic pocket), and rms distance between the MMP1 catalytic site and the cleavage sites on three collagen chains for active (blue) and inactive (orange) MMP1. Two-dimensional projections of the scatter plots are in gray. The clusters encircled in red in (A) represent the plausible catalytically relevant conformations. To see this figure in color, go online.