Supplementary Figure 3: MD simulation analyses.
From: Copper-transporting P-type ATPases use a unique ion-release pathway
(a), Evolution of the simulation box cell height. (b), The corresponding relative cell area (X,Y) evolution. (c-d), Backbone RMSD measured over the MD trajectory for states E2.Pi and E2P, and E2.Pi mutants P94A and P710A in the full protein (c) and the TM domain (d). (e), Centers of mass in x, y and z dimensions of the intracellular domains during the E2.Pi simulation. (f-g), Residence times for water molecules within 7 Å of Glu189 associated with the release pathway in the E2.Pi (f) and E2P (g) simulations. Two crystal waters remained associated with the internal water pockets within the release pathway for the entire E2P simulation and hence have residency times of 85 ns (not included in (f)). (h-i), Radii analyses. To determine structural variations of the release pathway within the 10 ns average from the MD simulations presented in Fig. 3d, the last 10 ns of the E2P (h) and E2.Pi (i) simulations were divided into 10 equally spaced 100 ps averages and subjected to Caver analyses.
