FIGURE 3.

Hydrogen bonds and lipid recruitment upon MLKL binding. (A) Bar plots of the total number of hydrogen bonds between protein and lipids for each replica during the first 500 ns (in blue) versus the last 500 ns (in orange). Close-up of hydrogen bonds between PIP lipids and the 4HB domain at: (B) 200 ns, and (C). 2000 ns. The 4HB domain is shown in blue, PIP lipid headgroup in black, R30 residue in yellow, K25 and K31 in pink, and G01 in red. (D) Cumulative plot of the lateral distribution of PIP lipids as estimated from the location of the lipid phosphate atoms for the last 200 ns. Blue points indicate the phosphate atom positions in the xy-plane, while orange points show representative positions of the atoms of the protein domains in contact (4HB and Brace). Panels (B–D) show analysis for Rep3, the replica of focus as discussed in subsequent sections. Similar plots for the remaining replicas are found in the SM, Supplementary Figure S6. (E) 2D surface charge distribution maps for the binding leaflets of each replica averaged over the last 500 ns of simulation. The cumulative negative charge is shown by the yellow/green regions, clearly localized in regions that correspond to the protein binding sites in each replica. The darker regions correspond to DOPC/DOPE-rich regions, with overall net charge of zero.