Figure 4

MD simulation of non-palmitoylated AnkG.

(A) Long-term (1 μs) coarse-grained MD simulation of nonpalmitoylated AnkG (R1-R5). The left panels show representative orientations observed during the simulations. The time course of the proximities of the AnkG to the lipid bilayer is shown in the right panel. The subtotal represents the ratio of trajectories in which “contact” events were observed during the prior 10 ns. (B) Long-term (1 μs) coarse-grained MD simulation of dimeric AnkG. The left panel is a representative initial structure of the system. The right panel represents the time course of the observed protein-membrane association events in 16 trials (same as shown in (A)). (C) Contact probabilities for the interaction between the lipid membrane and each residue. Details of the calculation of contact probabilities are provided in the Methods section. The black and red lines represent the contact probabilities for the AnkG dimer and nonpalmitoylated AnkG simulations, respectively. The perpendicular gray line shows the terminal of the former monomeric subunit. The residue numbers of the nonpalmitoylated AnkG are duplicated corresponding to the two monomeric subunits of the AnkG dimer.