Figure 3

MD simulation of palmitoylated AnkG.

(A) Long-term (1 μs) coarse-grained MD simulation of a palmitoylated AnkG (R1-R5)-membrane system. Representative initial (left) and final (right) orientations of AnkG are shown. (B) The time course of proximities between AnkG and the lipid membrane was analyzed as two kinds of events: “contact” and “contact after insertion; inserted.” (The definition of “contact” and “insertion” are provided in the Methods section.) For “contact,” cumulative and subtotals of the membrane contacts were analyzed for all 100 trials (blue lines), where subtotal is the ratio of trajectories in which the “contact” events were observed during the prior 10 ns. For “inserted,” the ratios of “contact” trajectories undergoing “insertion” events were analyzed for the 72 trajectories in which insertion was observed (red lines). The cumulative and subtotal curves overlap (red lines). (C) Contact probability for the interaction between the lipid membrane and each residue. Details of the calculation of contact probability are provided in the Methods section. The black and red lines represent the respective contact probabilities calculated for the snapshots after and before the “insertion” event.