Figure 4
Monitoring of local secondary structure and contacts between NEU1/TM2 peptides.
(A) Average secondary structure and standard deviations were computed for the twenty-four independent simulations performed in DPPC. (B) Time evolution of the secondary structure corresponding to the simulation with a starting conformation angle equal to 30 degrees. Green indicates residues in a turn structure, pink in an α-helix structure and white in a coil structure. The nature of the peptides is indicated on the y-axis (P1 or P2). (C) Contact map obtained over the last 10 ns of the trajectory corresponding to a starting conformation angle of 30 degrees. For each pair of residues, the average smallest atomic distance was computed over the last 1000 snapshots of the trajectory. The contacts displayed in the central square correspond to contacts within the membrane. (D) Snapshot extracted from a simulation highlighting the presence of a H-bond between two serine residues (S326-S327). (E) Key-residues (bold letters) involved in contacts between the two helices according to the analysis of the twenty-four contact maps.
