Fig 5. MD simulations showing the stability of the N-terminal loop of the E protein protomers within a dimer in the E^I6 and E^M6 systems.

The initial (t = 0 ns, top) and final (t = 300 ns, bottom) conformations of the N-terminal loop (residues 1–10) are shown for both protomers (chains A and B) of the (A) E^I6 and (B) E^M6 systems. The protein backbone is shown as ribbons and colored according to the secondary structure. Residue number 6 is shown as sphere (carbon in cyan, nitrogen in blue, oxygen in red and hydrogen in grey). The per-residue secondary structure propensity for the N-terminal loop over simulation time is shown for each chain in the (C) E^I6 and (D) E^M6 systems.