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The Structural Dynamics of the Flavivirus Fusion Peptide–Membrane Interaction

Figure 3

Molecular dynamics studies of the POPE membrane environment.

(A) The RMSD of FLAG (black) and FLAH (red). (B) The distance between the peptide and membrane was determined as follows: the distance between the center of mass of the peptide and the membrane in the axis perpendicular to the membrane surface plane for both FLAG (black) and FLAH (red); and the minimal distance between Gly104 (green) or His104 (blue) atoms and the phosphorus atoms of the lipids. (C and D) The number of intramolecular hydrogen bonds (black) and those formed between the fusion peptides FLAG (C) or FLAH (D) and the water (green) or the POPE membrane (red). (E and F) The minimal distance between the Trp101 residue and the POPE membrane (red) and between the Phe108 residue and the POPE membrane (black) during MD simulation in the presence of the POPE membrane at 35°C. The intermolecular distance between Trp101 and Phe108 is also presented (green). The results for MD simulation of FLAG and FLAH are shown in E and F, respectively.

Figure 3