Figure 6.

Lipid contacts elucidated from MD simulations of Fab-ctMPER-TMD complexes inserted into VL bilayers. Representative snapshots of the Fabs with a chemical modification engineered to contain a single Cys residue at position 65 within the Fab’s FRL3 to which (A) Fus4 and (B) Lin3 were attached in the presence of the MPER-TMD inserted in the viral-like membrane. The protein is shown in cyan using a cartoon representation, and the point mutations are displayed as van der Waals spheres within the snapshot. Cys-Fus4 and Cys-Lin3 are also depicted separately in the licorice representation. A zoomed-in view highlights some of the lipid–protein interactions observed, which are established with Cys-Fus4 and Cys-Lin3 represented in van der Waals in cyan. The right panels show the evolution with simulation time of the number of contacts between each lipid component of the viral-like membrane and each single mutated residue in the antibody, either Cys-Fus4 or Cys-Lin3. A contact is considered when the distance between any heavy atom of the mutated residue and any heavy atom of a lipid residue is ≤3.5 Å.