Figure 9.

Spatial Disposition of Membrane Proteins

(A) Comparison of interprotein distance histograms in final snapshots of simulations (excluding the M2 proton channel). The centroids of each protein were employed and the closest five neighboring proteins were included for 460 distances.

(B) Assessment of influenza A spike glycoprotein fractional surface volume in final snapshots of production simulations. The phosphate particles in each virion (red) were used to define the inner boundary of the outer surface layer (contained within a diffuse meshgrid), while the outer boundary was assigned 13 nm farther from the virion centroid (contained within outermost diffuse meshgrid). The coordinates of particles representing the convex hulls of the spike glycoproteins are shown for HA (green) and NA (purple). The percentage of the outer surface layer volume (V_f) occupied by the spike glycoproteins is indicated above each condition. See also Figures S11–S15 and S19.