PMC

Association rates (log-scale) of SIA to the NA active site, NA secondary site, and HA.

An illustration of the atomic-resolution viral-surface models, shown with reduced resolution to illustrate differences in the NA stalk heights. 09H1 and H5 are colored in blue and green, respectively. 09N1 and avian N1 are colored in white and yellow, respectively. (A) The wild-type H1N1 virus (long-stalk NA). (B) The H5N1 virus with a short-stalk H1N1 NA. (C) The reassortant H5N1 virus studied by Imai et al. (D) The reassortant H1N1 virus studied by Blumenkrantz et al.

Virion reconstruction. (A) The asymmetrical virus membrane represented as points (from the tomographic data). (B) The proteins within the tomographic map are represented as vectors. (C) HAs are positioned according to their vectors. (D) NAs are similarly positioned. (E) The lipid envelope is constructed through surface meshing via tessellation. (F) The M2 ion channels are inserted randomly into the membrane construct. (G) All-atom lipid molecules are added to the individual triangles that represent the membrane. (H) The full influenza viral surface.

(A, B) H1N1 and H5N1, respectively, plotted by surface protein type and location. Hemagglutinins (circles) and neuraminidases (triangles) are colored by their absolute curvature. Curvature is calculated from fitting a sphere to the surrounding neighborhood of proteins within a 440 Å radius. (C, D) Distributions of curvature values associated with hemagglutinins (top, royal blue) and neuraminidases (bottom, sky blue). H5N1 shows a more significant shift to lower curvatures (flatter surfaces) for neuraminidase compared to the total protein shell than those of H1N1.

An atomic-resolution virtual model of the viral envelope derived from integrative modeling. (A) The whole viral envelope is shown, with HAs in blue, NAs in white, and membrane in pink. Glowing green points on glycoproteins indicate SIA binding sites. SIA is shown diffusing from the b-surface (starting coordinate) toward the virus or escaping to the q-surface. If SIA escapes, the simulation ends. (B) Close-up of HA (blue) and NA (white), in more detail. SIA binding sites are shown with glowing red and blue points. (C) The encounter-complex definitions of SIA (shown in sticks, illustrated with polar hydrogens) bound to the NA-secondary (blue shading on white surface) and NA-active (red shading on white surface) sites. Atom–atom interactions between the glycoprotein and SIA are visible. (D) The encounter-complex definition of SIA bound to the HA receptor binding domain (blue).