Fig. 2.

Structural comparison of P domain dimers of 2004 and 1996 GII.4 variants. (A) Superposition of the 2004 (orange) and 1996 (cyan) P domain dimer structures. The N and C termini of the dimeric subunits in the 2004 P domain structure are indicated. HBGA binding sites observed for the 1996 variant structure are indicated by arrows. Red and black boxes indicate locations of site 1 and site 2, respectively, in the P domain dimer. A conformational change in the site 2 loop (black box) between the two variants is clearly evident. The alignment of residues in site 1 and site 2 of the 1996 and 2004 GII.4 variants is shown below. (B and C) Side-by-side comparison of the electrostatic potential surfaces of the 2004 and 1996 P domain dimers. (B) Side (above) and top (below) views of the 2004 variant. (C) Side (above) and top (below) views of the 1996 variant. The electrostatic potential variation from negative (red) to positive (blue) is indicated by a bar at the bottom. Significant differences in the electrostatic potential surfaces between the variants are indicated by colored dashed arrows, with each color representing a different region. The temporally varying residues that contribute to these changes are also indicated. For reference, the locations of the HBGA binding sites in the P domain dimer are indicated by black arrows in the side views and by black boxes in the top views. Residues 340 (pink), 393 to 395 (black), and 412 (blue) have all been identified as hot spots for GII.4 epochal evolution.