Fig. 6.
Location of sites predicted to differentiate the mild acidic pH-dependence of locked and closed forms. Tube plots of spike protein backbone are shown with colour-coding from d-SASA of 0 Å2 (yellow) to 80 Å2 (red) for open/7a98 [9] (a), closed/6zp1 [31] (b), and locked/6zp2 [31] (c) forms. Within the regions of increased d-SASA in locked relative to closed forms are amino acids with acidic sidechains, shown in a coarse view with magenta tube plot (one of 3 symmetry-related representatives) on a background of spike trimer S1 (grey) and S2 (orange) subunits (d). This region is drawn in greater detail (e) with backbone tube and amino acid stick plots, noting that this one of the 3 representatives consists of regions from all 3 monomers (colour-coded tube). Sites of interest with regard to conformational change and stability within the trimer are also indicated. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)