Fig. 9: Weak neutralizers bind to Spike variants at cryptic epitope site.
From: Defining neutralization and allostery by antibodies against COVID-19 variants
Plots comparing differences in deuterium exchange across the S1 subunit of a, b Spikeo2 and c, d Spikeδ complexed to a, c LSI-CoVA-014 and b, d LSI-CoVA-016 versus the apo states are shown at various labelling times. Residue numbers for the peptides are labeled on x axis of the bottom plots of a, b Spikeo2 and c, d Spikeδ, with domain organization shown. Average (n = 3 independent experiments) values with standard deviations (error bars) were used to generate the plots (Microsoft Excel). Yellow zones highlight the peptides spanning the cryptic epitope site, as observed for SpikeWuhan. LSI-CoVA-016 showed larger decreases in deuterium exchange to the two variants. Differences in HDX of Spike variants—e Delta and f Omicron BA.2 in the presence and absence of (left) LSI-CoVA-014 and (right) LSI-CoVA-016 antibody are mapped onto a monomer of delta Spike (PDB: 7W98) and Omicron Spike (PDB: 7WPA), shown in surface representation. The insets show a transverse view of the conformational changes across the trimer. Source data is provided as Source data file.
