Fig. 3: Defining epitope sites for antibodies recognizing NTD.

Difference plots for NTD showing changes in deuterium exchange for a LSI-CoVA-017 and b 4A8 antibody complexes with Spike (purified from insect cell culture) compared to apo Spike, at different labelling times as indicated. Pepsin-proteolyzed fragment peptides spanning NTD of the Spike are represented by a dot and their residue numbers are indicated on the x axis. Average values (n = 3 independent experiments each for two biological replicates) and the standard deviations (error bars) are plotted using Microsoft Excel. A significant value of ± 0.5 D was considered as threshold and is indicated by red-dashed line. Epitope sites are highlighted in yellow. Right panels: Differences at 1 min labeling time mapped on to NTD of Spike is shown in cartoon representation. Comparative HDXMS analysis of Spike trimer in the presence and absence of c LSI-CoVA-017 and d 4A8 mapped onto the S1 subunit (left) and trimeric Spike protein (right), as indicated. Peptides spanning key regions are highlighted by arrows with epitopes on NTD (92–110, 136–143, 243–265) indicated by yellow ellipse. Inset highlights a close-up view of Spike trimer along the transverse axis. Differences are mapped onto all the three monomers of Spike. NTD-binding LSI-CoVA-017 reduce overall conformational dynamics (shades of blue). Peptides spanning residues 304–317, fusion peptide (FP), and heptad repeat 1 (HR1) constituting a part of intermonomer interaction interface are indicated. Source data is provided as Source data file.