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. 2023 Mar 17;12:e82584. doi: 10.7554/eLife.82584

Figure 6. Enhanced trimer stability and N-terminal domain (NTD) dynamics in Omicron BA.1 S.

(A) Relative fractional uptake (Dex = 10 min) for Omicron BA.1 S mapped onto a wild-type (WT) spike (S) structure with three down receptor-binding domains (RBDs) (PDB ID: 6VXX) coverage maps shown in Figure 6—figure supplement 1). Deuterium exchange heat map (gradient of white (0%) -red (70%) as mapped on WT S structure (PDB ID: 6VXX). (B) Differences in deuterium exchange (ΔRFU) (Dex = 10 min) for Omicron BA.1 S minus Delta S were mapped onto a WT S structure (PDB ID: 6VXX). Shades of blue correspond to negative differences in deuterium exchange and shades of red correspond to a positive difference in deuterium exchange. (C–E) Stacked mass spectra for peptides 92–103, 177–191, and 900–913 with undeuterated reference spectra, 1 min, and 10 min exchange (left to right). For each peptide, the top row contains spectra for Delta S and the bottom row contains spectra for Omicron BA.1 S. Absolute intensities are indicated at the top right of each spectrum. (F) Differences in deuterium exchange (deuterons) mapped at peptide resolution from N to C terminus for Omicron BA.1 S minus Delta S are shown in difference plots for 1-, 2-, 10-, and 30 min exchange. Select peptides showing significant differences in exchange are annotated. Significance was determined by hybrid significance testing (p<0.01, Figure 6—figure supplement 2). Differences are tabulated in Figure 6—source data 1 with corresponding peptide numbers* shown on the x-axis of the difference plot.

Figure 6—source data 1. Deuterium uptake differences for Omicron BA.1 S minus Delta S.
Figure 6—source data 2. Source data for the volcano plot; Figure 6, Figure 6—figure supplement 2.

Figure 6.

Figure 6—figure supplement 1. Primary sequence coverage map of pepsin fragment peptides for Omicron S versus Delta S.

Figure 6—figure supplement 1.

Coverage map of Omicron S compared to Delta S using the D614G 2P sequence showing 95 peptides spanning 36.4% of the spike (S) protein. The domain organization of S is indicated.
Figure 6—figure supplement 2. Volcano plot analysis of Omicron variant S versus Delta variant S.

Figure 6—figure supplement 2.

Volcano plots for 1 min (A), 2 min (B), 10 min (C), and 30 min (D) exchange (Figure 6—source data 2). Significantly protected (blue) or deprotected (red) peptides were identified using a hybrid significance test and a p-value <0.01.
Figure 6—figure supplement 3. Mass spectral envelopes from overlapping peptides from two stalk loci in Omicron S.

Figure 6—figure supplement 3.

(A) Peptide locus 899–913 (blue) mapped onto the wild-type (WT) spike (S) structure (PDB ID: 7TGX). (B) Peptide locus 988–998 (orange) mapped onto WT S structure (PDB ID: 7TGX). (C) Spectra from three overlapping peptides in the 899–913 locus of Omicron BA.1 S. Reference state as well as spectra for 1 and 10 min exchange are shown from top to bottom for each peptide. (D) Spectra from three overlapping peptides in the 988–998 locus of Omicron BA.1 S. Reference state as well as spectra for 1 and 10 min exchange are shown from top to bottom for each peptide. Absolute intensities are indicated at the top right of each spectrum.