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

Figure 5. Increased stability at trimer stalk and decreased N-terminal domain (NTD) dynamics in Delta S.

(A) Relative fractional uptake (Dex = 10 min) for Delta S mapped onto a wild-type (WT) spike (S) protein structure with three down receptor-binding domain s (RBDs) (PDB ID: 6VXX) coverage maps shown in Figure 5—figure supplement 1). Deuterium exchange heat map (gradient of white (0%) -red (70%) as mapped on S structure (PDB ID: 6VXX). (B) Differences in deuterium exchange (ΔRFU) (Dex = 10 min) for Delta S minus Alpha 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 positive differences 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 Alpha S and the bottom row contains spectra for Delta 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 Delta S minus Alpha 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 5—figure supplement 2). Differences are tabulated in Figure 5—source data 1 with corresponding peptide numbers* shown on the x-axis of the difference plot.

Figure 5—source data 1. Deuterium uptake differences for Delta S minus Alpha S.
Figure 5—source data 2. Source data for the volcano plot; Figure 5, Figure 5—figure supplement 2.
elife-82584-fig5-data2.xlsx (100.4KB, xlsx)

Figure 5.

Figure 5—figure supplement 1. Primary sequence coverage map of pepsin fragment peptides for Delta S versus Alpha S.

Figure 5—figure supplement 1.

Coverage map of Delta S compared to Alpha S using the D614G 2P sequence showing 123 peptides spanning 47.0% of the spike (S) protein. The domain organization of S is indicated.
Figure 5—figure supplement 2. Volcano plot analysis of Delta variant S versus Alpha variant S.

Figure 5—figure supplement 2.

Volcano plots for 1 min (A), 2 min (B), 10 min (C), and 30 min (D) exchange (Figure 5—source data 2). Significantly protected (blue) or deprotected (red) peptides were identified using a hybrid significance test and a p-value <0.01.
Figure 5—figure supplement 3. Mass spectra from overlapping peptides from two stalk loci in Delta S.

Figure 5—figure supplement 3.

(A) Peptide locus 899–913 (blue) mapped onto the wild-type (WT) spike (S) protein 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 Delta 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 Delta 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.