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

Figure 4. Increased N-terminal domain (NTD) dynamics in Alpha S.

(A) Relative fractional uptake (Dex = 10 min) for Alpha S mapped onto an spike (S) protein structure with three down RBDs (PDB ID: 6VXX) coverage map is shown in Figure 4—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 (Δ RFU) (Dex = 10 min) for Alpha S minus D614G S were mapped onto an 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 the undeuterated mass spectral envelope as a reference, 1 min and 10 min exchange (left to right). For each peptide, the top row contains spectra for D614G S and the bottom row contains spectra for Alpha 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 Alpha S minus D614G 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 4—figure supplement 2). Differences are tabulated in Figure 4—source data 1 with corresponding peptide numbers* shown on the x-axis of the difference plot.

Figure 4—source data 1. Deuterium uptake differences for Alpha S minus D614G S.
Figure 4—source data 2. Source data for the volcano plot; Figure 4, Figure 4—figure supplement 2.
elife-82584-fig4-data2.xlsx (101.2KB, xlsx)

Figure 4.

Figure 4—figure supplement 1. Primary sequence coverage map of pepsin fragment peptides for Alpha S versus D614G S.

Figure 4—figure supplement 1.

Coverage map of Alpha S compared to D614G S using the D614G 2P sequence showing 127 peptides spanning 45.9% of the spike (S) protein. The domain organization of S is indicated.
Figure 4—figure supplement 2. Volcano plot analysis of Alpha S versus D614G S.

Figure 4—figure supplement 2.

Volcano plots for 1 min (A), 2 min (B), 10 min (C), and 30 min (D) exchange (Figure 4—source data 2). Significantly protected (blue) or deprotected (red) peptides were identified using a hybrid significance test and a p-value <0.01.
Figure 4—figure supplement 3. Mass spectral envelopes for overlapping peptides from two stalk loci in Alpha S.

Figure 4—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 Alpha 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 Alpha 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.