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. 2021 Feb 18;120(6):983–993. doi: 10.1016/j.bpj.2021.01.037

Figure 4.

Figure 4

Accessible surface area (ASA) of Y674-R685 region in the context of the fully glycosylated full-length SARS-CoV-2 spike. (A) Shown is a snapshot taken from the simulations by Casalino et al. (31) of the glycosylated full-length SARS-CoV-2 spike in the closed state showing Y674-R685 loop protruding into the solvent. The protein is depicted with a gray surface, whereas 674–685 loop is shown as a cyan ribbon. The glycans are illustrated with blue sticks. (B–C) The ASA of the of residues 674–685 (corresponding to the S-peptide) and the area shielded by glycans at multiple probe radii from 1.4 Å (water molecule) to 15 Å are calculated using the available MD trajectories of the full-length models of the glycosylated SARS-CoV-2 spike protein in the closed (B) and open states (C) from Casalino et al. (31). The area of 674–685 shielded by the glycans is presented in blue, whereas the gray line represents the accessible area of 674–685 in the absence of glycans. Highlighted in cyan is the area of 674–685 that remains accessible in the presence of glycans. The calculated values have been averaged across the three chains and across the different replicas performed for each system by Casalino et al. (31). Error bars correspond to ± SD. To see this figure in color, go online.