PMC:7443692 / 26947-28586 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7443692","sourcedb":"PMC","sourceid":"7443692","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7443692","text":"The percentage of simulation time that each S protein residue is accessible to a probe that approximates the size of an antibody variable domain was calculated for a model of the S trimer by using the Abundance glycoforms (Table S1) (Ferreira et al., 2018). The predicted antibody accessibility is visualized across the sequence, as well as mapped onto the 3D surface, via color shading (Figures 4A and 4C; Table S13; Video S1). Additionally, the Oxford Class glycoforms model (Table S1), which is arguably the most encompassing means for representing glycan microheterogeneity because it captures abundant structural topologies (Table S8), is shown with the sequence variant information (Figure 4D; Table S11). A substantial number of these variants occur (directly by comparison to Figure 4A or visually by comparison to Figure 4C) in regions of high calculated epitope accessibility (e.g., N74K, T76I, R78M, D138H, H146Y, S151I, D253G, V483A, etc.; Table S14), suggesting potential selective pressure to avoid host immune response. Also, it is interesting to note that three of the emerging variants would eliminate N-linked sequons in S; N74K and T76I would eliminate N-glycosylation of N74 (found in the insert variable region 1 of CoV-2 S compared to CoV-1 S), and S151I eliminates N-glycosylation of N149 (found in the insert variable region 2) (Figures 4A and S7; Table S11). Lastly, the SARS-CoV-2 S Processed glycoform model is shown (Table S1), along with marking amino acid T0323 that has a modest (11% occupancy, Figure S6; Table S10) amount of O-glycosylation to represent the most heavily glycosylated form of S 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