Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2020 Sep 14;10(1):14991.
doi: 10.1038/s41598-020-71748-7.

Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition

Oliver C Grant  1 , David Montgomery  1 , Keigo Ito  1 , Robert J Woods  2
Affiliations

Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition

Oliver C Grant et al. Sci Rep. .

Abstract

Here we have generated 3D structures of glycoforms of the spike (S) glycoprotein from SARS-CoV-2, based on reported 3D structures and glycomics data for the protein produced in HEK293 cells. We also analyze structures for glycoforms representing those present in the nascent glycoproteins (prior to enzymatic modifications in the Golgi), as well as those that are commonly observed on antigens present in other viruses. These models were subjected to molecular dynamics (MD) simulation to determine the extent to which glycan microheterogeneity impacts the antigenicity of the S glycoprotein. Lastly, we have identified peptides in the S glycoprotein that are likely to be presented in human leukocyte antigen (HLA) complexes, and discuss the role of S protein glycosylation in potentially modulating the innate and adaptive immune response to the SARS-CoV-2 virus or to a related vaccine. The 3D structures show that the protein surface is extensively shielded from antibody recognition by glycans, with the notable exception of the ACE2 receptor binding domain, and also that the degree of shielding is largely insensitive to the specific glycoform. Despite the relatively modest contribution of the glycans to the total molecular weight of the S trimer (17% for the HEK293 glycoform) they shield approximately 40% of the protein surface.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Side and top views of the S glycoprotein trimer with site-specific glycosylation shown as overlaid snapshots (moss surface) from MD simulations. The glycans are shown in ball-and-stick representation: M9 (green), M5 (dark yellow), hybrid (orange), complex (pink) (See Supplementary Table S1 for details). The protein surface is colored according to antibody accessibility from black to red (least to most accessible). The residues comprising the RBD in the “up” or “open” protomer are circled in blue. Images generated using Visual Molecular Dynamics (VMD) version 1.9.3.
Figure 2
Figure 2
Superimpositions of neutralizing antibodies from co-complexes for the SARS, MERS and SARS-CoV-2 S proteins onto the HEK293 S trimer model for SARS-Cov-2. Upper panels, the antibody fragments are shown as pastel transparent surfaces with the mAb name and PDB ID for each co-complex shown in the same color–. Lower panel, the alignments of the RBD sequences of MERS, SARS, and CoV-2 spike proteins with the experimentally derived antibody contact areas shaded from white to green (least to most contact) compared to the predicted AbASA values for the HEK293 glycoform, shaded from white to red (least to most exposed). Glycosites in the SARS-CoV-2 sequence are indicated with an asterisk above the aligned sequences. Images generated using VMD version 1.9.3; antibody contact areas computed with the naccess software using a water-sized probe.
Figure 3
Figure 3
Image of the S309 antibody (cyan) observed in the crystallographic co-complex (PDB ID 6WPS) compared to a single pose from an MD simulation of the S-glycoprotein trimer. While numerous poses of the glycan at N343 were incompatible with antibody binding, there are poses within the MD trajectory that are similar to that found in the crystal structure co-complex with S309 that would permit binding.
Figure 4
Figure 4
Sequence of the S protein (NCBI: YP_009724390.1) used to generate the 3D model of the glycoprotein. Residues 1–26 and 1,147–1,273 were not included in the 3D structure due to a lack of relevant template structures. Sequences within a rectangle were predicted to consist of one or more HLA antigens using the RankPep server (imed.med.ucm.es/Tools/rankpep,). Glycosites are indicated with asterisks, residues reported to interact with the ACE2 receptor are underlined, and the protease cleavage site is indicated with a triangle above the RS junction. (a) The sequence is colored according to antibody accessibility computed for the site-specific glycoform from white to red (least to most accessible). (b) Antibody accessibility computed for the non-glycosylated (nude) protein. (c) The difference in accessibilities between the site-specific and non-glycosylated glycoforms is plotted as the fold change in epitope accessibility during the simulation, from − 4 (blue) to 0 (white), where blue indicates glycosylation-dependent surface shielding.
Figure 5
Figure 5
Antibody accessible surface area estimation using a pair of spherical probes. To estimate the AbASA, a CDR spherical probe was derived (radius 7.2 Å, smaller sphere) that approximates the average size of the hypervariable loops in the CDR from four anti-gp120 antibodies, in which the epitopes were either protein surface residues (PDB IDs: 2B4C, 2NY7, 1G9M) or both carbohydrate and protein residues: (3TYG). Additionally, to account for the presence of the beta-sheet framework in the antibody variable fragment (Fv), we introduced a second larger probe (18.6 Å) sufficient to approximately enclose that domain. Images generated with UCSF Chimera.
See this image and copyright information in PMC

Update of

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. W.H.O. Coronavirus disease 2019 (Covid-19) Situation Report. Report No. 77, (2020).
    1. Depetris RS, et al. Partial enzymatic deglycosylation preserves the structure of cleaved recombinant HIV-1 envelope glycoprotein trimers. J. Biol. Chem. 2012;287:24239–24254. doi: 10.1074/jbc.M112.371898. - DOI - PMC - PubMed
    1. Tate MD, et al. Playing hide and seek: how glycosylation of the influenza virus hemagglutinin can modulate the immune response to infection. Viruses. 2014;6:1294–1316. doi: 10.3390/v6031294. - DOI - PMC - PubMed
    1. Helle F, Duverlie G, Dubuisson J. The hepatitis C virus glycan shield and evasion of the humoral immune response. Viruses. 2011;3:1909–1932. doi: 10.3390/v3101909. - DOI - PMC - PubMed
    1. Marth JD, Grewal PK. Mammalian glycosylation in immunity. Nat. Rev. Immunol. 2008;8:874–887. doi: 10.1038/nri2417. - DOI - PMC - PubMed

Publication types

MeSH terms

LinkOut - more resources