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

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 e...

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Vydáno v:	Scientific reports Ročník 10; číslo 1; s. 14991
Hlavní autoři:	Grant, Oliver C., Montgomery, David, Ito, Keigo, Woods, Robert J.
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	London Nature Publishing Group UK 14.09.2020 Nature Publishing Group
Témata:	631/114/2411 631/250 ACE2 Adaptive Immunity Amino Acid Sequence Angiotensin-Converting Enzyme 2 Antibodies, Neutralizing - immunology Antigen-Antibody Complex Betacoronavirus - immunology Betacoronavirus - isolation & purification Betacoronavirus - metabolism Binding Sites Cadmium Coronavirus Infections - immunology Coronavirus Infections - pathology Coronavirus Infections - virology COVID-19 Fourier analysis Glycoproteins Glycosylation HEK293 Cells HLA Antigens - metabolism Humanities and Social Sciences Humans Immune response Immunity, Innate Molecular Dynamics Simulation multidisciplinary Nanotechnology Pandemics Peptides Peptidyl-Dipeptidase A - chemistry Peptidyl-Dipeptidase A - metabolism Physicochemical properties Pneumonia, Viral - immunology Pneumonia, Viral - pathology Pneumonia, Viral - virology Polysaccharides - chemistry Protein Binding Protein Structure, Tertiary SARS-CoV-2 Scanning electron microscopy Science Science (multidisciplinary) Sensors Sequence Alignment Severe acute respiratory syndrome coronavirus 2 Spike Glycoprotein, Coronavirus - genetics Spike Glycoprotein, Coronavirus - immunology Spike Glycoprotein, Coronavirus - metabolism Transmission electron microscopy X-ray diffraction
ISSN:	2045-2322, 2045-2322
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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.
AbstractList	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. 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.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.
ArticleNumber	14991
Author	Grant, Oliver C. Ito, Keigo Montgomery, David Woods, Robert J.
Author_xml	– sequence: 1 givenname: Oliver C. surname: Grant fullname: Grant, Oliver C. organization: Complex Carbohydrate Research Center, University of Georgia – sequence: 2 givenname: David surname: Montgomery fullname: Montgomery, David organization: Complex Carbohydrate Research Center, University of Georgia – sequence: 3 givenname: Keigo surname: Ito fullname: Ito, Keigo organization: Complex Carbohydrate Research Center, University of Georgia – sequence: 4 givenname: Robert J. surname: Woods fullname: Woods, Robert J. email: rwoods@ccrc.uga.edu organization: Complex Carbohydrate Research Center, University of Georgia
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/32929138$$D View this record in MEDLINE/PubMed
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Snippet	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...
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SubjectTerms	631/114/2411 631/250 ACE2 Adaptive Immunity Amino Acid Sequence Angiotensin-Converting Enzyme 2 Antibodies, Neutralizing - immunology Antigen-Antibody Complex Betacoronavirus - immunology Betacoronavirus - isolation & purification Betacoronavirus - metabolism Binding Sites Cadmium Coronavirus Infections - immunology Coronavirus Infections - pathology Coronavirus Infections - virology COVID-19 Fourier analysis Glycoproteins Glycosylation HEK293 Cells HLA Antigens - metabolism Humanities and Social Sciences Humans Immune response Immunity, Innate Molecular Dynamics Simulation multidisciplinary Nanotechnology Pandemics Peptides Peptidyl-Dipeptidase A - chemistry Peptidyl-Dipeptidase A - metabolism Physicochemical properties Pneumonia, Viral - immunology Pneumonia, Viral - pathology Pneumonia, Viral - virology Polysaccharides - chemistry Protein Binding Protein Structure, Tertiary SARS-CoV-2 Scanning electron microscopy Science Science (multidisciplinary) Sensors Sequence Alignment Severe acute respiratory syndrome coronavirus 2 Spike Glycoprotein, Coronavirus - genetics Spike Glycoprotein, Coronavirus - immunology Spike Glycoprotein, Coronavirus - metabolism Transmission electron microscopy X-ray diffraction
Title	Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition
URI	https://link.springer.com/article/10.1038/s41598-020-71748-7 https://www.ncbi.nlm.nih.gov/pubmed/32929138 https://www.proquest.com/docview/2023453805 https://www.proquest.com/docview/2442848716 https://pubmed.ncbi.nlm.nih.gov/PMC7490396
Volume	10
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