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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| Veröffentlicht in: | Scientific reports 2020-09, Vol.10 (1), p.14991, Article 14991 |
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| description | 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. |
| doi_str_mv | 10.1038/s41598-020-71748-7 |
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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.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/s41598-020-71748-7</identifier><identifier>PMID: 32929138</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>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</subject><ispartof>Scientific reports, 2020-09, Vol.10 (1), p.14991, Article 14991</ispartof><rights>The Author(s) 2020</rights><rights>The Author(s) 2020. 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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.</description><subject>631/114/2411</subject><subject>631/250</subject><subject>ACE2</subject><subject>Adaptive Immunity</subject><subject>Amino Acid Sequence</subject><subject>Angiotensin-Converting Enzyme 2</subject><subject>Antibodies, Neutralizing - immunology</subject><subject>Antigen-Antibody Complex</subject><subject>Betacoronavirus - immunology</subject><subject>Betacoronavirus - isolation & purification</subject><subject>Betacoronavirus - metabolism</subject><subject>Binding Sites</subject><subject>Cadmium</subject><subject>Coronavirus Infections - immunology</subject><subject>Coronavirus Infections - pathology</subject><subject>Coronavirus Infections - virology</subject><subject>COVID-19</subject><subject>Fourier analysis</subject><subject>Glycoproteins</subject><subject>Glycosylation</subject><subject>HEK293 Cells</subject><subject>HLA Antigens - 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genetics</subject><subject>Spike Glycoprotein, Coronavirus - immunology</subject><subject>Spike Glycoprotein, Coronavirus - metabolism</subject><subject>Transmission electron microscopy</subject><subject>X-ray diffraction</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNp9kV9vFCEUxYnR2Kb2C_hgSHzxZSp_B3gx2WyqNWliYtVXwrB3dqkzMMJMk_32sm6t1Qd5gdzzu-cCB6GXlFxQwvXbIqg0uiGMNIoqoRv1BJ0yImTDOGNPH51P0Hkpt6QuyYyg5jk64cwwQ7k-Rd0qumFfQsGpx_MO8M3q802zTt8ahssUvgOecpohRLwd9t5FXHYBhg3OcAduKDiM0xC8m0OKBfcp18K4RKi6T9sYDvUX6FlfUTi_38_Q1_eXX9ZXzfWnDx_Xq-vGS6XmRmptBKPOtx3lxBECysmOesZaTrQgrRJEtX1VnXYMQPUagMjOb7jshTH8DL07-k5LN8LGQ5yzG-yUw-jy3iYX7N9KDDu7TXdWCUO4aavBm3uDnH4sUGY7huJhGFyEtBTLhGBaaEUP6Ot_0Nu05PqVlSKMC8k1kZViR8rnVEqG_uEylNhDivaYoq0p2l8pWlWbXj1-xkPL78wqwI9AqVLcQv4z-z-2PwGD5qf6</recordid><startdate>20200914</startdate><enddate>20200914</enddate><creator>Grant, Oliver C.</creator><creator>Montgomery, David</creator><creator>Ito, Keigo</creator><creator>Woods, Robert J.</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20200914</creationdate><title>Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition</title><author>Grant, Oliver C. ; Montgomery, David ; Ito, Keigo ; Woods, Robert J.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c577t-5889421ac6b130a00e7a5b1c22630840674076f6b1a8a2ee7f8ee05bcd35f4993</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>631/114/2411</topic><topic>631/250</topic><topic>ACE2</topic><topic>Adaptive Immunity</topic><topic>Amino Acid Sequence</topic><topic>Angiotensin-Converting Enzyme 2</topic><topic>Antibodies, Neutralizing - immunology</topic><topic>Antigen-Antibody Complex</topic><topic>Betacoronavirus - immunology</topic><topic>Betacoronavirus - isolation & purification</topic><topic>Betacoronavirus - metabolism</topic><topic>Binding Sites</topic><topic>Cadmium</topic><topic>Coronavirus Infections - immunology</topic><topic>Coronavirus Infections - pathology</topic><topic>Coronavirus Infections - virology</topic><topic>COVID-19</topic><topic>Fourier analysis</topic><topic>Glycoproteins</topic><topic>Glycosylation</topic><topic>HEK293 Cells</topic><topic>HLA Antigens - metabolism</topic><topic>Humanities and Social Sciences</topic><topic>Humans</topic><topic>Immune response</topic><topic>Immunity, Innate</topic><topic>Molecular Dynamics Simulation</topic><topic>multidisciplinary</topic><topic>Nanotechnology</topic><topic>Pandemics</topic><topic>Peptides</topic><topic>Peptidyl-Dipeptidase A - chemistry</topic><topic>Peptidyl-Dipeptidase A - metabolism</topic><topic>Physicochemical properties</topic><topic>Pneumonia, Viral - immunology</topic><topic>Pneumonia, Viral - pathology</topic><topic>Pneumonia, Viral - virology</topic><topic>Polysaccharides - chemistry</topic><topic>Protein Binding</topic><topic>Protein Structure, Tertiary</topic><topic>SARS-CoV-2</topic><topic>Scanning electron microscopy</topic><topic>Science</topic><topic>Science (multidisciplinary)</topic><topic>Sensors</topic><topic>Sequence Alignment</topic><topic>Severe acute respiratory syndrome coronavirus 2</topic><topic>Spike Glycoprotein, Coronavirus - genetics</topic><topic>Spike Glycoprotein, Coronavirus - immunology</topic><topic>Spike Glycoprotein, Coronavirus - metabolism</topic><topic>Transmission electron microscopy</topic><topic>X-ray diffraction</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Grant, Oliver C.</creatorcontrib><creatorcontrib>Montgomery, David</creatorcontrib><creatorcontrib>Ito, Keigo</creatorcontrib><creatorcontrib>Woods, Robert J.</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Grant, Oliver C.</au><au>Montgomery, David</au><au>Ito, Keigo</au><au>Woods, Robert J.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2020-09-14</date><risdate>2020</risdate><volume>10</volume><issue>1</issue><spage>14991</spage><pages>14991-</pages><artnum>14991</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><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.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>32929138</pmid><doi>10.1038/s41598-020-71748-7</doi><oa>free_for_read</oa></addata></record> |
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| subjects | 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 |
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