PMC:7253482 / 21961-22945 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"715","span":{"begin":25,"end":31},"obj":"Chemical"},{"id":"731","span":{"begin":247,"end":250},"obj":"Gene"},{"id":"732","span":{"begin":258,"end":261},"obj":"Gene"},{"id":"733","span":{"begin":321,"end":324},"obj":"Gene"},{"id":"734","span":{"begin":895,"end":898},"obj":"Gene"},{"id":"735","span":{"begin":252,"end":257},"obj":"Species"},{"id":"736","span":{"begin":281,"end":285},"obj":"Species"},{"id":"737","span":{"begin":271,"end":280},"obj":"Species"},{"id":"738","span":{"begin":74,"end":80},"obj":"Chemical"},{"id":"739","span":{"begin":403,"end":415},"obj":"Chemical"},{"id":"740","span":{"begin":511,"end":527},"obj":"Chemical"},{"id":"741","span":{"begin":566,"end":578},"obj":"Chemical"},{"id":"742","span":{"begin":651,"end":667},"obj":"Chemical"},{"id":"743","span":{"begin":780,"end":786},"obj":"Chemical"},{"id":"744","span":{"begin":226,"end":230},"obj":"Disease"},{"id":"745","span":{"begin":865,"end":872},"obj":"CellLine"}],"attributes":[{"id":"A715","pred":"tao:has_database_id","subj":"715","obj":"MESH:D011134"},{"id":"A731","pred":"tao:has_database_id","subj":"731","obj":"Gene:2995"},{"id":"A732","pred":"tao:has_database_id","subj":"732","obj":"Gene:64006"},{"id":"A733","pred":"tao:has_database_id","subj":"733","obj":"Gene:64006"},{"id":"A734","pred":"tao:has_database_id","subj":"734","obj":"Gene:2995"},{"id":"A735","pred":"tao:has_database_id","subj":"735","obj":"Tax:11676"},{"id":"A736","pred":"tao:has_database_id","subj":"736","obj":"Tax:119210"},{"id":"A737","pred":"tao:has_database_id","subj":"737","obj":"Tax:11320"},{"id":"A738","pred":"tao:has_database_id","subj":"738","obj":"MESH:D011134"},{"id":"A741","pred":"tao:has_database_id","subj":"741","obj":"MESH:D011342"},{"id":"A743","pred":"tao:has_database_id","subj":"743","obj":"MESH:D011134"},{"id":"A744","pred":"tao:has_database_id","subj":"744","obj":"MESH:D018352"},{"id":"A745","pred":"tao:has_database_id","subj":"745","obj":"CVCL:6642"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Fig. 6 Comparison of the glycan shields of viral class I fusion proteins.\nGlycan shield densities were calculated using Proteins, Interfaces, Structures and Assemblies (PISA)83 analyses of fully glycosylated models of SARS S, MERS S, HKU1 S, LASV GPC, HIV-1 Env (BG505), Influenza H3N2 hemagglutinin (Victoria 2011), SIV Env (PDB ID 5X58, 5X59, 5I08, 5VK2, 4ZMJ, 4O5N, 6OHY, respectively)9,11,53,84–86. Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T126","span":{"begin":64,"end":72},"obj":"Body_part"},{"id":"T127","span":{"begin":120,"end":128},"obj":"Body_part"},{"id":"T128","span":{"begin":252,"end":255},"obj":"Body_part"},{"id":"T129","span":{"begin":436,"end":449},"obj":"Body_part"},{"id":"T130","span":{"begin":614,"end":624},"obj":"Body_part"},{"id":"T131","span":{"begin":716,"end":726},"obj":"Body_part"},{"id":"T132","span":{"begin":743,"end":755},"obj":"Body_part"},{"id":"T133","span":{"begin":813,"end":826},"obj":"Body_part"},{"id":"T134","span":{"begin":873,"end":878},"obj":"Body_part"},{"id":"T135","span":{"begin":968,"end":974},"obj":"Body_part"},{"id":"T136","span":{"begin":978,"end":983},"obj":"Body_part"}],"attributes":[{"id":"A126","pred":"fma_id","subj":"T126","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A127","pred":"fma_id","subj":"T127","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A128","pred":"fma_id","subj":"T128","obj":"http://purl.org/sig/ont/fma/fma278683"},{"id":"A129","pred":"fma_id","subj":"T129","obj":"http://purl.org/sig/ont/fma/fma62925"},{"id":"A130","pred":"fma_id","subj":"T130","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A131","pred":"fma_id","subj":"T131","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A132","pred":"fma_id","subj":"T132","obj":"http://purl.org/sig/ont/fma/fma62925"},{"id":"A133","pred":"fma_id","subj":"T133","obj":"http://purl.org/sig/ont/fma/fma62925"},{"id":"A134","pred":"fma_id","subj":"T134","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A135","pred":"fma_id","subj":"T135","obj":"http://purl.org/sig/ont/fma/fma7203"},{"id":"A136","pred":"fma_id","subj":"T136","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"Fig. 6 Comparison of the glycan shields of viral class I fusion proteins.\nGlycan shield densities were calculated using Proteins, Interfaces, Structures and Assemblies (PISA)83 analyses of fully glycosylated models of SARS S, MERS S, HKU1 S, LASV GPC, HIV-1 Env (BG505), Influenza H3N2 hemagglutinin (Victoria 2011), SIV Env (PDB ID 5X58, 5X59, 5I08, 5VK2, 4ZMJ, 4O5N, 6OHY, respectively)9,11,53,84–86. Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T5","span":{"begin":968,"end":974},"obj":"Body_part"}],"attributes":[{"id":"A5","pred":"uberon_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/UBERON_0002113"}],"text":"Fig. 6 Comparison of the glycan shields of viral class I fusion proteins.\nGlycan shield densities were calculated using Proteins, Interfaces, Structures and Assemblies (PISA)83 analyses of fully glycosylated models of SARS S, MERS S, HKU1 S, LASV GPC, HIV-1 Env (BG505), Influenza H3N2 hemagglutinin (Victoria 2011), SIV Env (PDB ID 5X58, 5X59, 5I08, 5VK2, 4ZMJ, 4O5N, 6OHY, respectively)9,11,53,84–86. Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T74","span":{"begin":218,"end":222},"obj":"Disease"},{"id":"T75","span":{"begin":271,"end":280},"obj":"Disease"},{"id":"T76","span":{"begin":317,"end":320},"obj":"Disease"}],"attributes":[{"id":"A74","pred":"mondo_id","subj":"T74","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A75","pred":"mondo_id","subj":"T75","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"},{"id":"A76","pred":"mondo_id","subj":"T76","obj":"http://purl.obolibrary.org/obo/MONDO_0010029"}],"text":"Fig. 6 Comparison of the glycan shields of viral class I fusion proteins.\nGlycan shield densities were calculated using Proteins, Interfaces, Structures and Assemblies (PISA)83 analyses of fully glycosylated models of SARS S, MERS S, HKU1 S, LASV GPC, HIV-1 Env (BG505), Influenza H3N2 hemagglutinin (Victoria 2011), SIV Env (PDB ID 5X58, 5X59, 5I08, 5VK2, 4ZMJ, 4O5N, 6OHY, respectively)9,11,53,84–86. Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T126","span":{"begin":552,"end":560},"obj":"http://purl.obolibrary.org/obo/CLO_0007225"},{"id":"T127","span":{"begin":614,"end":633},"obj":"http://purl.obolibrary.org/obo/CHEBI_33708"},{"id":"T128","span":{"begin":614,"end":633},"obj":"http://purl.obolibrary.org/obo/PR_000036907"},{"id":"T129","span":{"begin":716,"end":735},"obj":"http://purl.obolibrary.org/obo/CHEBI_33708"},{"id":"T130","span":{"begin":716,"end":735},"obj":"http://purl.obolibrary.org/obo/PR_000036907"},{"id":"T131","span":{"begin":759,"end":760},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T132","span":{"begin":873,"end":878},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T133","span":{"begin":923,"end":928},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T134","span":{"begin":968,"end":974},"obj":"http://purl.obolibrary.org/obo/UBERON_0002113"},{"id":"T135","span":{"begin":968,"end":974},"obj":"http://www.ebi.ac.uk/efo/EFO_0000927"},{"id":"T136","span":{"begin":968,"end":974},"obj":"http://www.ebi.ac.uk/efo/EFO_0000929"},{"id":"T137","span":{"begin":978,"end":983},"obj":"http://purl.obolibrary.org/obo/GO_0005623"}],"text":"Fig. 6 Comparison of the glycan shields of viral class I fusion proteins.\nGlycan shield densities were calculated using Proteins, Interfaces, Structures and Assemblies (PISA)83 analyses of fully glycosylated models of SARS S, MERS S, HKU1 S, LASV GPC, HIV-1 Env (BG505), Influenza H3N2 hemagglutinin (Victoria 2011), SIV Env (PDB ID 5X58, 5X59, 5I08, 5VK2, 4ZMJ, 4O5N, 6OHY, respectively)9,11,53,84–86. Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}

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Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T125","span":{"begin":64,"end":72},"obj":"Body_part"},{"id":"T126","span":{"begin":120,"end":128},"obj":"Body_part"},{"id":"T127","span":{"begin":252,"end":255},"obj":"Body_part"},{"id":"T128","span":{"begin":436,"end":449},"obj":"Body_part"},{"id":"T129","span":{"begin":614,"end":624},"obj":"Body_part"},{"id":"T130","span":{"begin":716,"end":726},"obj":"Body_part"},{"id":"T131","span":{"begin":743,"end":755},"obj":"Body_part"},{"id":"T132","span":{"begin":813,"end":826},"obj":"Body_part"},{"id":"T133","span":{"begin":873,"end":878},"obj":"Body_part"},{"id":"T134","span":{"begin":968,"end":974},"obj":"Body_part"},{"id":"T135","span":{"begin":978,"end":983},"obj":"Body_part"}],"attributes":[{"id":"A126","pred":"fma_id","subj":"T126","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A133","pred":"fma_id","subj":"T133","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A135","pred":"fma_id","subj":"T135","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A127","pred":"fma_id","subj":"T127","obj":"http://purl.org/sig/ont/fma/fma278683"},{"id":"A131","pred":"fma_id","subj":"T131","obj":"http://purl.org/sig/ont/fma/fma62925"},{"id":"A130","pred":"fma_id","subj":"T130","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A128","pred":"fma_id","subj":"T128","obj":"http://purl.org/sig/ont/fma/fma62925"},{"id":"A129","pred":"fma_id","subj":"T129","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A125","pred":"fma_id","subj":"T125","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A132","pred":"fma_id","subj":"T132","obj":"http://purl.org/sig/ont/fma/fma62925"},{"id":"A134","pred":"fma_id","subj":"T134","obj":"http://purl.org/sig/ont/fma/fma7203"}],"text":"Fig. 6 Comparison of the glycan shields of viral class I fusion proteins.\nGlycan shield densities were calculated using Proteins, Interfaces, Structures and Assemblies (PISA)83 analyses of fully glycosylated models of SARS S, MERS S, HKU1 S, LASV GPC, HIV-1 Env (BG505), Influenza H3N2 hemagglutinin (Victoria 2011), SIV Env (PDB ID 5X58, 5X59, 5I08, 5VK2, 4ZMJ, 4O5N, 6OHY, respectively)9,11,53,84–86. Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}

{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T154","span":{"begin":64,"end":72},"obj":"Chemical"},{"id":"T155","span":{"begin":74,"end":80},"obj":"Chemical"},{"id":"T156","span":{"begin":436,"end":449},"obj":"Chemical"},{"id":"T157","span":{"begin":520,"end":527},"obj":"Chemical"},{"id":"T158","span":{"begin":614,"end":633},"obj":"Chemical"},{"id":"T159","span":{"begin":660,"end":667},"obj":"Chemical"},{"id":"T160","span":{"begin":716,"end":735},"obj":"Chemical"},{"id":"T161","span":{"begin":743,"end":755},"obj":"Chemical"},{"id":"T162","span":{"begin":813,"end":826},"obj":"Chemical"}],"attributes":[{"id":"A162","pred":"chebi_id","subj":"T162","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"},{"id":"A154","pred":"chebi_id","subj":"T154","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A160","pred":"chebi_id","subj":"T160","obj":"http://purl.obolibrary.org/obo/CHEBI_33708"},{"id":"A155","pred":"chebi_id","subj":"T155","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"},{"id":"A156","pred":"chebi_id","subj":"T156","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"},{"id":"A161","pred":"chebi_id","subj":"T161","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"},{"id":"A158","pred":"chebi_id","subj":"T158","obj":"http://purl.obolibrary.org/obo/CHEBI_33708"},{"id":"A157","pred":"chebi_id","subj":"T157","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"},{"id":"A159","pred":"chebi_id","subj":"T159","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"}],"text":"Fig. 6 Comparison of the glycan shields of viral class I fusion proteins.\nGlycan shield densities were calculated using Proteins, Interfaces, Structures and Assemblies (PISA)83 analyses of fully glycosylated models of SARS S, MERS S, HKU1 S, LASV GPC, HIV-1 Env (BG505), Influenza H3N2 hemagglutinin (Victoria 2011), SIV Env (PDB ID 5X58, 5X59, 5I08, 5VK2, 4ZMJ, 4O5N, 6OHY, respectively)9,11,53,84–86. Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}

{"project":"LitCovid-sample-PD-NCBITaxon","denotations":[{"id":"T153","span":{"begin":218,"end":222},"obj":"Species"},{"id":"T154","span":{"begin":226,"end":230},"obj":"Species"},{"id":"T155","span":{"begin":242,"end":246},"obj":"Species"},{"id":"T156","span":{"begin":252,"end":257},"obj":"Species"},{"id":"T157","span":{"begin":281,"end":285},"obj":"Species"},{"id":"T158","span":{"begin":301,"end":309},"obj":"Species"},{"id":"T159","span":{"begin":317,"end":320},"obj":"Species"},{"id":"T160","span":{"begin":890,"end":894},"obj":"Species"}],"attributes":[{"id":"A155","pred":"ncbi_taxonomy_id","subj":"T155","obj":"NCBItxid:11620"},{"id":"A158","pred":"ncbi_taxonomy_id","subj":"T158","obj":"NCBItxid:4420"},{"id":"A157","pred":"ncbi_taxonomy_id","subj":"T157","obj":"NCBItxid:119210"},{"id":"A159","pred":"ncbi_taxonomy_id","subj":"T159","obj":"NCBItxid:11723"},{"id":"A156","pred":"ncbi_taxonomy_id","subj":"T156","obj":"NCBItxid:11676"},{"id":"A160","pred":"ncbi_taxonomy_id","subj":"T160","obj":"NCBItxid:11620"},{"id":"A153","pred":"ncbi_taxonomy_id","subj":"T153","obj":"NCBItxid:694009"},{"id":"A154","pred":"ncbi_taxonomy_id","subj":"T154","obj":"NCBItxid:1335626"}],"namespaces":[{"prefix":"NCBItxid","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"text":"Fig. 6 Comparison of the glycan shields of viral class I fusion proteins.\nGlycan shield densities were calculated using Proteins, Interfaces, Structures and Assemblies (PISA)83 analyses of fully glycosylated models of SARS S, MERS S, HKU1 S, LASV GPC, HIV-1 Env (BG505), Influenza H3N2 hemagglutinin (Victoria 2011), SIV Env (PDB ID 5X58, 5X59, 5I08, 5VK2, 4ZMJ, 4O5N, 6OHY, respectively)9,11,53,84–86. Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T126","span":{"begin":0,"end":73},"obj":"Sentence"},{"id":"T127","span":{"begin":74,"end":402},"obj":"Sentence"},{"id":"T128","span":{"begin":403,"end":599},"obj":"Sentence"},{"id":"T129","span":{"begin":600,"end":802},"obj":"Sentence"},{"id":"T130","span":{"begin":803,"end":984},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Fig. 6 Comparison of the glycan shields of viral class I fusion proteins.\nGlycan shield densities were calculated using Proteins, Interfaces, Structures and Assemblies (PISA)83 analyses of fully glycosylated models of SARS S, MERS S, HKU1 S, LASV GPC, HIV-1 Env (BG505), Influenza H3N2 hemagglutinin (Victoria 2011), SIV Env (PDB ID 5X58, 5X59, 5I08, 5VK2, 4ZMJ, 4O5N, 6OHY, respectively)9,11,53,84–86. Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}

{"project":"LitCovid-sample-PD-UBERON","denotations":[{"id":"T5","span":{"begin":968,"end":974},"obj":"Body_part"}],"attributes":[{"id":"A5","pred":"uberon_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/UBERON_0002113"}],"text":"Fig. 6 Comparison of the glycan shields of viral class I fusion proteins.\nGlycan shield densities were calculated using Proteins, Interfaces, Structures and Assemblies (PISA)83 analyses of fully glycosylated models of SARS S, MERS S, HKU1 S, LASV GPC, HIV-1 Env (BG505), Influenza H3N2 hemagglutinin (Victoria 2011), SIV Env (PDB ID 5X58, 5X59, 5I08, 5VK2, 4ZMJ, 4O5N, 6OHY, respectively)9,11,53,84–86. Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}

{"project":"LitCovid-sample-PD-MONDO","denotations":[{"id":"T69","span":{"begin":218,"end":222},"obj":"Disease"},{"id":"T70","span":{"begin":271,"end":280},"obj":"Disease"},{"id":"T71","span":{"begin":317,"end":320},"obj":"Disease"}],"attributes":[{"id":"A69","pred":"mondo_id","subj":"T69","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A70","pred":"mondo_id","subj":"T70","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"},{"id":"A71","pred":"mondo_id","subj":"T71","obj":"http://purl.obolibrary.org/obo/MONDO_0010029"}],"text":"Fig. 6 Comparison of the glycan shields of viral class I fusion proteins.\nGlycan shield densities were calculated using Proteins, Interfaces, Structures and Assemblies (PISA)83 analyses of fully glycosylated models of SARS S, MERS S, HKU1 S, LASV GPC, HIV-1 Env (BG505), Influenza H3N2 hemagglutinin (Victoria 2011), SIV Env (PDB ID 5X58, 5X59, 5I08, 5VK2, 4ZMJ, 4O5N, 6OHY, respectively)9,11,53,84–86. Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}

{"project":"LitCovid-sample-Pubtator","denotations":[{"id":"715","span":{"begin":25,"end":31},"obj":"Chemical"},{"id":"744","span":{"begin":226,"end":230},"obj":"Disease"},{"id":"731","span":{"begin":247,"end":250},"obj":"Gene"},{"id":"735","span":{"begin":252,"end":257},"obj":"Species"},{"id":"732","span":{"begin":258,"end":261},"obj":"Gene"},{"id":"737","span":{"begin":271,"end":280},"obj":"Species"},{"id":"736","span":{"begin":281,"end":285},"obj":"Species"},{"id":"733","span":{"begin":321,"end":324},"obj":"Gene"},{"id":"739","span":{"begin":403,"end":415},"obj":"Chemical"},{"id":"740","span":{"begin":511,"end":527},"obj":"Chemical"},{"id":"741","span":{"begin":566,"end":578},"obj":"Chemical"},{"id":"742","span":{"begin":651,"end":667},"obj":"Chemical"},{"id":"743","span":{"begin":780,"end":786},"obj":"Chemical"},{"id":"745","span":{"begin":865,"end":872},"obj":"CellLine"},{"id":"734","span":{"begin":895,"end":898},"obj":"Gene"}],"attributes":[{"id":"A731","pred":"pubann:denotes","subj":"731","obj":"Gene:2995"},{"id":"A715","pred":"pubann:denotes","subj":"715","obj":"MESH:D011134"},{"id":"A736","pred":"pubann:denotes","subj":"736","obj":"Tax:119210"},{"id":"A737","pred":"pubann:denotes","subj":"737","obj":"Tax:11320"},{"id":"A743","pred":"pubann:denotes","subj":"743","obj":"MESH:D011134"},{"id":"A745","pred":"pubann:denotes","subj":"745","obj":"CVCL:6642"},{"id":"A744","pred":"pubann:denotes","subj":"744","obj":"MESH:D018352"},{"id":"A733","pred":"pubann:denotes","subj":"733","obj":"Gene:64006"},{"id":"A741","pred":"pubann:denotes","subj":"741","obj":"MESH:D011342"},{"id":"A734","pred":"pubann:denotes","subj":"734","obj":"Gene:2995"},{"id":"A732","pred":"pubann:denotes","subj":"732","obj":"Gene:64006"},{"id":"A735","pred":"pubann:denotes","subj":"735","obj":"Tax:11676"}],"text":"Fig. 6 Comparison of the glycan shields of viral class I fusion proteins.\nGlycan shield densities were calculated using Proteins, Interfaces, Structures and Assemblies (PISA)83 analyses of fully glycosylated models of SARS S, MERS S, HKU1 S, LASV GPC, HIV-1 Env (BG505), Influenza H3N2 hemagglutinin (Victoria 2011), SIV Env (PDB ID 5X58, 5X59, 5I08, 5VK2, 4ZMJ, 4O5N, 6OHY, respectively)9,11,53,84–86. Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}

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6 Comparison of the glycan shields of viral class I fusion proteins.\nGlycan shield densities were calculated using Proteins, Interfaces, Structures and Assemblies (PISA)83 analyses of fully glycosylated models of SARS S, MERS S, HKU1 S, LASV GPC, HIV-1 Env (BG505), Influenza H3N2 hemagglutinin (Victoria 2011), SIV Env (PDB ID 5X58, 5X59, 5I08, 5VK2, 4ZMJ, 4O5N, 6OHY, respectively)9,11,53,84–86. Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}

{"project":"LitCovid-sample-PD-MAT","denotations":[{"id":"T3","span":{"begin":968,"end":974},"obj":"http://purl.obolibrary.org/obo/MAT_0000119"}],"text":"Fig. 6 Comparison of the glycan shields of viral class I fusion proteins.\nGlycan shield densities were calculated using Proteins, Interfaces, Structures and Assemblies (PISA)83 analyses of fully glycosylated models of SARS S, MERS S, HKU1 S, LASV GPC, HIV-1 Env (BG505), Influenza H3N2 hemagglutinin (Victoria 2011), SIV Env (PDB ID 5X58, 5X59, 5I08, 5VK2, 4ZMJ, 4O5N, 6OHY, respectively)9,11,53,84–86. Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}

{"project":"LitCovid-sample-PD-GO-BP-0","denotations":[{"id":"T44","span":{"begin":493,"end":501},"obj":"http://purl.obolibrary.org/obo/GO_0000224"}],"text":"Fig. 6 Comparison of the glycan shields of viral class I fusion proteins.\nGlycan shield densities were calculated using Proteins, Interfaces, Structures and Assemblies (PISA)83 analyses of fully glycosylated models of SARS S, MERS S, HKU1 S, LASV GPC, HIV-1 Env (BG505), Influenza H3N2 hemagglutinin (Victoria 2011), SIV Env (PDB ID 5X58, 5X59, 5I08, 5VK2, 4ZMJ, 4O5N, 6OHY, respectively)9,11,53,84–86. Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}

{"project":"LitCovid-sentences","denotations":[{"id":"T126","span":{"begin":0,"end":73},"obj":"Sentence"},{"id":"T127","span":{"begin":74,"end":402},"obj":"Sentence"},{"id":"T128","span":{"begin":403,"end":599},"obj":"Sentence"},{"id":"T129","span":{"begin":600,"end":802},"obj":"Sentence"},{"id":"T130","span":{"begin":803,"end":984},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Fig. 6 Comparison of the glycan shields of viral class I fusion proteins.\nGlycan shield densities were calculated using Proteins, Interfaces, Structures and Assemblies (PISA)83 analyses of fully glycosylated models of SARS S, MERS S, HKU1 S, LASV GPC, HIV-1 Env (BG505), Influenza H3N2 hemagglutinin (Victoria 2011), SIV Env (PDB ID 5X58, 5X59, 5I08, 5VK2, 4ZMJ, 4O5N, 6OHY, respectively)9,11,53,84–86. Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}

{"project":"LitCovid-sample-Glycan","denotations":[{"id":"T49","span":{"begin":803,"end":806},"obj":"https://glytoucan.org/Structures/Glycans/G05518TD"}],"text":"Fig. 6 Comparison of the glycan shields of viral class I fusion proteins.\nGlycan shield densities were calculated using Proteins, Interfaces, Structures and Assemblies (PISA)83 analyses of fully glycosylated models of SARS S, MERS S, HKU1 S, LASV GPC, HIV-1 Env (BG505), Influenza H3N2 hemagglutinin (Victoria 2011), SIV Env (PDB ID 5X58, 5X59, 5I08, 5VK2, 4ZMJ, 4O5N, 6OHY, respectively)9,11,53,84–86. Oligomannose abundances of viral glycoproteins were ascertained by HILIC-UPLC analysis of PNGase F released N-linked glycans that were fluorescently labelled with procainamide24,45,53 (SI Fig. 5). The number of amino-acid residues interacting with N-linked glycans was divided by the number of solvent-accessible amino-acid residues of the glycoprotein as a measure for global glycan shield density. All viral glycoproteins analysed were expressed as trimers in HEK293F cells apart from LASV GPC, which was derived from virus-like particles from Madin-Darby canine kidney II cells."}