PMC:7443692 / 24844-26946 JSONTXT

{"project":"LitCovid-sample-MedDRA","denotations":[{"id":"T12","span":{"begin":721,"end":734},"obj":"http://purl.bioontology.org/ontology/MEDDRA/10022891"}],"attributes":[{"id":"A12","pred":"meddra_id","subj":"T12","obj":"http://purl.bioontology.org/ontology/MEDDRA/10062026"}],"text":"The three glycoform models were subjected to multiple all-atom MD simulations with explicit water. Information from analyses of these structures is presented in Figure 4 A along with the sequence of the SARS-CoV-2 S protomer. We also determined variants in S that are emerging in the virus that have been sequenced to date (Table S11). The inter-residue distances were measured between the most α-carbon-distal atoms of the N-glycan sites and Spike glycoprotein population variant sites in 3D space (Figure 4B). Notable from this analysis, there are several variants that don’t ablate the N-linked sequon but are sufficiently close in 3D space to N-glycosites, such as D138H, H655Y, S939F, and L1203F, to warrant further investigation.\nFigure 4 3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T161","span":{"begin":58,"end":62},"obj":"Chemical"},{"id":"T162","span":{"begin":92,"end":97},"obj":"Chemical"},{"id":"T163","span":{"begin":397,"end":403},"obj":"Chemical"},{"id":"T165","span":{"begin":411,"end":416},"obj":"Chemical"},{"id":"T166","span":{"begin":424,"end":432},"obj":"Chemical"},{"id":"T167","span":{"begin":449,"end":461},"obj":"Chemical"},{"id":"T168","span":{"begin":1249,"end":1259},"obj":"Chemical"},{"id":"T169","span":{"begin":1870,"end":1880},"obj":"Chemical"},{"id":"T170","span":{"begin":2038,"end":2041},"obj":"Chemical"}],"attributes":[{"id":"A170","pred":"chebi_id","subj":"T170","obj":"http://purl.obolibrary.org/obo/CHEBI_16857"},{"id":"A171","pred":"chebi_id","subj":"T170","obj":"http://purl.obolibrary.org/obo/CHEBI_30013"},{"id":"A162","pred":"chebi_id","subj":"T162","obj":"http://purl.obolibrary.org/obo/CHEBI_15377"},{"id":"A165","pred":"chebi_id","subj":"T165","obj":"http://purl.obolibrary.org/obo/CHEBI_33250"},{"id":"A169","pred":"chebi_id","subj":"T169","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A161","pred":"chebi_id","subj":"T161","obj":"http://purl.obolibrary.org/obo/CHEBI_33250"},{"id":"A163","pred":"chebi_id","subj":"T163","obj":"http://purl.obolibrary.org/obo/CHEBI_27594"},{"id":"A164","pred":"chebi_id","subj":"T163","obj":"http://purl.obolibrary.org/obo/CHEBI_33415"},{"id":"A166","pred":"chebi_id","subj":"T166","obj":"http://purl.obolibrary.org/obo/CHEBI_59520"},{"id":"A167","pred":"chebi_id","subj":"T167","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"},{"id":"A168","pred":"chebi_id","subj":"T168","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"}],"text":"The three glycoform models were subjected to multiple all-atom MD simulations with explicit water. Information from analyses of these structures is presented in Figure 4 A along with the sequence of the SARS-CoV-2 S protomer. We also determined variants in S that are emerging in the virus that have been sequenced to date (Table S11). The inter-residue distances were measured between the most α-carbon-distal atoms of the N-glycan sites and Spike glycoprotein population variant sites in 3D space (Figure 4B). Notable from this analysis, there are several variants that don’t ablate the N-linked sequon but are sufficiently close in 3D space to N-glycosites, such as D138H, H655Y, S939F, and L1203F, to warrant further investigation.\nFigure 4 3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

{"project":"LitCovid-sample-PD-NCBITaxon","denotations":[{"id":"T70","span":{"begin":203,"end":213},"obj":"Species"},{"id":"T71","span":{"begin":784,"end":794},"obj":"Species"},{"id":"T72","span":{"begin":1049,"end":1059},"obj":"Species"},{"id":"T73","span":{"begin":1100,"end":1110},"obj":"Species"},{"id":"T74","span":{"begin":1383,"end":1393},"obj":"Species"},{"id":"T75","span":{"begin":1478,"end":1488},"obj":"Species"},{"id":"T76","span":{"begin":1692,"end":1702},"obj":"Species"},{"id":"T77","span":{"begin":1935,"end":1945},"obj":"Species"}],"attributes":[{"id":"A76","pred":"ncbi_taxonomy_id","subj":"T76","obj":"NCBItxid:2697049"},{"id":"A72","pred":"ncbi_taxonomy_id","subj":"T72","obj":"NCBItxid:2697049"},{"id":"A71","pred":"ncbi_taxonomy_id","subj":"T71","obj":"NCBItxid:2697049"},{"id":"A75","pred":"ncbi_taxonomy_id","subj":"T75","obj":"NCBItxid:2697049"},{"id":"A73","pred":"ncbi_taxonomy_id","subj":"T73","obj":"NCBItxid:2697049"},{"id":"A77","pred":"ncbi_taxonomy_id","subj":"T77","obj":"NCBItxid:2697049"},{"id":"A74","pred":"ncbi_taxonomy_id","subj":"T74","obj":"NCBItxid:2697049"},{"id":"A70","pred":"ncbi_taxonomy_id","subj":"T70","obj":"NCBItxid:2697049"}],"namespaces":[{"prefix":"NCBItxid","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"text":"The three glycoform models were subjected to multiple all-atom MD simulations with explicit water. Information from analyses of these structures is presented in Figure 4 A along with the sequence of the SARS-CoV-2 S protomer. We also determined variants in S that are emerging in the virus that have been sequenced to date (Table S11). The inter-residue distances were measured between the most α-carbon-distal atoms of the N-glycan sites and Spike glycoprotein population variant sites in 3D space (Figure 4B). Notable from this analysis, there are several variants that don’t ablate the N-linked sequon but are sufficiently close in 3D space to N-glycosites, such as D138H, H655Y, S939F, and L1203F, to warrant further investigation.\nFigure 4 3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T139","span":{"begin":0,"end":98},"obj":"Sentence"},{"id":"T140","span":{"begin":99,"end":225},"obj":"Sentence"},{"id":"T141","span":{"begin":226,"end":335},"obj":"Sentence"},{"id":"T142","span":{"begin":336,"end":511},"obj":"Sentence"},{"id":"T143","span":{"begin":512,"end":735},"obj":"Sentence"},{"id":"T144","span":{"begin":736,"end":886},"obj":"Sentence"},{"id":"T145","span":{"begin":887,"end":1079},"obj":"Sentence"},{"id":"T146","span":{"begin":1080,"end":1187},"obj":"Sentence"},{"id":"T147","span":{"begin":1188,"end":1269},"obj":"Sentence"},{"id":"T148","span":{"begin":1270,"end":1473},"obj":"Sentence"},{"id":"T149","span":{"begin":1474,"end":1687},"obj":"Sentence"},{"id":"T150","span":{"begin":1688,"end":1804},"obj":"Sentence"},{"id":"T151","span":{"begin":1805,"end":1930},"obj":"Sentence"},{"id":"T152","span":{"begin":1931,"end":2102},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The three glycoform models were subjected to multiple all-atom MD simulations with explicit water. Information from analyses of these structures is presented in Figure 4 A along with the sequence of the SARS-CoV-2 S protomer. We also determined variants in S that are emerging in the virus that have been sequenced to date (Table S11). The inter-residue distances were measured between the most α-carbon-distal atoms of the N-glycan sites and Spike glycoprotein population variant sites in 3D space (Figure 4B). Notable from this analysis, there are several variants that don’t ablate the N-linked sequon but are sufficiently close in 3D space to N-glycosites, such as D138H, H655Y, S939F, and L1203F, to warrant further investigation.\nFigure 4 3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

{"project":"LitCovid-sample-PD-MONDO","denotations":[{"id":"T49","span":{"begin":203,"end":213},"obj":"Disease"},{"id":"T50","span":{"begin":784,"end":794},"obj":"Disease"},{"id":"T51","span":{"begin":1049,"end":1059},"obj":"Disease"},{"id":"T52","span":{"begin":1100,"end":1110},"obj":"Disease"},{"id":"T53","span":{"begin":1383,"end":1393},"obj":"Disease"},{"id":"T54","span":{"begin":1478,"end":1488},"obj":"Disease"},{"id":"T55","span":{"begin":1692,"end":1702},"obj":"Disease"},{"id":"T56","span":{"begin":1935,"end":1945},"obj":"Disease"}],"attributes":[{"id":"A51","pred":"mondo_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A50","pred":"mondo_id","subj":"T50","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A52","pred":"mondo_id","subj":"T52","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A53","pred":"mondo_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A49","pred":"mondo_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A54","pred":"mondo_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A55","pred":"mondo_id","subj":"T55","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A56","pred":"mondo_id","subj":"T56","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"The three glycoform models were subjected to multiple all-atom MD simulations with explicit water. Information from analyses of these structures is presented in Figure 4 A along with the sequence of the SARS-CoV-2 S protomer. We also determined variants in S that are emerging in the virus that have been sequenced to date (Table S11). The inter-residue distances were measured between the most α-carbon-distal atoms of the N-glycan sites and Spike glycoprotein population variant sites in 3D space (Figure 4B). Notable from this analysis, there are several variants that don’t ablate the N-linked sequon but are sufficiently close in 3D space to N-glycosites, such as D138H, H655Y, S939F, and L1203F, to warrant further investigation.\nFigure 4 3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

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1924","pred":"uniprot_id","subj":"T1831","obj":"https://www.uniprot.org/uniprot/P0DTC2"},{"id":"A1925","pred":"uniprot_id","subj":"T1831","obj":"https://www.uniprot.org/uniprot/P07946"},{"id":"A1926","pred":"uniprot_id","subj":"T1831","obj":"https://www.uniprot.org/uniprot/P07923"},{"id":"A1927","pred":"uniprot_id","subj":"T1831","obj":"https://www.uniprot.org/uniprot/P05135"},{"id":"A1928","pred":"uniprot_id","subj":"T1831","obj":"https://www.uniprot.org/uniprot/P05134"},{"id":"A1929","pred":"uniprot_id","subj":"T1831","obj":"https://www.uniprot.org/uniprot/O90304"},{"id":"A1930","pred":"uniprot_id","subj":"T1831","obj":"https://www.uniprot.org/uniprot/O39227"},{"id":"A1931","pred":"uniprot_id","subj":"T1831","obj":"https://www.uniprot.org/uniprot/K9N5Q8"},{"id":"A1932","pred":"uniprot_id","subj":"T1831","obj":"https://www.uniprot.org/uniprot/A3EXG6"},{"id":"A1933","pred":"uniprot_id","subj":"T1831","obj":"https://www.uniprot.org/uniprot/A3EXD0"},{"id":"A1934","pred":"uniprot_id","subj":"T1831","obj":"https://www.uniprot.org/uniprot/A3EX94"}],"text":"The three glycoform models were subjected to multiple all-atom MD simulations with explicit water. Information from analyses of these structures is presented in Figure 4 A along with the sequence of the SARS-CoV-2 S protomer. We also determined variants in S that are emerging in the virus that have been sequenced to date (Table S11). The inter-residue distances were measured between the most α-carbon-distal atoms of the N-glycan sites and Spike glycoprotein population variant sites in 3D space (Figure 4B). Notable from this analysis, there are several variants that don’t ablate the N-linked sequon but are sufficiently close in 3D space to N-glycosites, such as D138H, H655Y, S939F, and L1203F, to warrant further investigation.\nFigure 4 3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

{"project":"LitCovid-sample-PD-IDO","denotations":[{"id":"T80","span":{"begin":284,"end":289},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T81","span":{"begin":433,"end":438},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T82","span":{"begin":481,"end":486},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"},{"id":"T83","span":{"begin":1467,"end":1472},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"}],"text":"The three glycoform models were subjected to multiple all-atom MD simulations with explicit water. Information from analyses of these structures is presented in Figure 4 A along with the sequence of the SARS-CoV-2 S protomer. We also determined variants in S that are emerging in the virus that have been sequenced to date (Table S11). The inter-residue distances were measured between the most α-carbon-distal atoms of the N-glycan sites and Spike glycoprotein population variant sites in 3D space (Figure 4B). Notable from this analysis, there are several variants that don’t ablate the N-linked sequon but are sufficiently close in 3D space to N-glycosites, such as D138H, H655Y, S939F, and L1203F, to warrant further investigation.\nFigure 4 3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T88","span":{"begin":449,"end":461},"obj":"Body_part"},{"id":"T89","span":{"begin":1249,"end":1259},"obj":"Body_part"},{"id":"T90","span":{"begin":1870,"end":1880},"obj":"Body_part"}],"attributes":[{"id":"A88","pred":"fma_id","subj":"T88","obj":"http://purl.org/sig/ont/fma/fma62925"},{"id":"A89","pred":"fma_id","subj":"T89","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A90","pred":"fma_id","subj":"T90","obj":"http://purl.org/sig/ont/fma/fma82739"}],"text":"The three glycoform models were subjected to multiple all-atom MD simulations with explicit water. Information from analyses of these structures is presented in Figure 4 A along with the sequence of the SARS-CoV-2 S protomer. We also determined variants in S that are emerging in the virus that have been sequenced to date (Table S11). The inter-residue distances were measured between the most α-carbon-distal atoms of the N-glycan sites and Spike glycoprotein population variant sites in 3D space (Figure 4B). Notable from this analysis, there are several variants that don’t ablate the N-linked sequon but are sufficiently close in 3D space to N-glycosites, such as D138H, H655Y, S939F, and L1203F, to warrant further investigation.\nFigure 4 3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

{"project":"LitCovid-sample-PD-MAT","denotations":[{"id":"T5","span":{"begin":1410,"end":1419},"obj":"http://purl.obolibrary.org/obo/MAT_0000491"}],"text":"The three glycoform models were subjected to multiple all-atom MD simulations with explicit water. Information from analyses of these structures is presented in Figure 4 A along with the sequence of the SARS-CoV-2 S protomer. We also determined variants in S that are emerging in the virus that have been sequenced to date (Table S11). The inter-residue distances were measured between the most α-carbon-distal atoms of the N-glycan sites and Spike glycoprotein population variant sites in 3D space (Figure 4B). Notable from this analysis, there are several variants that don’t ablate the N-linked sequon but are sufficiently close in 3D space to N-glycosites, such as D138H, H655Y, S939F, and L1203F, to warrant further investigation.\nFigure 4 3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

{"project":"LitCovid-sample-PD-GO-BP-0","denotations":[{"id":"T63","span":{"begin":1453,"end":1466},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T64","span":{"begin":2057,"end":2070},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"The three glycoform models were subjected to multiple all-atom MD simulations with explicit water. Information from analyses of these structures is presented in Figure 4 A along with the sequence of the SARS-CoV-2 S protomer. We also determined variants in S that are emerging in the virus that have been sequenced to date (Table S11). The inter-residue distances were measured between the most α-carbon-distal atoms of the N-glycan sites and Spike glycoprotein population variant sites in 3D space (Figure 4B). Notable from this analysis, there are several variants that don’t ablate the N-linked sequon but are sufficiently close in 3D space to N-glycosites, such as D138H, H655Y, S939F, and L1203F, to warrant further investigation.\nFigure 4 3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

{"project":"LitCovid-sample-GO-BP","denotations":[{"id":"T59","span":{"begin":1453,"end":1466},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T60","span":{"begin":2057,"end":2070},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"The three glycoform models were subjected to multiple all-atom MD simulations with explicit water. Information from analyses of these structures is presented in Figure 4 A along with the sequence of the SARS-CoV-2 S protomer. We also determined variants in S that are emerging in the virus that have been sequenced to date (Table S11). The inter-residue distances were measured between the most α-carbon-distal atoms of the N-glycan sites and Spike glycoprotein population variant sites in 3D space (Figure 4B). Notable from this analysis, there are several variants that don’t ablate the N-linked sequon but are sufficiently close in 3D space to N-glycosites, such as D138H, H655Y, S939F, and L1203F, to warrant further investigation.\nFigure 4 3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}

{"project":"LitCovid-sample-Glycan","denotations":[{"id":"T61","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G69371PB"},{"id":"T62","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G00134PL"},{"id":"T63","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G52865ZM"},{"id":"T64","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G50601AY"},{"id":"T65","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G27898GL"},{"id":"T66","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G90753WM"},{"id":"T67","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G57814GP"},{"id":"T68","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G42918SL"},{"id":"T69","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G81521LC"},{"id":"T70","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G19289PT"},{"id":"T71","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G23779KC"},{"id":"T72","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G94729UX"},{"id":"T73","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G49708JS"},{"id":"T74","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G60349YI"},{"id":"T75","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G63317ON"},{"id":"T76","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G71284FA"},{"id":"T77","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G42091PK"},{"id":"T78","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G39722QK"},{"id":"T79","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G76637LW"},{"id":"T80","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G46130CG"},{"id":"T81","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G05333AM"},{"id":"T82","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G77428YW"},{"id":"T83","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G15142RK"},{"id":"T84","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G06824UZ"},{"id":"T85","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G48723MN"},{"id":"T86","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G35093GE"},{"id":"T87","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G34845TQ"},{"id":"T88","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G71815PL"},{"id":"T89","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G97173UR"},{"id":"T90","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G53453JD"},{"id":"T91","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G81407LL"},{"id":"T92","span":{"begin":2038,"end":2041},"obj":"https://glytoucan.org/Structures/Glycans/G46430YF"}],"text":"The three glycoform models were subjected to multiple all-atom MD simulations with explicit water. Information from analyses of these structures is presented in Figure 4 A along with the sequence of the SARS-CoV-2 S protomer. We also determined variants in S that are emerging in the virus that have been sequenced to date (Table S11). The inter-residue distances were measured between the most α-carbon-distal atoms of the N-glycan sites and Spike glycoprotein population variant sites in 3D space (Figure 4B). Notable from this analysis, there are several variants that don’t ablate the N-linked sequon but are sufficiently close in 3D space to N-glycosites, such as D138H, H655Y, S939F, and L1203F, to warrant further investigation.\nFigure 4 3D Structural Modeling of Glycosylated SARS-CoV-2 Spike Trimer Immunogen Reveals Predictions for Antigen Accessibility and Other Key Features\nResults from glycomics and glycoproteomics experiments were combined with results from bioinformatics analyses and used to model several versions of glycosylated SARS-CoV-2 S trimer immunogen.\n(A) Sequence of the SARS-CoV-2 S immunogen displaying computed antigen accessibility and other information. Antigen accessibility is indicated by red shading across the amino acid sequence.\n(B) Emerging variants confirmed by independent sequencing experiments were analyzed based on the 3D structure of SARS-CoV-2 S to generate a proximity chart to the determined N-linked glycosylation sites.\n(C) SARS-CoV-2 S trimer immunogen model from MD simulation displaying abundance glycoforms and antigen accessibility shaded in red for most accessible, white for partial, and black for inaccessible (see Video S1).\n(D) SARS-CoV-2 S trimer immunogen model from MD simulation displaying Oxford Class glycoforms and sequence variants. Asterisk indicates not visible, whereas the box represents three amino acid variants that are clustered together in 3D space.\n(E) SARS-CoV-2 S trimer immunogen model from MD simulation displaying processed glycoforms plus shading of Thr-323 that has O-glycosylation at low stoichiometry in yellow."}