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LitCovid_Glycan-Motif-Structure

LitCovid-PMC-OGER-BB

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T6","span":{"begin":565,"end":580},"obj":"Body_part"},{"id":"T7","span":{"begin":3177,"end":3181},"obj":"Body_part"},{"id":"T8","span":{"begin":3442,"end":3448},"obj":"Body_part"},{"id":"T9","span":{"begin":3453,"end":3458},"obj":"Body_part"},{"id":"T10","span":{"begin":3704,"end":3714},"obj":"Body_part"}],"attributes":[{"id":"A6","pred":"uberon_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/UBERON_4200047"},{"id":"A7","pred":"uberon_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A8","pred":"uberon_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/UBERON_0001836"},{"id":"A9","pred":"uberon_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/UBERON_0000912"},{"id":"A10","pred":"uberon_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/UBERON_2000106"}],"text":"1.3 The great diversity of sialic acid glycans\nThe seeming challenge for research into non-covalent binding to glycans is that they are diverse molecules, and that remains true even among the sialic acid glycans. At first consideration, this would seem to suggest that the prediction of glycan binding sites will be difficult. Critical features that distinguish glycans of interest in the present paper are the terminal sugar residues on the oligosaccharide chains at the distal ends (i.e. the “tips”), where sialic acids are important, and the amino acid residue attachment site (N- or. O-) to the membrane protein at the base. The N (nitrogen) protein attachment point attachment is asparagine and the O (oxygen) protein attachment point is usually serine or threonine, but sometimes tyrosine, or occasionally other amino acids which are hydoxylated as a post-translational modification. Covalent connections of that kind are those to the host cell surface proteins but, as indicated above, it is the non-covalent binding of a virus to them that is of interest here. Covalent binding is controlled by host enzymes and so would appear, again at first consideration, to be more specific. Enveloped viruses such as SARS-CoV-2 also have their own bound sialic acid glycans (the spike protein is usually referred to as the spike glycoprotein), but these are of less direct interest here although they can clearly influence binding of a virus to various receptors.\nDespite their diversity, and perhaps because of it (i.e. because that diversity implies more information content) sialic acid glycans of host cells are key molecular recognition features not only for entry of viruses such as influenza, but also in embryonic development, neurodevelopment, reprogramming, and oncogenesis. Correctly speaking, even sialic acid itself is diverse. It is a generic term for a family of derivatives of the nine-carbon sugar neuraminic acid. The sialic acid family includes some 43 derivatives of neuraminic acid, but these acids rarely appear free in nature. Members include N-acetylneuraminic acid, 2-keto-3-deoxy-d-glycero-d-galacto-nonulosonic acid, 5,7-diamino-3,5,7,9-tetra-deoxy-d-glycero-d-galacto- nonulosonic acid, and 5,7-diamino-3,5,7,9-tetra-deoxy-l-glycero-l-manno-nonulosonic acid. If the term “sialic acid” is used unqualified, it usually refers to the representative member of this group, N-acetylneuraminic acid. The variability of glycans is not random but reflects their modes of synthesis. In eukaryotes generally, a typical N-linked glycan has an initial core that consists of 14 residues (3 glucose, 9 mannose, and 2 N-acetylglucosamine). This preassembled glycan is usually transferred by a glycosyltransferase oligosaccharyltransferase to a nascent peptide chain within the reticular lumen. This initial core 14-sugar unit is assembled in the cytoplasm and endoplasmic reticulum and other sugars may be added later. In contrast, O-linked glycans are assembled one sugar at a time at the outset on proteins in the Golgi apparatus.\nThere are some specific features of medical interest as relevant to the human host of viruses (but by no means unique to humans). The lung epithelial glycans are typical by having sialic acids as the distal residues, and it is these that the influenza neuraminidase cleaves away. Most soluble secreted proteins are also similarly decorated with such glycans. That includes the proteins that make up saliva and mucus in the airway, and are in general important for viral infection. Both N- and O- and glycosphingolipid-glycans are found in human lungs, and they include large and complex-type N-glycans with linear poly-N-acetyllactosamine [-3Galβ1–4GlcNAcβ1-]n extensions, which are predominantly terminated in α2,3-linked sialic acid. In contrast, the smaller N-glycans lack poly-N-acetyllactosamine but are enriched in α2,6-linked sialic acids. There are also large glycosphingolipid glycans, which also consists of poly-N-acetyllactosamine, usually terminating in α2,3-linked sialic acid. While it is commonly maintained that viruses such as influenza virus bind to the sialylated glycans, and this is assumed in the present paper, some care is required, because there are also non-sialylated glycans in human lungs on which viral binding could occur."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T28","span":{"begin":1215,"end":1223},"obj":"Disease"},{"id":"T29","span":{"begin":1687,"end":1696},"obj":"Disease"},{"id":"T30","span":{"begin":3285,"end":3294},"obj":"Disease"},{"id":"T31","span":{"begin":3507,"end":3522},"obj":"Disease"},{"id":"T32","span":{"begin":3513,"end":3522},"obj":"Disease"},{"id":"T33","span":{"begin":4088,"end":4097},"obj":"Disease"}],"attributes":[{"id":"A28","pred":"mondo_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A29","pred":"mondo_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"},{"id":"A30","pred":"mondo_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"},{"id":"A31","pred":"mondo_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/MONDO_0005108"},{"id":"A32","pred":"mondo_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A33","pred":"mondo_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"}],"text":"1.3 The great diversity of sialic acid glycans\nThe seeming challenge for research into non-covalent binding to glycans is that they are diverse molecules, and that remains true even among the sialic acid glycans. At first consideration, this would seem to suggest that the prediction of glycan binding sites will be difficult. Critical features that distinguish glycans of interest in the present paper are the terminal sugar residues on the oligosaccharide chains at the distal ends (i.e. the “tips”), where sialic acids are important, and the amino acid residue attachment site (N- or. O-) to the membrane protein at the base. The N (nitrogen) protein attachment point attachment is asparagine and the O (oxygen) protein attachment point is usually serine or threonine, but sometimes tyrosine, or occasionally other amino acids which are hydoxylated as a post-translational modification. Covalent connections of that kind are those to the host cell surface proteins but, as indicated above, it is the non-covalent binding of a virus to them that is of interest here. Covalent binding is controlled by host enzymes and so would appear, again at first consideration, to be more specific. Enveloped viruses such as SARS-CoV-2 also have their own bound sialic acid glycans (the spike protein is usually referred to as the spike glycoprotein), but these are of less direct interest here although they can clearly influence binding of a virus to various receptors.\nDespite their diversity, and perhaps because of it (i.e. because that diversity implies more information content) sialic acid glycans of host cells are key molecular recognition features not only for entry of viruses such as influenza, but also in embryonic development, neurodevelopment, reprogramming, and oncogenesis. Correctly speaking, even sialic acid itself is diverse. It is a generic term for a family of derivatives of the nine-carbon sugar neuraminic acid. The sialic acid family includes some 43 derivatives of neuraminic acid, but these acids rarely appear free in nature. Members include N-acetylneuraminic acid, 2-keto-3-deoxy-d-glycero-d-galacto-nonulosonic acid, 5,7-diamino-3,5,7,9-tetra-deoxy-d-glycero-d-galacto- nonulosonic acid, and 5,7-diamino-3,5,7,9-tetra-deoxy-l-glycero-l-manno-nonulosonic acid. If the term “sialic acid” is used unqualified, it usually refers to the representative member of this group, N-acetylneuraminic acid. The variability of glycans is not random but reflects their modes of synthesis. In eukaryotes generally, a typical N-linked glycan has an initial core that consists of 14 residues (3 glucose, 9 mannose, and 2 N-acetylglucosamine). This preassembled glycan is usually transferred by a glycosyltransferase oligosaccharyltransferase to a nascent peptide chain within the reticular lumen. This initial core 14-sugar unit is assembled in the cytoplasm and endoplasmic reticulum and other sugars may be added later. In contrast, O-linked glycans are assembled one sugar at a time at the outset on proteins in the Golgi apparatus.\nThere are some specific features of medical interest as relevant to the human host of viruses (but by no means unique to humans). The lung epithelial glycans are typical by having sialic acids as the distal residues, and it is these that the influenza neuraminidase cleaves away. Most soluble secreted proteins are also similarly decorated with such glycans. That includes the proteins that make up saliva and mucus in the airway, and are in general important for viral infection. Both N- and O- and glycosphingolipid-glycans are found in human lungs, and they include large and complex-type N-glycans with linear poly-N-acetyllactosamine [-3Galβ1–4GlcNAcβ1-]n extensions, which are predominantly terminated in α2,3-linked sialic acid. In contrast, the smaller N-glycans lack poly-N-acetyllactosamine but are enriched in α2,6-linked sialic acids. There are also large glycosphingolipid glycans, which also consists of poly-N-acetyllactosamine, usually terminating in α2,3-linked sialic acid. While it is commonly maintained that viruses such as influenza virus bind to the sialylated glycans, and this is assumed in the present paper, some care is required, because there are also non-sialylated glycans in human lungs on which viral binding could occur."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T19597","span":{"begin":858,"end":889},"obj":"http://purl.obolibrary.org/obo/GO_0043687"},{"id":"T3","span":{"begin":1710,"end":1731},"obj":"http://purl.obolibrary.org/obo/GO_0009790"},{"id":"T4","span":{"begin":2488,"end":2497},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T5","span":{"begin":3507,"end":3522},"obj":"http://purl.obolibrary.org/obo/GO_0016032"}],"text":"1.3 The great diversity of sialic acid glycans\nThe seeming challenge for research into non-covalent binding to glycans is that they are diverse molecules, and that remains true even among the sialic acid glycans. At first consideration, this would seem to suggest that the prediction of glycan binding sites will be difficult. Critical features that distinguish glycans of interest in the present paper are the terminal sugar residues on the oligosaccharide chains at the distal ends (i.e. the “tips”), where sialic acids are important, and the amino acid residue attachment site (N- or. O-) to the membrane protein at the base. The N (nitrogen) protein attachment point attachment is asparagine and the O (oxygen) protein attachment point is usually serine or threonine, but sometimes tyrosine, or occasionally other amino acids which are hydoxylated as a post-translational modification. Covalent connections of that kind are those to the host cell surface proteins but, as indicated above, it is the non-covalent binding of a virus to them that is of interest here. Covalent binding is controlled by host enzymes and so would appear, again at first consideration, to be more specific. Enveloped viruses such as SARS-CoV-2 also have their own bound sialic acid glycans (the spike protein is usually referred to as the spike glycoprotein), but these are of less direct interest here although they can clearly influence binding of a virus to various receptors.\nDespite their diversity, and perhaps because of it (i.e. because that diversity implies more information content) sialic acid glycans of host cells are key molecular recognition features not only for entry of viruses such as influenza, but also in embryonic development, neurodevelopment, reprogramming, and oncogenesis. Correctly speaking, even sialic acid itself is diverse. It is a generic term for a family of derivatives of the nine-carbon sugar neuraminic acid. The sialic acid family includes some 43 derivatives of neuraminic acid, but these acids rarely appear free in nature. Members include N-acetylneuraminic acid, 2-keto-3-deoxy-d-glycero-d-galacto-nonulosonic acid, 5,7-diamino-3,5,7,9-tetra-deoxy-d-glycero-d-galacto- nonulosonic acid, and 5,7-diamino-3,5,7,9-tetra-deoxy-l-glycero-l-manno-nonulosonic acid. If the term “sialic acid” is used unqualified, it usually refers to the representative member of this group, N-acetylneuraminic acid. The variability of glycans is not random but reflects their modes of synthesis. In eukaryotes generally, a typical N-linked glycan has an initial core that consists of 14 residues (3 glucose, 9 mannose, and 2 N-acetylglucosamine). This preassembled glycan is usually transferred by a glycosyltransferase oligosaccharyltransferase to a nascent peptide chain within the reticular lumen. This initial core 14-sugar unit is assembled in the cytoplasm and endoplasmic reticulum and other sugars may be added later. In contrast, O-linked glycans are assembled one sugar at a time at the outset on proteins in the Golgi apparatus.\nThere are some specific features of medical interest as relevant to the human host of viruses (but by no means unique to humans). The lung epithelial glycans are typical by having sialic acids as the distal residues, and it is these that the influenza neuraminidase cleaves away. Most soluble secreted proteins are also similarly decorated with such glycans. That includes the proteins that make up saliva and mucus in the airway, and are in general important for viral infection. Both N- and O- and glycosphingolipid-glycans are found in human lungs, and they include large and complex-type N-glycans with linear poly-N-acetyllactosamine [-3Galβ1–4GlcNAcβ1-]n extensions, which are predominantly terminated in α2,3-linked sialic acid. In contrast, the smaller N-glycans lack poly-N-acetyllactosamine but are enriched in α2,6-linked sialic acids. There are also large glycosphingolipid glycans, which also consists of poly-N-acetyllactosamine, usually terminating in α2,3-linked sialic acid. While it is commonly maintained that viruses such as influenza virus bind to the sialylated glycans, and this is assumed in the present paper, some care is required, because there are also non-sialylated glycans in human lungs on which viral binding could occur."}

LitCovid-sentences

LitCovid-PubTator

PMC:7278709 / 7949-12246 JSONTXT

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PMC:7278709 / 7949-12246 JSON TXT