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LitCovid-PubTator

LitCovid_Glycan-Motif-Structure

{"project":"LitCovid_Glycan-Motif-Structure","denotations":[{"id":"T1","span":{"begin":2346,"end":2365},"obj":"https://glytoucan.org/Structures/Glycans/G64581RP"},{"id":"T2","span":{"begin":2472,"end":2494},"obj":"https://glytoucan.org/Structures/Glycans/G27025MB"},{"id":"T3","span":{"begin":4103,"end":4110},"obj":"https://glytoucan.org/Structures/Glycans/G15021LG"}],"text":"3 Certain characteristics of SARS-CoV2\n\n3.1 SARS-CoV2 has acquired an S glycoprotein that highly underwent genetic variation and glycosylation\n\n3.1.1 Polybasic cleavage site\nAs evidenced by sequence analysis, there is a residue insertion formed of four amino acids (12 nucleotides) at the boundary between S1 and S2 subunits of the SARS-CoV 2 S. It defines a polybasic furin cleavage site of RRAR for the human SARS-CoV 2 that was absent in human SARS-CoV, bat SARS-like CoVs, and pangolin SARS-like CoV while might be present in other species [3]. After the introduction of mutation to the residue insertion and furin cleavage site, the S1/S2 cleavage of the SARS-CoV 2 S did not longer take place. However, the SARS-CoV 2 S entry raised for VeroE6 cells and remained high in BHK cells that express human ACE. Therefore, it seems that SARS-CoV2 transmissibility does not depend on the S1/S2 cleavage.\nA polybasic cleavage site explains a virus that is highly-pathogenic for humans while it is low-pathogenic for other species. For example, using reverse genetic tools, an avian paramyxovirus type 7 (APMV-7) was developed by mutating the fusion (F) protein cleavage site [4]. The constructed APMV-7 showed furin cleavage and increased replication and syncytium formation in cell cultures. However, chicken exposed to the virus did not exhibit infection.\n\n3.1.2 Glycosylation\nGlycosylation and its related products, i.e., glycans, introduce changes to the viral envelope that make the virus fitted for interaction with the host cell membrane [5]. Generally, glycans are oligosaccharides linked to the dense decoration of the spike glycoprotein. In particular, these oligosaccharides have shown to influence the folding of the S protein and proteolytic process so that they facilitate the virus cell entry. Moreover, a virus with the glycosylated glycoprotein gains an extra feature for an escape from the immune responses. Therefore, glycans are a good target for vaccine design.\nTwo main types of glycans are N-linked and O-linked glycans. Both are released from glycoproteins. Whereas enzymes fulfill the construction of N-glycans, chemical methods perform the release of O-glycans. N-glycans are linked to the amino acid asparagine (Asn) residues (Asn-any amino acids except for proline- Ser or Thr) utilizing an N-glycosidic bond, mostly N-acetylglucosamine. O-glycans are attached to the amino acid serine (Ser) and threonine (Thr) residues by the addition of an N-acetyl galactosamine (GalNAc). For example, N-glycans exist in Hendra virus, SARS-CoV, influenza virus, hepatitis virus, HIV-1, and West Nile virus [6], and O-glycans have occurred in the Ebola virus.\nThe 2019-nCoV S protein includes 13 and 9N-linked glycosylation sequons in the S1 and S2 subunit, respectively [3]. All of these have previously occurred in the SARS-CoV S glycoprotein, except for four-linked glycosylation sequons in the S1. Also, due to the existence of an amino acid proline in the polybasic cleavage site, which makes the inserted sequence PRRA, there are three O-linked glycans introduced to the 2019-nCoV RBD residues S673, T678, and S686 [7].\n\n3.1.3 SARS-CoV2 receptor binding domain contains six amino acids providing favorable positions for binding to human ACE2\nWhen compared to SARS-CoV SB, the motif binding the human ACE2 to the SARS-CoV 2 SB showed a relatively higher binding affinity for human ACE2 as indicated in smaller equilibrium dissociation constant (2.9 nM vs. 7.7 nM) [3]. Structural analysis has demonstrated that fourteen positions critically take part in the receptor-binding domain of the SARS-CoV SB that contain eight conserved (T402, Y436, Y440, N473, Y475, T486, G488, and Y491) positions and six semi-conserved (R426 to N448, Y442 to L464, L472 to F495, N479 to Q502, Y484 to Q507, and T487 to N510) substitutions with respect to the SARS-CoV 2 SB.\n\n3.1.4 SARS-CoV2 receptor binding domain contains cyclic regions that can make interaction with cell-surface GRP78\nPep42 is a cyclic oligopeptide that, with its hydrophobic character, can selectively interact with cell surface glucose‐regulated protein 78 (GRP78), a member of 70 kDa heat shock proteins. GRP78, also known as BiP or HSPA5, under endoplasmic reticulum stress, can be translocated from the endoplasmic reticulum to the membrane and helps to maintain cellular integrity under physiologic and pathological stress. It critically contributes to various functions ranging from protein folding, transportation, and degradation to cell-signaling, proliferation, survival, apoptosis, inflammation, and immunity. The expression of GRP78 decreases with age.\nOn the 2019-nCoV spike protein, 13 disulfide bonds are corresponding to 13 different cyclic regions thought to be similar to the cyclic form of Pep42 [8]. Among these, four regions I-IV take place in the outer surface of a putative receptor-binding domain (RBD) on the viral spike., including C361, C379, C391, and C480. These regions share sequence similarity with Pep42, ranging from 15.38% to 46.15%. However, only one of them, i.e., region IV (GRAVY = 0.08), is a hydrophobic region, like Pep42 (GRAVY = 1.1). Structural models evaluate the energy contribution for region IV as a part of region III to the GRP78 to be about (−9.8 out of −14.0 kcal/mol), and the docking platform proposes region IV as the best region binding to GRP78. The region IV can be linked to the substrate-binding domain β (SBDB) of GRP78 using five H-bonds (through P479, N481, E484, and N487) and four hydrophobic interactions (through T478, E484, and F486)."}

LitCovid-PD-FMA-UBERON

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-sample-MedDRA

{"project":"LitCovid-sample-MedDRA","denotations":[{"id":"T4","span":{"begin":809,"end":812},"obj":"http://purl.bioontology.org/ontology/MEDDRA/10022891"},{"id":"T5","span":{"begin":1283,"end":1291},"obj":"http://purl.bioontology.org/ontology/MEDDRA/10022891"}],"attributes":[{"id":"A4","pred":"meddra_id","subj":"T4","obj":"http://purl.bioontology.org/ontology/MEDDRA/10050289"},{"id":"A5","pred":"meddra_id","subj":"T5","obj":"http://purl.bioontology.org/ontology/MEDDRA/10061447"}],"text":"3 Certain characteristics of SARS-CoV2\n\n3.1 SARS-CoV2 has acquired an S glycoprotein that highly underwent genetic variation and glycosylation\n\n3.1.1 Polybasic cleavage site\nAs evidenced by sequence analysis, there is a residue insertion formed of four amino acids (12 nucleotides) at the boundary between S1 and S2 subunits of the SARS-CoV 2 S. It defines a polybasic furin cleavage site of RRAR for the human SARS-CoV 2 that was absent in human SARS-CoV, bat SARS-like CoVs, and pangolin SARS-like CoV while might be present in other species [3]. After the introduction of mutation to the residue insertion and furin cleavage site, the S1/S2 cleavage of the SARS-CoV 2 S did not longer take place. However, the SARS-CoV 2 S entry raised for VeroE6 cells and remained high in BHK cells that express human ACE. Therefore, it seems that SARS-CoV2 transmissibility does not depend on the S1/S2 cleavage.\nA polybasic cleavage site explains a virus that is highly-pathogenic for humans while it is low-pathogenic for other species. For example, using reverse genetic tools, an avian paramyxovirus type 7 (APMV-7) was developed by mutating the fusion (F) protein cleavage site [4]. The constructed APMV-7 showed furin cleavage and increased replication and syncytium formation in cell cultures. However, chicken exposed to the virus did not exhibit infection.\n\n3.1.2 Glycosylation\nGlycosylation and its related products, i.e., glycans, introduce changes to the viral envelope that make the virus fitted for interaction with the host cell membrane [5]. Generally, glycans are oligosaccharides linked to the dense decoration of the spike glycoprotein. In particular, these oligosaccharides have shown to influence the folding of the S protein and proteolytic process so that they facilitate the virus cell entry. Moreover, a virus with the glycosylated glycoprotein gains an extra feature for an escape from the immune responses. Therefore, glycans are a good target for vaccine design.\nTwo main types of glycans are N-linked and O-linked glycans. Both are released from glycoproteins. Whereas enzymes fulfill the construction of N-glycans, chemical methods perform the release of O-glycans. N-glycans are linked to the amino acid asparagine (Asn) residues (Asn-any amino acids except for proline- Ser or Thr) utilizing an N-glycosidic bond, mostly N-acetylglucosamine. O-glycans are attached to the amino acid serine (Ser) and threonine (Thr) residues by the addition of an N-acetyl galactosamine (GalNAc). For example, N-glycans exist in Hendra virus, SARS-CoV, influenza virus, hepatitis virus, HIV-1, and West Nile virus [6], and O-glycans have occurred in the Ebola virus.\nThe 2019-nCoV S protein includes 13 and 9N-linked glycosylation sequons in the S1 and S2 subunit, respectively [3]. All of these have previously occurred in the SARS-CoV S glycoprotein, except for four-linked glycosylation sequons in the S1. Also, due to the existence of an amino acid proline in the polybasic cleavage site, which makes the inserted sequence PRRA, there are three O-linked glycans introduced to the 2019-nCoV RBD residues S673, T678, and S686 [7].\n\n3.1.3 SARS-CoV2 receptor binding domain contains six amino acids providing favorable positions for binding to human ACE2\nWhen compared to SARS-CoV SB, the motif binding the human ACE2 to the SARS-CoV 2 SB showed a relatively higher binding affinity for human ACE2 as indicated in smaller equilibrium dissociation constant (2.9 nM vs. 7.7 nM) [3]. Structural analysis has demonstrated that fourteen positions critically take part in the receptor-binding domain of the SARS-CoV SB that contain eight conserved (T402, Y436, Y440, N473, Y475, T486, G488, and Y491) positions and six semi-conserved (R426 to N448, Y442 to L464, L472 to F495, N479 to Q502, Y484 to Q507, and T487 to N510) substitutions with respect to the SARS-CoV 2 SB.\n\n3.1.4 SARS-CoV2 receptor binding domain contains cyclic regions that can make interaction with cell-surface GRP78\nPep42 is a cyclic oligopeptide that, with its hydrophobic character, can selectively interact with cell surface glucose‐regulated protein 78 (GRP78), a member of 70 kDa heat shock proteins. GRP78, also known as BiP or HSPA5, under endoplasmic reticulum stress, can be translocated from the endoplasmic reticulum to the membrane and helps to maintain cellular integrity under physiologic and pathological stress. It critically contributes to various functions ranging from protein folding, transportation, and degradation to cell-signaling, proliferation, survival, apoptosis, inflammation, and immunity. The expression of GRP78 decreases with age.\nOn the 2019-nCoV spike protein, 13 disulfide bonds are corresponding to 13 different cyclic regions thought to be similar to the cyclic form of Pep42 [8]. Among these, four regions I-IV take place in the outer surface of a putative receptor-binding domain (RBD) on the viral spike., including C361, C379, C391, and C480. These regions share sequence similarity with Pep42, ranging from 15.38% to 46.15%. However, only one of them, i.e., region IV (GRAVY = 0.08), is a hydrophobic region, like Pep42 (GRAVY = 1.1). Structural models evaluate the energy contribution for region IV as a part of region III to the GRP78 to be about (−9.8 out of −14.0 kcal/mol), and the docking platform proposes region IV as the best region binding to GRP78. The region IV can be linked to the substrate-binding domain β (SBDB) of GRP78 using five H-bonds (through P479, N481, E484, and N487) and four hydrophobic interactions (through T478, E484, and F486)."}

LitCovid-sample-PD-IDO

LitCovid-sample-CHEBI

LitCovid-sample-PD-NCBITaxon

LitCovid-sample-sentences

LitCovid-sample-Pubtator

LitCovid-sample-UniProt

LitCovid-sample-Enju

LitCovid-sample-PD-GO-BP-0

{"project":"LitCovid-sample-PD-GO-BP-0","denotations":[{"id":"T5","span":{"begin":131,"end":144},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T6","span":{"begin":1255,"end":1274},"obj":"http://purl.obolibrary.org/obo/GO_0006949"},{"id":"T7","span":{"begin":1265,"end":1274},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T8","span":{"begin":1366,"end":1379},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T9","span":{"begin":1380,"end":1393},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T10","span":{"begin":1506,"end":1531},"obj":"http://purl.obolibrary.org/obo/GO_0051701"},{"id":"T11","span":{"begin":1909,"end":1925},"obj":"http://purl.obolibrary.org/obo/GO_0006955"},{"id":"T12","span":{"begin":2725,"end":2738},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T13","span":{"begin":2884,"end":2897},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T14","span":{"begin":4463,"end":4478},"obj":"http://purl.obolibrary.org/obo/GO_0006457"},{"id":"T15","span":{"begin":4500,"end":4511},"obj":"http://purl.obolibrary.org/obo/GO_0009056"},{"id":"T16","span":{"begin":4520,"end":4529},"obj":"http://purl.obolibrary.org/obo/GO_0023052"},{"id":"T17","span":{"begin":4556,"end":4565},"obj":"http://purl.obolibrary.org/obo/GO_0006915"},{"id":"T18","span":{"begin":4556,"end":4565},"obj":"http://purl.obolibrary.org/obo/GO_0097194"},{"id":"T19","span":{"begin":4567,"end":4579},"obj":"http://purl.obolibrary.org/obo/GO_0006954"}],"text":"3 Certain characteristics of SARS-CoV2\n\n3.1 SARS-CoV2 has acquired an S glycoprotein that highly underwent genetic variation and glycosylation\n\n3.1.1 Polybasic cleavage site\nAs evidenced by sequence analysis, there is a residue insertion formed of four amino acids (12 nucleotides) at the boundary between S1 and S2 subunits of the SARS-CoV 2 S. It defines a polybasic furin cleavage site of RRAR for the human SARS-CoV 2 that was absent in human SARS-CoV, bat SARS-like CoVs, and pangolin SARS-like CoV while might be present in other species [3]. After the introduction of mutation to the residue insertion and furin cleavage site, the S1/S2 cleavage of the SARS-CoV 2 S did not longer take place. However, the SARS-CoV 2 S entry raised for VeroE6 cells and remained high in BHK cells that express human ACE. Therefore, it seems that SARS-CoV2 transmissibility does not depend on the S1/S2 cleavage.\nA polybasic cleavage site explains a virus that is highly-pathogenic for humans while it is low-pathogenic for other species. For example, using reverse genetic tools, an avian paramyxovirus type 7 (APMV-7) was developed by mutating the fusion (F) protein cleavage site [4]. The constructed APMV-7 showed furin cleavage and increased replication and syncytium formation in cell cultures. However, chicken exposed to the virus did not exhibit infection.\n\n3.1.2 Glycosylation\nGlycosylation and its related products, i.e., glycans, introduce changes to the viral envelope that make the virus fitted for interaction with the host cell membrane [5]. Generally, glycans are oligosaccharides linked to the dense decoration of the spike glycoprotein. In particular, these oligosaccharides have shown to influence the folding of the S protein and proteolytic process so that they facilitate the virus cell entry. Moreover, a virus with the glycosylated glycoprotein gains an extra feature for an escape from the immune responses. Therefore, glycans are a good target for vaccine design.\nTwo main types of glycans are N-linked and O-linked glycans. Both are released from glycoproteins. Whereas enzymes fulfill the construction of N-glycans, chemical methods perform the release of O-glycans. N-glycans are linked to the amino acid asparagine (Asn) residues (Asn-any amino acids except for proline- Ser or Thr) utilizing an N-glycosidic bond, mostly N-acetylglucosamine. O-glycans are attached to the amino acid serine (Ser) and threonine (Thr) residues by the addition of an N-acetyl galactosamine (GalNAc). For example, N-glycans exist in Hendra virus, SARS-CoV, influenza virus, hepatitis virus, HIV-1, and West Nile virus [6], and O-glycans have occurred in the Ebola virus.\nThe 2019-nCoV S protein includes 13 and 9N-linked glycosylation sequons in the S1 and S2 subunit, respectively [3]. All of these have previously occurred in the SARS-CoV S glycoprotein, except for four-linked glycosylation sequons in the S1. Also, due to the existence of an amino acid proline in the polybasic cleavage site, which makes the inserted sequence PRRA, there are three O-linked glycans introduced to the 2019-nCoV RBD residues S673, T678, and S686 [7].\n\n3.1.3 SARS-CoV2 receptor binding domain contains six amino acids providing favorable positions for binding to human ACE2\nWhen compared to SARS-CoV SB, the motif binding the human ACE2 to the SARS-CoV 2 SB showed a relatively higher binding affinity for human ACE2 as indicated in smaller equilibrium dissociation constant (2.9 nM vs. 7.7 nM) [3]. Structural analysis has demonstrated that fourteen positions critically take part in the receptor-binding domain of the SARS-CoV SB that contain eight conserved (T402, Y436, Y440, N473, Y475, T486, G488, and Y491) positions and six semi-conserved (R426 to N448, Y442 to L464, L472 to F495, N479 to Q502, Y484 to Q507, and T487 to N510) substitutions with respect to the SARS-CoV 2 SB.\n\n3.1.4 SARS-CoV2 receptor binding domain contains cyclic regions that can make interaction with cell-surface GRP78\nPep42 is a cyclic oligopeptide that, with its hydrophobic character, can selectively interact with cell surface glucose‐regulated protein 78 (GRP78), a member of 70 kDa heat shock proteins. GRP78, also known as BiP or HSPA5, under endoplasmic reticulum stress, can be translocated from the endoplasmic reticulum to the membrane and helps to maintain cellular integrity under physiologic and pathological stress. It critically contributes to various functions ranging from protein folding, transportation, and degradation to cell-signaling, proliferation, survival, apoptosis, inflammation, and immunity. The expression of GRP78 decreases with age.\nOn the 2019-nCoV spike protein, 13 disulfide bonds are corresponding to 13 different cyclic regions thought to be similar to the cyclic form of Pep42 [8]. Among these, four regions I-IV take place in the outer surface of a putative receptor-binding domain (RBD) on the viral spike., including C361, C379, C391, and C480. These regions share sequence similarity with Pep42, ranging from 15.38% to 46.15%. However, only one of them, i.e., region IV (GRAVY = 0.08), is a hydrophobic region, like Pep42 (GRAVY = 1.1). Structural models evaluate the energy contribution for region IV as a part of region III to the GRP78 to be about (−9.8 out of −14.0 kcal/mol), and the docking platform proposes region IV as the best region binding to GRP78. The region IV can be linked to the substrate-binding domain β (SBDB) of GRP78 using five H-bonds (through P479, N481, E484, and N487) and four hydrophobic interactions (through T478, E484, and F486)."}

LitCovid-sample-PD-FMA

LitCovid-sample-PD-MONDO

LitCovid-sample-PD-HP

{"project":"LitCovid-sample-PD-HP","denotations":[{"id":"T1","span":{"begin":2578,"end":2587},"obj":"Phenotype"},{"id":"T2","span":{"begin":4165,"end":4170},"obj":"Phenotype"}],"attributes":[{"id":"A1","pred":"hp_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/HP_0012115"},{"id":"A2","pred":"hp_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/HP_0031273"}],"text":"3 Certain characteristics of SARS-CoV2\n\n3.1 SARS-CoV2 has acquired an S glycoprotein that highly underwent genetic variation and glycosylation\n\n3.1.1 Polybasic cleavage site\nAs evidenced by sequence analysis, there is a residue insertion formed of four amino acids (12 nucleotides) at the boundary between S1 and S2 subunits of the SARS-CoV 2 S. It defines a polybasic furin cleavage site of RRAR for the human SARS-CoV 2 that was absent in human SARS-CoV, bat SARS-like CoVs, and pangolin SARS-like CoV while might be present in other species [3]. After the introduction of mutation to the residue insertion and furin cleavage site, the S1/S2 cleavage of the SARS-CoV 2 S did not longer take place. However, the SARS-CoV 2 S entry raised for VeroE6 cells and remained high in BHK cells that express human ACE. Therefore, it seems that SARS-CoV2 transmissibility does not depend on the S1/S2 cleavage.\nA polybasic cleavage site explains a virus that is highly-pathogenic for humans while it is low-pathogenic for other species. For example, using reverse genetic tools, an avian paramyxovirus type 7 (APMV-7) was developed by mutating the fusion (F) protein cleavage site [4]. The constructed APMV-7 showed furin cleavage and increased replication and syncytium formation in cell cultures. However, chicken exposed to the virus did not exhibit infection.\n\n3.1.2 Glycosylation\nGlycosylation and its related products, i.e., glycans, introduce changes to the viral envelope that make the virus fitted for interaction with the host cell membrane [5]. Generally, glycans are oligosaccharides linked to the dense decoration of the spike glycoprotein. In particular, these oligosaccharides have shown to influence the folding of the S protein and proteolytic process so that they facilitate the virus cell entry. Moreover, a virus with the glycosylated glycoprotein gains an extra feature for an escape from the immune responses. Therefore, glycans are a good target for vaccine design.\nTwo main types of glycans are N-linked and O-linked glycans. Both are released from glycoproteins. Whereas enzymes fulfill the construction of N-glycans, chemical methods perform the release of O-glycans. N-glycans are linked to the amino acid asparagine (Asn) residues (Asn-any amino acids except for proline- Ser or Thr) utilizing an N-glycosidic bond, mostly N-acetylglucosamine. O-glycans are attached to the amino acid serine (Ser) and threonine (Thr) residues by the addition of an N-acetyl galactosamine (GalNAc). For example, N-glycans exist in Hendra virus, SARS-CoV, influenza virus, hepatitis virus, HIV-1, and West Nile virus [6], and O-glycans have occurred in the Ebola virus.\nThe 2019-nCoV S protein includes 13 and 9N-linked glycosylation sequons in the S1 and S2 subunit, respectively [3]. All of these have previously occurred in the SARS-CoV S glycoprotein, except for four-linked glycosylation sequons in the S1. Also, due to the existence of an amino acid proline in the polybasic cleavage site, which makes the inserted sequence PRRA, there are three O-linked glycans introduced to the 2019-nCoV RBD residues S673, T678, and S686 [7].\n\n3.1.3 SARS-CoV2 receptor binding domain contains six amino acids providing favorable positions for binding to human ACE2\nWhen compared to SARS-CoV SB, the motif binding the human ACE2 to the SARS-CoV 2 SB showed a relatively higher binding affinity for human ACE2 as indicated in smaller equilibrium dissociation constant (2.9 nM vs. 7.7 nM) [3]. Structural analysis has demonstrated that fourteen positions critically take part in the receptor-binding domain of the SARS-CoV SB that contain eight conserved (T402, Y436, Y440, N473, Y475, T486, G488, and Y491) positions and six semi-conserved (R426 to N448, Y442 to L464, L472 to F495, N479 to Q502, Y484 to Q507, and T487 to N510) substitutions with respect to the SARS-CoV 2 SB.\n\n3.1.4 SARS-CoV2 receptor binding domain contains cyclic regions that can make interaction with cell-surface GRP78\nPep42 is a cyclic oligopeptide that, with its hydrophobic character, can selectively interact with cell surface glucose‐regulated protein 78 (GRP78), a member of 70 kDa heat shock proteins. GRP78, also known as BiP or HSPA5, under endoplasmic reticulum stress, can be translocated from the endoplasmic reticulum to the membrane and helps to maintain cellular integrity under physiologic and pathological stress. It critically contributes to various functions ranging from protein folding, transportation, and degradation to cell-signaling, proliferation, survival, apoptosis, inflammation, and immunity. The expression of GRP78 decreases with age.\nOn the 2019-nCoV spike protein, 13 disulfide bonds are corresponding to 13 different cyclic regions thought to be similar to the cyclic form of Pep42 [8]. Among these, four regions I-IV take place in the outer surface of a putative receptor-binding domain (RBD) on the viral spike., including C361, C379, C391, and C480. These regions share sequence similarity with Pep42, ranging from 15.38% to 46.15%. However, only one of them, i.e., region IV (GRAVY = 0.08), is a hydrophobic region, like Pep42 (GRAVY = 1.1). Structural models evaluate the energy contribution for region IV as a part of region III to the GRP78 to be about (−9.8 out of −14.0 kcal/mol), and the docking platform proposes region IV as the best region binding to GRP78. The region IV can be linked to the substrate-binding domain β (SBDB) of GRP78 using five H-bonds (through P479, N481, E484, and N487) and four hydrophobic interactions (through T478, E484, and F486)."}

LitCovid-sample-GO-BP

{"project":"LitCovid-sample-GO-BP","denotations":[{"id":"T3","span":{"begin":131,"end":144},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T4","span":{"begin":1255,"end":1274},"obj":"http://purl.obolibrary.org/obo/GO_0006949"},{"id":"T5","span":{"begin":1265,"end":1274},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T6","span":{"begin":1366,"end":1379},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T7","span":{"begin":1380,"end":1393},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T8","span":{"begin":1506,"end":1531},"obj":"http://purl.obolibrary.org/obo/GO_0051701"},{"id":"T9","span":{"begin":1909,"end":1925},"obj":"http://purl.obolibrary.org/obo/GO_0006955"},{"id":"T10","span":{"begin":2725,"end":2738},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T11","span":{"begin":2884,"end":2897},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T12","span":{"begin":4463,"end":4478},"obj":"http://purl.obolibrary.org/obo/GO_0006457"},{"id":"T13","span":{"begin":4500,"end":4511},"obj":"http://purl.obolibrary.org/obo/GO_0009056"},{"id":"T14","span":{"begin":4520,"end":4529},"obj":"http://purl.obolibrary.org/obo/GO_0023052"},{"id":"T15","span":{"begin":4556,"end":4565},"obj":"http://purl.obolibrary.org/obo/GO_0097194"},{"id":"T16","span":{"begin":4556,"end":4565},"obj":"http://purl.obolibrary.org/obo/GO_0006915"},{"id":"T17","span":{"begin":4567,"end":4579},"obj":"http://purl.obolibrary.org/obo/GO_0006954"}],"text":"3 Certain characteristics of SARS-CoV2\n\n3.1 SARS-CoV2 has acquired an S glycoprotein that highly underwent genetic variation and glycosylation\n\n3.1.1 Polybasic cleavage site\nAs evidenced by sequence analysis, there is a residue insertion formed of four amino acids (12 nucleotides) at the boundary between S1 and S2 subunits of the SARS-CoV 2 S. It defines a polybasic furin cleavage site of RRAR for the human SARS-CoV 2 that was absent in human SARS-CoV, bat SARS-like CoVs, and pangolin SARS-like CoV while might be present in other species [3]. After the introduction of mutation to the residue insertion and furin cleavage site, the S1/S2 cleavage of the SARS-CoV 2 S did not longer take place. However, the SARS-CoV 2 S entry raised for VeroE6 cells and remained high in BHK cells that express human ACE. Therefore, it seems that SARS-CoV2 transmissibility does not depend on the S1/S2 cleavage.\nA polybasic cleavage site explains a virus that is highly-pathogenic for humans while it is low-pathogenic for other species. For example, using reverse genetic tools, an avian paramyxovirus type 7 (APMV-7) was developed by mutating the fusion (F) protein cleavage site [4]. The constructed APMV-7 showed furin cleavage and increased replication and syncytium formation in cell cultures. However, chicken exposed to the virus did not exhibit infection.\n\n3.1.2 Glycosylation\nGlycosylation and its related products, i.e., glycans, introduce changes to the viral envelope that make the virus fitted for interaction with the host cell membrane [5]. Generally, glycans are oligosaccharides linked to the dense decoration of the spike glycoprotein. In particular, these oligosaccharides have shown to influence the folding of the S protein and proteolytic process so that they facilitate the virus cell entry. Moreover, a virus with the glycosylated glycoprotein gains an extra feature for an escape from the immune responses. Therefore, glycans are a good target for vaccine design.\nTwo main types of glycans are N-linked and O-linked glycans. Both are released from glycoproteins. Whereas enzymes fulfill the construction of N-glycans, chemical methods perform the release of O-glycans. N-glycans are linked to the amino acid asparagine (Asn) residues (Asn-any amino acids except for proline- Ser or Thr) utilizing an N-glycosidic bond, mostly N-acetylglucosamine. O-glycans are attached to the amino acid serine (Ser) and threonine (Thr) residues by the addition of an N-acetyl galactosamine (GalNAc). For example, N-glycans exist in Hendra virus, SARS-CoV, influenza virus, hepatitis virus, HIV-1, and West Nile virus [6], and O-glycans have occurred in the Ebola virus.\nThe 2019-nCoV S protein includes 13 and 9N-linked glycosylation sequons in the S1 and S2 subunit, respectively [3]. All of these have previously occurred in the SARS-CoV S glycoprotein, except for four-linked glycosylation sequons in the S1. Also, due to the existence of an amino acid proline in the polybasic cleavage site, which makes the inserted sequence PRRA, there are three O-linked glycans introduced to the 2019-nCoV RBD residues S673, T678, and S686 [7].\n\n3.1.3 SARS-CoV2 receptor binding domain contains six amino acids providing favorable positions for binding to human ACE2\nWhen compared to SARS-CoV SB, the motif binding the human ACE2 to the SARS-CoV 2 SB showed a relatively higher binding affinity for human ACE2 as indicated in smaller equilibrium dissociation constant (2.9 nM vs. 7.7 nM) [3]. Structural analysis has demonstrated that fourteen positions critically take part in the receptor-binding domain of the SARS-CoV SB that contain eight conserved (T402, Y436, Y440, N473, Y475, T486, G488, and Y491) positions and six semi-conserved (R426 to N448, Y442 to L464, L472 to F495, N479 to Q502, Y484 to Q507, and T487 to N510) substitutions with respect to the SARS-CoV 2 SB.\n\n3.1.4 SARS-CoV2 receptor binding domain contains cyclic regions that can make interaction with cell-surface GRP78\nPep42 is a cyclic oligopeptide that, with its hydrophobic character, can selectively interact with cell surface glucose‐regulated protein 78 (GRP78), a member of 70 kDa heat shock proteins. GRP78, also known as BiP or HSPA5, under endoplasmic reticulum stress, can be translocated from the endoplasmic reticulum to the membrane and helps to maintain cellular integrity under physiologic and pathological stress. It critically contributes to various functions ranging from protein folding, transportation, and degradation to cell-signaling, proliferation, survival, apoptosis, inflammation, and immunity. The expression of GRP78 decreases with age.\nOn the 2019-nCoV spike protein, 13 disulfide bonds are corresponding to 13 different cyclic regions thought to be similar to the cyclic form of Pep42 [8]. Among these, four regions I-IV take place in the outer surface of a putative receptor-binding domain (RBD) on the viral spike., including C361, C379, C391, and C480. These regions share sequence similarity with Pep42, ranging from 15.38% to 46.15%. However, only one of them, i.e., region IV (GRAVY = 0.08), is a hydrophobic region, like Pep42 (GRAVY = 1.1). Structural models evaluate the energy contribution for region IV as a part of region III to the GRP78 to be about (−9.8 out of −14.0 kcal/mol), and the docking platform proposes region IV as the best region binding to GRP78. The region IV can be linked to the substrate-binding domain β (SBDB) of GRP78 using five H-bonds (through P479, N481, E484, and N487) and four hydrophobic interactions (through T478, E484, and F486)."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T3","span":{"begin":131,"end":144},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T4","span":{"begin":1255,"end":1274},"obj":"http://purl.obolibrary.org/obo/GO_0006949"},{"id":"T5","span":{"begin":1265,"end":1274},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T6","span":{"begin":1366,"end":1379},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T7","span":{"begin":1380,"end":1393},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T8","span":{"begin":1506,"end":1531},"obj":"http://purl.obolibrary.org/obo/GO_0051701"},{"id":"T9","span":{"begin":1909,"end":1925},"obj":"http://purl.obolibrary.org/obo/GO_0006955"},{"id":"T10","span":{"begin":2725,"end":2738},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T11","span":{"begin":2884,"end":2897},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T12","span":{"begin":4463,"end":4478},"obj":"http://purl.obolibrary.org/obo/GO_0006457"},{"id":"T13","span":{"begin":4500,"end":4511},"obj":"http://purl.obolibrary.org/obo/GO_0009056"},{"id":"T14","span":{"begin":4520,"end":4529},"obj":"http://purl.obolibrary.org/obo/GO_0023052"},{"id":"T15","span":{"begin":4556,"end":4565},"obj":"http://purl.obolibrary.org/obo/GO_0097194"},{"id":"T16","span":{"begin":4556,"end":4565},"obj":"http://purl.obolibrary.org/obo/GO_0006915"},{"id":"T17","span":{"begin":4567,"end":4579},"obj":"http://purl.obolibrary.org/obo/GO_0006954"}],"text":"3 Certain characteristics of SARS-CoV2\n\n3.1 SARS-CoV2 has acquired an S glycoprotein that highly underwent genetic variation and glycosylation\n\n3.1.1 Polybasic cleavage site\nAs evidenced by sequence analysis, there is a residue insertion formed of four amino acids (12 nucleotides) at the boundary between S1 and S2 subunits of the SARS-CoV 2 S. It defines a polybasic furin cleavage site of RRAR for the human SARS-CoV 2 that was absent in human SARS-CoV, bat SARS-like CoVs, and pangolin SARS-like CoV while might be present in other species [3]. After the introduction of mutation to the residue insertion and furin cleavage site, the S1/S2 cleavage of the SARS-CoV 2 S did not longer take place. However, the SARS-CoV 2 S entry raised for VeroE6 cells and remained high in BHK cells that express human ACE. Therefore, it seems that SARS-CoV2 transmissibility does not depend on the S1/S2 cleavage.\nA polybasic cleavage site explains a virus that is highly-pathogenic for humans while it is low-pathogenic for other species. For example, using reverse genetic tools, an avian paramyxovirus type 7 (APMV-7) was developed by mutating the fusion (F) protein cleavage site [4]. The constructed APMV-7 showed furin cleavage and increased replication and syncytium formation in cell cultures. However, chicken exposed to the virus did not exhibit infection.\n\n3.1.2 Glycosylation\nGlycosylation and its related products, i.e., glycans, introduce changes to the viral envelope that make the virus fitted for interaction with the host cell membrane [5]. Generally, glycans are oligosaccharides linked to the dense decoration of the spike glycoprotein. In particular, these oligosaccharides have shown to influence the folding of the S protein and proteolytic process so that they facilitate the virus cell entry. Moreover, a virus with the glycosylated glycoprotein gains an extra feature for an escape from the immune responses. Therefore, glycans are a good target for vaccine design.\nTwo main types of glycans are N-linked and O-linked glycans. Both are released from glycoproteins. Whereas enzymes fulfill the construction of N-glycans, chemical methods perform the release of O-glycans. N-glycans are linked to the amino acid asparagine (Asn) residues (Asn-any amino acids except for proline- Ser or Thr) utilizing an N-glycosidic bond, mostly N-acetylglucosamine. O-glycans are attached to the amino acid serine (Ser) and threonine (Thr) residues by the addition of an N-acetyl galactosamine (GalNAc). For example, N-glycans exist in Hendra virus, SARS-CoV, influenza virus, hepatitis virus, HIV-1, and West Nile virus [6], and O-glycans have occurred in the Ebola virus.\nThe 2019-nCoV S protein includes 13 and 9N-linked glycosylation sequons in the S1 and S2 subunit, respectively [3]. All of these have previously occurred in the SARS-CoV S glycoprotein, except for four-linked glycosylation sequons in the S1. Also, due to the existence of an amino acid proline in the polybasic cleavage site, which makes the inserted sequence PRRA, there are three O-linked glycans introduced to the 2019-nCoV RBD residues S673, T678, and S686 [7].\n\n3.1.3 SARS-CoV2 receptor binding domain contains six amino acids providing favorable positions for binding to human ACE2\nWhen compared to SARS-CoV SB, the motif binding the human ACE2 to the SARS-CoV 2 SB showed a relatively higher binding affinity for human ACE2 as indicated in smaller equilibrium dissociation constant (2.9 nM vs. 7.7 nM) [3]. Structural analysis has demonstrated that fourteen positions critically take part in the receptor-binding domain of the SARS-CoV SB that contain eight conserved (T402, Y436, Y440, N473, Y475, T486, G488, and Y491) positions and six semi-conserved (R426 to N448, Y442 to L464, L472 to F495, N479 to Q502, Y484 to Q507, and T487 to N510) substitutions with respect to the SARS-CoV 2 SB.\n\n3.1.4 SARS-CoV2 receptor binding domain contains cyclic regions that can make interaction with cell-surface GRP78\nPep42 is a cyclic oligopeptide that, with its hydrophobic character, can selectively interact with cell surface glucose‐regulated protein 78 (GRP78), a member of 70 kDa heat shock proteins. GRP78, also known as BiP or HSPA5, under endoplasmic reticulum stress, can be translocated from the endoplasmic reticulum to the membrane and helps to maintain cellular integrity under physiologic and pathological stress. It critically contributes to various functions ranging from protein folding, transportation, and degradation to cell-signaling, proliferation, survival, apoptosis, inflammation, and immunity. The expression of GRP78 decreases with age.\nOn the 2019-nCoV spike protein, 13 disulfide bonds are corresponding to 13 different cyclic regions thought to be similar to the cyclic form of Pep42 [8]. Among these, four regions I-IV take place in the outer surface of a putative receptor-binding domain (RBD) on the viral spike., including C361, C379, C391, and C480. These regions share sequence similarity with Pep42, ranging from 15.38% to 46.15%. However, only one of them, i.e., region IV (GRAVY = 0.08), is a hydrophobic region, like Pep42 (GRAVY = 1.1). Structural models evaluate the energy contribution for region IV as a part of region III to the GRP78 to be about (−9.8 out of −14.0 kcal/mol), and the docking platform proposes region IV as the best region binding to GRP78. The region IV can be linked to the substrate-binding domain β (SBDB) of GRP78 using five H-bonds (through P479, N481, E484, and N487) and four hydrophobic interactions (through T478, E484, and F486)."}

LitCovid-sentences

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T1","span":{"begin":2578,"end":2587},"obj":"Phenotype"},{"id":"T2","span":{"begin":4165,"end":4170},"obj":"Phenotype"}],"attributes":[{"id":"A1","pred":"hp_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/HP_0012115"},{"id":"A2","pred":"hp_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/HP_0031273"}],"text":"3 Certain characteristics of SARS-CoV2\n\n3.1 SARS-CoV2 has acquired an S glycoprotein that highly underwent genetic variation and glycosylation\n\n3.1.1 Polybasic cleavage site\nAs evidenced by sequence analysis, there is a residue insertion formed of four amino acids (12 nucleotides) at the boundary between S1 and S2 subunits of the SARS-CoV 2 S. It defines a polybasic furin cleavage site of RRAR for the human SARS-CoV 2 that was absent in human SARS-CoV, bat SARS-like CoVs, and pangolin SARS-like CoV while might be present in other species [3]. After the introduction of mutation to the residue insertion and furin cleavage site, the S1/S2 cleavage of the SARS-CoV 2 S did not longer take place. However, the SARS-CoV 2 S entry raised for VeroE6 cells and remained high in BHK cells that express human ACE. Therefore, it seems that SARS-CoV2 transmissibility does not depend on the S1/S2 cleavage.\nA polybasic cleavage site explains a virus that is highly-pathogenic for humans while it is low-pathogenic for other species. For example, using reverse genetic tools, an avian paramyxovirus type 7 (APMV-7) was developed by mutating the fusion (F) protein cleavage site [4]. The constructed APMV-7 showed furin cleavage and increased replication and syncytium formation in cell cultures. However, chicken exposed to the virus did not exhibit infection.\n\n3.1.2 Glycosylation\nGlycosylation and its related products, i.e., glycans, introduce changes to the viral envelope that make the virus fitted for interaction with the host cell membrane [5]. Generally, glycans are oligosaccharides linked to the dense decoration of the spike glycoprotein. In particular, these oligosaccharides have shown to influence the folding of the S protein and proteolytic process so that they facilitate the virus cell entry. Moreover, a virus with the glycosylated glycoprotein gains an extra feature for an escape from the immune responses. Therefore, glycans are a good target for vaccine design.\nTwo main types of glycans are N-linked and O-linked glycans. Both are released from glycoproteins. Whereas enzymes fulfill the construction of N-glycans, chemical methods perform the release of O-glycans. N-glycans are linked to the amino acid asparagine (Asn) residues (Asn-any amino acids except for proline- Ser or Thr) utilizing an N-glycosidic bond, mostly N-acetylglucosamine. O-glycans are attached to the amino acid serine (Ser) and threonine (Thr) residues by the addition of an N-acetyl galactosamine (GalNAc). For example, N-glycans exist in Hendra virus, SARS-CoV, influenza virus, hepatitis virus, HIV-1, and West Nile virus [6], and O-glycans have occurred in the Ebola virus.\nThe 2019-nCoV S protein includes 13 and 9N-linked glycosylation sequons in the S1 and S2 subunit, respectively [3]. All of these have previously occurred in the SARS-CoV S glycoprotein, except for four-linked glycosylation sequons in the S1. Also, due to the existence of an amino acid proline in the polybasic cleavage site, which makes the inserted sequence PRRA, there are three O-linked glycans introduced to the 2019-nCoV RBD residues S673, T678, and S686 [7].\n\n3.1.3 SARS-CoV2 receptor binding domain contains six amino acids providing favorable positions for binding to human ACE2\nWhen compared to SARS-CoV SB, the motif binding the human ACE2 to the SARS-CoV 2 SB showed a relatively higher binding affinity for human ACE2 as indicated in smaller equilibrium dissociation constant (2.9 nM vs. 7.7 nM) [3]. Structural analysis has demonstrated that fourteen positions critically take part in the receptor-binding domain of the SARS-CoV SB that contain eight conserved (T402, Y436, Y440, N473, Y475, T486, G488, and Y491) positions and six semi-conserved (R426 to N448, Y442 to L464, L472 to F495, N479 to Q502, Y484 to Q507, and T487 to N510) substitutions with respect to the SARS-CoV 2 SB.\n\n3.1.4 SARS-CoV2 receptor binding domain contains cyclic regions that can make interaction with cell-surface GRP78\nPep42 is a cyclic oligopeptide that, with its hydrophobic character, can selectively interact with cell surface glucose‐regulated protein 78 (GRP78), a member of 70 kDa heat shock proteins. GRP78, also known as BiP or HSPA5, under endoplasmic reticulum stress, can be translocated from the endoplasmic reticulum to the membrane and helps to maintain cellular integrity under physiologic and pathological stress. It critically contributes to various functions ranging from protein folding, transportation, and degradation to cell-signaling, proliferation, survival, apoptosis, inflammation, and immunity. The expression of GRP78 decreases with age.\nOn the 2019-nCoV spike protein, 13 disulfide bonds are corresponding to 13 different cyclic regions thought to be similar to the cyclic form of Pep42 [8]. Among these, four regions I-IV take place in the outer surface of a putative receptor-binding domain (RBD) on the viral spike., including C361, C379, C391, and C480. These regions share sequence similarity with Pep42, ranging from 15.38% to 46.15%. However, only one of them, i.e., region IV (GRAVY = 0.08), is a hydrophobic region, like Pep42 (GRAVY = 1.1). Structural models evaluate the energy contribution for region IV as a part of region III to the GRP78 to be about (−9.8 out of −14.0 kcal/mol), and the docking platform proposes region IV as the best region binding to GRP78. The region IV can be linked to the substrate-binding domain β (SBDB) of GRP78 using five H-bonds (through P479, N481, E484, and N487) and four hydrophobic interactions (through T478, E484, and F486)."}

LitCovid-sample-Glycan

2_test

{"project":"2_test","denotations":[{"id":"32413736-22258248-48112966","span":{"begin":1176,"end":1177},"obj":"22258248"},{"id":"32413736-29579213-48112967","span":{"begin":1547,"end":1548},"obj":"29579213"},{"id":"32413736-17398101-48112968","span":{"begin":2623,"end":2624},"obj":"17398101"},{"id":"T44212","span":{"begin":1176,"end":1177},"obj":"22258248"},{"id":"T49497","span":{"begin":1547,"end":1548},"obj":"29579213"},{"id":"T80973","span":{"begin":2623,"end":2624},"obj":"17398101"}],"text":"3 Certain characteristics of SARS-CoV2\n\n3.1 SARS-CoV2 has acquired an S glycoprotein that highly underwent genetic variation and glycosylation\n\n3.1.1 Polybasic cleavage site\nAs evidenced by sequence analysis, there is a residue insertion formed of four amino acids (12 nucleotides) at the boundary between S1 and S2 subunits of the SARS-CoV 2 S. It defines a polybasic furin cleavage site of RRAR for the human SARS-CoV 2 that was absent in human SARS-CoV, bat SARS-like CoVs, and pangolin SARS-like CoV while might be present in other species [3]. After the introduction of mutation to the residue insertion and furin cleavage site, the S1/S2 cleavage of the SARS-CoV 2 S did not longer take place. However, the SARS-CoV 2 S entry raised for VeroE6 cells and remained high in BHK cells that express human ACE. Therefore, it seems that SARS-CoV2 transmissibility does not depend on the S1/S2 cleavage.\nA polybasic cleavage site explains a virus that is highly-pathogenic for humans while it is low-pathogenic for other species. For example, using reverse genetic tools, an avian paramyxovirus type 7 (APMV-7) was developed by mutating the fusion (F) protein cleavage site [4]. The constructed APMV-7 showed furin cleavage and increased replication and syncytium formation in cell cultures. However, chicken exposed to the virus did not exhibit infection.\n\n3.1.2 Glycosylation\nGlycosylation and its related products, i.e., glycans, introduce changes to the viral envelope that make the virus fitted for interaction with the host cell membrane [5]. Generally, glycans are oligosaccharides linked to the dense decoration of the spike glycoprotein. In particular, these oligosaccharides have shown to influence the folding of the S protein and proteolytic process so that they facilitate the virus cell entry. Moreover, a virus with the glycosylated glycoprotein gains an extra feature for an escape from the immune responses. Therefore, glycans are a good target for vaccine design.\nTwo main types of glycans are N-linked and O-linked glycans. Both are released from glycoproteins. Whereas enzymes fulfill the construction of N-glycans, chemical methods perform the release of O-glycans. N-glycans are linked to the amino acid asparagine (Asn) residues (Asn-any amino acids except for proline- Ser or Thr) utilizing an N-glycosidic bond, mostly N-acetylglucosamine. O-glycans are attached to the amino acid serine (Ser) and threonine (Thr) residues by the addition of an N-acetyl galactosamine (GalNAc). For example, N-glycans exist in Hendra virus, SARS-CoV, influenza virus, hepatitis virus, HIV-1, and West Nile virus [6], and O-glycans have occurred in the Ebola virus.\nThe 2019-nCoV S protein includes 13 and 9N-linked glycosylation sequons in the S1 and S2 subunit, respectively [3]. All of these have previously occurred in the SARS-CoV S glycoprotein, except for four-linked glycosylation sequons in the S1. Also, due to the existence of an amino acid proline in the polybasic cleavage site, which makes the inserted sequence PRRA, there are three O-linked glycans introduced to the 2019-nCoV RBD residues S673, T678, and S686 [7].\n\n3.1.3 SARS-CoV2 receptor binding domain contains six amino acids providing favorable positions for binding to human ACE2\nWhen compared to SARS-CoV SB, the motif binding the human ACE2 to the SARS-CoV 2 SB showed a relatively higher binding affinity for human ACE2 as indicated in smaller equilibrium dissociation constant (2.9 nM vs. 7.7 nM) [3]. Structural analysis has demonstrated that fourteen positions critically take part in the receptor-binding domain of the SARS-CoV SB that contain eight conserved (T402, Y436, Y440, N473, Y475, T486, G488, and Y491) positions and six semi-conserved (R426 to N448, Y442 to L464, L472 to F495, N479 to Q502, Y484 to Q507, and T487 to N510) substitutions with respect to the SARS-CoV 2 SB.\n\n3.1.4 SARS-CoV2 receptor binding domain contains cyclic regions that can make interaction with cell-surface GRP78\nPep42 is a cyclic oligopeptide that, with its hydrophobic character, can selectively interact with cell surface glucose‐regulated protein 78 (GRP78), a member of 70 kDa heat shock proteins. GRP78, also known as BiP or HSPA5, under endoplasmic reticulum stress, can be translocated from the endoplasmic reticulum to the membrane and helps to maintain cellular integrity under physiologic and pathological stress. It critically contributes to various functions ranging from protein folding, transportation, and degradation to cell-signaling, proliferation, survival, apoptosis, inflammation, and immunity. The expression of GRP78 decreases with age.\nOn the 2019-nCoV spike protein, 13 disulfide bonds are corresponding to 13 different cyclic regions thought to be similar to the cyclic form of Pep42 [8]. Among these, four regions I-IV take place in the outer surface of a putative receptor-binding domain (RBD) on the viral spike., including C361, C379, C391, and C480. These regions share sequence similarity with Pep42, ranging from 15.38% to 46.15%. However, only one of them, i.e., region IV (GRAVY = 0.08), is a hydrophobic region, like Pep42 (GRAVY = 1.1). Structural models evaluate the energy contribution for region IV as a part of region III to the GRP78 to be about (−9.8 out of −14.0 kcal/mol), and the docking platform proposes region IV as the best region binding to GRP78. The region IV can be linked to the substrate-binding domain β (SBDB) of GRP78 using five H-bonds (through P479, N481, E484, and N487) and four hydrophobic interactions (through T478, E484, and F486)."}

PMC:7205724 / 3952-9529 JSONTXT

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PMC:7205724 / 3952-9529 JSON TXT