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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T14","span":{"begin":950,"end":954},"obj":"Body_part"},{"id":"T15","span":{"begin":1022,"end":1026},"obj":"Body_part"},{"id":"T16","span":{"begin":2042,"end":2046},"obj":"Body_part"},{"id":"T17","span":{"begin":2100,"end":2105},"obj":"Body_part"},{"id":"T18","span":{"begin":2261,"end":2265},"obj":"Body_part"}],"attributes":[{"id":"A14","pred":"uberon_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/UBERON_0002398"},{"id":"A15","pred":"uberon_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/UBERON_0002398"},{"id":"A16","pred":"uberon_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/UBERON_0000974"},{"id":"A17","pred":"uberon_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/UBERON_0002488"},{"id":"A18","pred":"uberon_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/UBERON_0000974"}],"text":"The ACE2 interacts with the spike (S) protein, thereby serves as an entry receptor for SARS-CoVs, and this event is likely followed by conformational changes, cleavages and fusion of both spike viral and ACE2 proteins at the level of infected host cell plasma-membrane. The SARS coronavirus surface spike glycoproteins consist of trimers formed by two spike, capsid-distal S1 and –proximal S2, protein regions, located on the outer envelope of the virion. Spike proteins are clove-shaped trimers with three S1 heads and a trimeric S2 stalk that can bind the cellular ACE2 receptor when one S1 (possessing the receptor-binding domain) in the trimer adopts an “up” conformation (see Figure later in the Section 4). The subsequent binding of ACE2 receptor to the spike glycoprotein triggers both the ADAM17-mediated ACE2 shedding and dissociation of S1 fragments by exogenous (furin-related or other) proteases from the spike trimer, which leads on one hand to one S1-ACE2 complex and two S1 free fragments, and on the other hand to fusion of S2 viral trimers and cellular membrane structures, finally producing cell infection. The molecular mechanism model for SARS-CoV recognition and infection was well described by Song and collaborators [26] and a similar molecular interactions between SARS-CoV-2 and ACE2 has been recently hypothesized [27,28]. To complete the picture, a recent structural work reveals that the full-length human ACE2 is assembled as a dimer associated or not with amino acid transporter B0AT1, which sandwich ACE2 [28]. Binding of the spike protein trimer onto the ACE2 dimer suggests simultaneous binding of two spike protein trimers to an ACE2 dimer [28]. Each monomer of the ACE2 homodimer is composed of a membrane-proximal collectrin-like domain mediating homodimerization and necessary to position the molecule to the cell membrane, and of a membrane-distal ACE2 peptidase domain responsible for ACE2 substrate cleavage. Collectrin-like domain consists of an extracellular ferredoxin-like fold domain, also called neck domain (residues 616 to 726), a single transmembrane helix and an intracellular segment. The ACE2 cleavage site mediated by ADAM17/TACE has been predicted between amino acids 716 and 741 [16], which corresponds to neck-transmembrane boundary of ACE2 collectrin-like domain. It is tempting to speculate that, after ACE2 shedding, S2 viral trimers may fuse with the residual ACE2 collectrin-like fragments (complexed or not with B0AT1 transporters) which are eventually exposed on the cell surface membranes. A model for SARS-CoV’s internalization by target cells that was already proposed several years ago [29]. Then, when the virus is inside the cell, a second proteolytic cleavage mediated by endosomal proteases (such as TMPRSS2) in the S2 region of the spike-ACE2 fusion protein might be necessary for intracellular virus “release” and active infection."}

LitCovid-PubTator

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T88","span":{"begin":87,"end":91},"obj":"Disease"},{"id":"T89","span":{"begin":274,"end":278},"obj":"Disease"},{"id":"T90","span":{"begin":1114,"end":1123},"obj":"Disease"},{"id":"T91","span":{"begin":1159,"end":1167},"obj":"Disease"},{"id":"T92","span":{"begin":1159,"end":1163},"obj":"Disease"},{"id":"T93","span":{"begin":1184,"end":1193},"obj":"Disease"},{"id":"T94","span":{"begin":1289,"end":1297},"obj":"Disease"},{"id":"T95","span":{"begin":1289,"end":1293},"obj":"Disease"},{"id":"T96","span":{"begin":2566,"end":2570},"obj":"Disease"},{"id":"T97","span":{"begin":2894,"end":2903},"obj":"Disease"}],"attributes":[{"id":"A88","pred":"mondo_id","subj":"T88","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A89","pred":"mondo_id","subj":"T89","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A90","pred":"mondo_id","subj":"T90","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A91","pred":"mondo_id","subj":"T91","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A92","pred":"mondo_id","subj":"T92","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A93","pred":"mondo_id","subj":"T93","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A94","pred":"mondo_id","subj":"T94","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A95","pred":"mondo_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A96","pred":"mondo_id","subj":"T96","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A97","pred":"mondo_id","subj":"T97","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"}],"text":"The ACE2 interacts with the spike (S) protein, thereby serves as an entry receptor for SARS-CoVs, and this event is likely followed by conformational changes, cleavages and fusion of both spike viral and ACE2 proteins at the level of infected host cell plasma-membrane. The SARS coronavirus surface spike glycoproteins consist of trimers formed by two spike, capsid-distal S1 and –proximal S2, protein regions, located on the outer envelope of the virion. Spike proteins are clove-shaped trimers with three S1 heads and a trimeric S2 stalk that can bind the cellular ACE2 receptor when one S1 (possessing the receptor-binding domain) in the trimer adopts an “up” conformation (see Figure later in the Section 4). The subsequent binding of ACE2 receptor to the spike glycoprotein triggers both the ADAM17-mediated ACE2 shedding and dissociation of S1 fragments by exogenous (furin-related or other) proteases from the spike trimer, which leads on one hand to one S1-ACE2 complex and two S1 free fragments, and on the other hand to fusion of S2 viral trimers and cellular membrane structures, finally producing cell infection. The molecular mechanism model for SARS-CoV recognition and infection was well described by Song and collaborators [26] and a similar molecular interactions between SARS-CoV-2 and ACE2 has been recently hypothesized [27,28]. To complete the picture, a recent structural work reveals that the full-length human ACE2 is assembled as a dimer associated or not with amino acid transporter B0AT1, which sandwich ACE2 [28]. Binding of the spike protein trimer onto the ACE2 dimer suggests simultaneous binding of two spike protein trimers to an ACE2 dimer [28]. Each monomer of the ACE2 homodimer is composed of a membrane-proximal collectrin-like domain mediating homodimerization and necessary to position the molecule to the cell membrane, and of a membrane-distal ACE2 peptidase domain responsible for ACE2 substrate cleavage. Collectrin-like domain consists of an extracellular ferredoxin-like fold domain, also called neck domain (residues 616 to 726), a single transmembrane helix and an intracellular segment. The ACE2 cleavage site mediated by ADAM17/TACE has been predicted between amino acids 716 and 741 [16], which corresponds to neck-transmembrane boundary of ACE2 collectrin-like domain. It is tempting to speculate that, after ACE2 shedding, S2 viral trimers may fuse with the residual ACE2 collectrin-like fragments (complexed or not with B0AT1 transporters) which are eventually exposed on the cell surface membranes. A model for SARS-CoV’s internalization by target cells that was already proposed several years ago [29]. Then, when the virus is inside the cell, a second proteolytic cleavage mediated by endosomal proteases (such as TMPRSS2) in the S2 region of the spike-ACE2 fusion protein might be necessary for intracellular virus “release” and active infection."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T54884","span":{"begin":1486,"end":1508},"obj":"http://purl.obolibrary.org/obo/GO_0006865"}],"text":"The ACE2 interacts with the spike (S) protein, thereby serves as an entry receptor for SARS-CoVs, and this event is likely followed by conformational changes, cleavages and fusion of both spike viral and ACE2 proteins at the level of infected host cell plasma-membrane. The SARS coronavirus surface spike glycoproteins consist of trimers formed by two spike, capsid-distal S1 and –proximal S2, protein regions, located on the outer envelope of the virion. Spike proteins are clove-shaped trimers with three S1 heads and a trimeric S2 stalk that can bind the cellular ACE2 receptor when one S1 (possessing the receptor-binding domain) in the trimer adopts an “up” conformation (see Figure later in the Section 4). The subsequent binding of ACE2 receptor to the spike glycoprotein triggers both the ADAM17-mediated ACE2 shedding and dissociation of S1 fragments by exogenous (furin-related or other) proteases from the spike trimer, which leads on one hand to one S1-ACE2 complex and two S1 free fragments, and on the other hand to fusion of S2 viral trimers and cellular membrane structures, finally producing cell infection. The molecular mechanism model for SARS-CoV recognition and infection was well described by Song and collaborators [26] and a similar molecular interactions between SARS-CoV-2 and ACE2 has been recently hypothesized [27,28]. To complete the picture, a recent structural work reveals that the full-length human ACE2 is assembled as a dimer associated or not with amino acid transporter B0AT1, which sandwich ACE2 [28]. Binding of the spike protein trimer onto the ACE2 dimer suggests simultaneous binding of two spike protein trimers to an ACE2 dimer [28]. Each monomer of the ACE2 homodimer is composed of a membrane-proximal collectrin-like domain mediating homodimerization and necessary to position the molecule to the cell membrane, and of a membrane-distal ACE2 peptidase domain responsible for ACE2 substrate cleavage. Collectrin-like domain consists of an extracellular ferredoxin-like fold domain, also called neck domain (residues 616 to 726), a single transmembrane helix and an intracellular segment. The ACE2 cleavage site mediated by ADAM17/TACE has been predicted between amino acids 716 and 741 [16], which corresponds to neck-transmembrane boundary of ACE2 collectrin-like domain. It is tempting to speculate that, after ACE2 shedding, S2 viral trimers may fuse with the residual ACE2 collectrin-like fragments (complexed or not with B0AT1 transporters) which are eventually exposed on the cell surface membranes. A model for SARS-CoV’s internalization by target cells that was already proposed several years ago [29]. Then, when the virus is inside the cell, a second proteolytic cleavage mediated by endosomal proteases (such as TMPRSS2) in the S2 region of the spike-ACE2 fusion protein might be necessary for intracellular virus “release” and active infection."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T41","span":{"begin":0,"end":269},"obj":"Sentence"},{"id":"T42","span":{"begin":270,"end":455},"obj":"Sentence"},{"id":"T43","span":{"begin":456,"end":712},"obj":"Sentence"},{"id":"T44","span":{"begin":713,"end":1124},"obj":"Sentence"},{"id":"T45","span":{"begin":1125,"end":1348},"obj":"Sentence"},{"id":"T46","span":{"begin":1349,"end":1541},"obj":"Sentence"},{"id":"T47","span":{"begin":1542,"end":1679},"obj":"Sentence"},{"id":"T48","span":{"begin":1680,"end":1948},"obj":"Sentence"},{"id":"T49","span":{"begin":1949,"end":2135},"obj":"Sentence"},{"id":"T50","span":{"begin":2136,"end":2320},"obj":"Sentence"},{"id":"T51","span":{"begin":2321,"end":2553},"obj":"Sentence"},{"id":"T52","span":{"begin":2554,"end":2658},"obj":"Sentence"},{"id":"T53","span":{"begin":2659,"end":2904},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The ACE2 interacts with the spike (S) protein, thereby serves as an entry receptor for SARS-CoVs, and this event is likely followed by conformational changes, cleavages and fusion of both spike viral and ACE2 proteins at the level of infected host cell plasma-membrane. The SARS coronavirus surface spike glycoproteins consist of trimers formed by two spike, capsid-distal S1 and –proximal S2, protein regions, located on the outer envelope of the virion. Spike proteins are clove-shaped trimers with three S1 heads and a trimeric S2 stalk that can bind the cellular ACE2 receptor when one S1 (possessing the receptor-binding domain) in the trimer adopts an “up” conformation (see Figure later in the Section 4). The subsequent binding of ACE2 receptor to the spike glycoprotein triggers both the ADAM17-mediated ACE2 shedding and dissociation of S1 fragments by exogenous (furin-related or other) proteases from the spike trimer, which leads on one hand to one S1-ACE2 complex and two S1 free fragments, and on the other hand to fusion of S2 viral trimers and cellular membrane structures, finally producing cell infection. The molecular mechanism model for SARS-CoV recognition and infection was well described by Song and collaborators [26] and a similar molecular interactions between SARS-CoV-2 and ACE2 has been recently hypothesized [27,28]. To complete the picture, a recent structural work reveals that the full-length human ACE2 is assembled as a dimer associated or not with amino acid transporter B0AT1, which sandwich ACE2 [28]. Binding of the spike protein trimer onto the ACE2 dimer suggests simultaneous binding of two spike protein trimers to an ACE2 dimer [28]. Each monomer of the ACE2 homodimer is composed of a membrane-proximal collectrin-like domain mediating homodimerization and necessary to position the molecule to the cell membrane, and of a membrane-distal ACE2 peptidase domain responsible for ACE2 substrate cleavage. Collectrin-like domain consists of an extracellular ferredoxin-like fold domain, also called neck domain (residues 616 to 726), a single transmembrane helix and an intracellular segment. The ACE2 cleavage site mediated by ADAM17/TACE has been predicted between amino acids 716 and 741 [16], which corresponds to neck-transmembrane boundary of ACE2 collectrin-like domain. It is tempting to speculate that, after ACE2 shedding, S2 viral trimers may fuse with the residual ACE2 collectrin-like fragments (complexed or not with B0AT1 transporters) which are eventually exposed on the cell surface membranes. A model for SARS-CoV’s internalization by target cells that was already proposed several years ago [29]. Then, when the virus is inside the cell, a second proteolytic cleavage mediated by endosomal proteases (such as TMPRSS2) in the S2 region of the spike-ACE2 fusion protein might be necessary for intracellular virus “release” and active infection."}

2_test

{"project":"2_test","denotations":[{"id":"32708755-30102747-20678677","span":{"begin":1240,"end":1242},"obj":"30102747"},{"id":"32708755-32075877-20678678","span":{"begin":1341,"end":1343},"obj":"32075877"},{"id":"32708755-32132184-20678679","span":{"begin":1344,"end":1346},"obj":"32132184"},{"id":"32708755-32132184-20678680","span":{"begin":1537,"end":1539},"obj":"32132184"},{"id":"32708755-32132184-20678681","span":{"begin":1675,"end":1677},"obj":"32132184"},{"id":"32708755-17522231-20678682","span":{"begin":2654,"end":2656},"obj":"17522231"}],"text":"The ACE2 interacts with the spike (S) protein, thereby serves as an entry receptor for SARS-CoVs, and this event is likely followed by conformational changes, cleavages and fusion of both spike viral and ACE2 proteins at the level of infected host cell plasma-membrane. The SARS coronavirus surface spike glycoproteins consist of trimers formed by two spike, capsid-distal S1 and –proximal S2, protein regions, located on the outer envelope of the virion. Spike proteins are clove-shaped trimers with three S1 heads and a trimeric S2 stalk that can bind the cellular ACE2 receptor when one S1 (possessing the receptor-binding domain) in the trimer adopts an “up” conformation (see Figure later in the Section 4). The subsequent binding of ACE2 receptor to the spike glycoprotein triggers both the ADAM17-mediated ACE2 shedding and dissociation of S1 fragments by exogenous (furin-related or other) proteases from the spike trimer, which leads on one hand to one S1-ACE2 complex and two S1 free fragments, and on the other hand to fusion of S2 viral trimers and cellular membrane structures, finally producing cell infection. The molecular mechanism model for SARS-CoV recognition and infection was well described by Song and collaborators [26] and a similar molecular interactions between SARS-CoV-2 and ACE2 has been recently hypothesized [27,28]. To complete the picture, a recent structural work reveals that the full-length human ACE2 is assembled as a dimer associated or not with amino acid transporter B0AT1, which sandwich ACE2 [28]. Binding of the spike protein trimer onto the ACE2 dimer suggests simultaneous binding of two spike protein trimers to an ACE2 dimer [28]. Each monomer of the ACE2 homodimer is composed of a membrane-proximal collectrin-like domain mediating homodimerization and necessary to position the molecule to the cell membrane, and of a membrane-distal ACE2 peptidase domain responsible for ACE2 substrate cleavage. Collectrin-like domain consists of an extracellular ferredoxin-like fold domain, also called neck domain (residues 616 to 726), a single transmembrane helix and an intracellular segment. The ACE2 cleavage site mediated by ADAM17/TACE has been predicted between amino acids 716 and 741 [16], which corresponds to neck-transmembrane boundary of ACE2 collectrin-like domain. It is tempting to speculate that, after ACE2 shedding, S2 viral trimers may fuse with the residual ACE2 collectrin-like fragments (complexed or not with B0AT1 transporters) which are eventually exposed on the cell surface membranes. A model for SARS-CoV’s internalization by target cells that was already proposed several years ago [29]. Then, when the virus is inside the cell, a second proteolytic cleavage mediated by endosomal proteases (such as TMPRSS2) in the S2 region of the spike-ACE2 fusion protein might be necessary for intracellular virus “release” and active infection."}

PMC:7408073 / 7989-10893 JSONTXT

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PMC:7408073 / 7989-10893 JSON TXT