PMC:7556165 / 49779-52427 JSON TXT

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LitCovid-sample-CHEBI

{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T162","span":{"begin":426,"end":433},"obj":"Chemical"},{"id":"T163","span":{"begin":657,"end":664},"obj":"Chemical"},{"id":"T164","span":{"begin":1636,"end":1647},"obj":"Chemical"},{"id":"T165","span":{"begin":1674,"end":1685},"obj":"Chemical"},{"id":"T166","span":{"begin":1686,"end":1689},"obj":"Chemical"},{"id":"T167","span":{"begin":1916,"end":1919},"obj":"Chemical"}],"attributes":[{"id":"A162","pred":"chebi_id","subj":"T162","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A163","pred":"chebi_id","subj":"T163","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A164","pred":"chebi_id","subj":"T164","obj":"http://purl.obolibrary.org/obo/CHEBI_162578"},{"id":"A165","pred":"chebi_id","subj":"T165","obj":"http://purl.obolibrary.org/obo/CHEBI_164159"},{"id":"A166","pred":"chebi_id","subj":"T166","obj":"http://purl.obolibrary.org/obo/CHEBI_15428"},{"id":"A167","pred":"chebi_id","subj":"T167","obj":"http://purl.obolibrary.org/obo/CHEBI_17191"},{"id":"A168","pred":"chebi_id","subj":"T167","obj":"http://purl.obolibrary.org/obo/CHEBI_30009"}],"text":"In spite of the recent emergence of SARS-CoV-2, multiple authors have already highlighted the structure of ACE2/SARS-CoV-2 RBD complex by either X-ray (Lan et al., 2020; Shang et al., 2020b; Wang et al., 2020) or cryo-EM (Walls et al., 2020; Wrapp et al., 2020; Yan et al., 2020). Pleasantly, all data converged to a consistent tridimensional arrangement of the receptor (Wang et al., 2020). In the “closed” conformation of S protein, the RBD is buried at the interface between protomers (Walls et al., 2020). Only in the “open” S conformation, RBD engages PD of ACE2 (Wrapp et al., 2020), and the complex may involve a dimeric ACE2 that accommodates two S protein trimers (Yan et al., 2020). In keeping with their sequence similarity, strong structural homology was found between ACE2/SARS-CoV RBD and ACE2/SARS-CoV-2 RBD (Lan et al., 2020; Shang et al., 2020b; Wang et al., 2020). SARS-CoV-2 RBM spans from residue 438–506 of S sequence and, likewise SARS-CoV RBM, it approaches the outer surface of ACE2 by a gently concave surface with a ridge on one side (Figure 8). The concave surface is made up by the two short β5 and β6 sheets of the external RBD subdomain, whereas the ridge contains the β5/β6 loop (loop 1: residues 474–489). A second smaller loop (loop 2: residues 498–505) is visible on the other side of the concave surface. Inspection of the complex structure and molecular dynamics (MD) highlighted that the motifs 453–456 (in β5), 484–489 (in the loop 1), and 500–505 (in the loop 2) are at the basis of the largest differences between SARS-CoV-2 and SARS-CoV RBM interactions with ACE2. SARS-CoV RBM ridge contains a Pro-Pro-Ala motif that is replaced by Gly-Val-Glu-Gly in SARS-CoV-2 (residues 482–485), yielding a more compact loop able to engage more interactions with proximal ACE2 residues (e.g., Ser19 and Gln24) (Shang et al., 2020b). Additionally, Phe486 of SARS-CoV-2 RBM (which replaces Ile of SARS) inserts into a hydrophobic pocket on the receptor surface, establishing strong aromatic interactions with Tyr83 of ACE2 (Wang et al., 2020). Asn501 in loop 2 further engages recognized hotspots on the ACE2 surface (Shang et al., 2020b). Consistently, MD studies confirmed that loop 1 and 2 are much more rigid in RBM-ACE2 complex of SARS-CoV-2 with respect to SARS (Brielle et al., 2020). These subtle structural differences probably account for the higher affinity of SARS-CoV-2 for ACE2 (Wang et al., 2020). Interestingly, MD simulations suggest that the difference in affinity is largely due to the solvation energy, emphasizing the relevant role of hydrophobic patches in RBM/ACE2 binding surface (He et al., 2020)."}

LitCovid-sample-PD-NCBITaxon

LitCovid-sample-sentences

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T312","span":{"begin":0,"end":280},"obj":"Sentence"},{"id":"T313","span":{"begin":281,"end":391},"obj":"Sentence"},{"id":"T314","span":{"begin":392,"end":509},"obj":"Sentence"},{"id":"T315","span":{"begin":510,"end":692},"obj":"Sentence"},{"id":"T316","span":{"begin":693,"end":882},"obj":"Sentence"},{"id":"T317","span":{"begin":883,"end":1071},"obj":"Sentence"},{"id":"T318","span":{"begin":1072,"end":1237},"obj":"Sentence"},{"id":"T319","span":{"begin":1238,"end":1339},"obj":"Sentence"},{"id":"T320","span":{"begin":1340,"end":1605},"obj":"Sentence"},{"id":"T321","span":{"begin":1606,"end":1860},"obj":"Sentence"},{"id":"T322","span":{"begin":1861,"end":2069},"obj":"Sentence"},{"id":"T323","span":{"begin":2070,"end":2165},"obj":"Sentence"},{"id":"T324","span":{"begin":2166,"end":2317},"obj":"Sentence"},{"id":"T325","span":{"begin":2318,"end":2438},"obj":"Sentence"},{"id":"T326","span":{"begin":2439,"end":2648},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"In spite of the recent emergence of SARS-CoV-2, multiple authors have already highlighted the structure of ACE2/SARS-CoV-2 RBD complex by either X-ray (Lan et al., 2020; Shang et al., 2020b; Wang et al., 2020) or cryo-EM (Walls et al., 2020; Wrapp et al., 2020; Yan et al., 2020). Pleasantly, all data converged to a consistent tridimensional arrangement of the receptor (Wang et al., 2020). In the “closed” conformation of S protein, the RBD is buried at the interface between protomers (Walls et al., 2020). Only in the “open” S conformation, RBD engages PD of ACE2 (Wrapp et al., 2020), and the complex may involve a dimeric ACE2 that accommodates two S protein trimers (Yan et al., 2020). In keeping with their sequence similarity, strong structural homology was found between ACE2/SARS-CoV RBD and ACE2/SARS-CoV-2 RBD (Lan et al., 2020; Shang et al., 2020b; Wang et al., 2020). SARS-CoV-2 RBM spans from residue 438–506 of S sequence and, likewise SARS-CoV RBM, it approaches the outer surface of ACE2 by a gently concave surface with a ridge on one side (Figure 8). The concave surface is made up by the two short β5 and β6 sheets of the external RBD subdomain, whereas the ridge contains the β5/β6 loop (loop 1: residues 474–489). A second smaller loop (loop 2: residues 498–505) is visible on the other side of the concave surface. Inspection of the complex structure and molecular dynamics (MD) highlighted that the motifs 453–456 (in β5), 484–489 (in the loop 1), and 500–505 (in the loop 2) are at the basis of the largest differences between SARS-CoV-2 and SARS-CoV RBM interactions with ACE2. SARS-CoV RBM ridge contains a Pro-Pro-Ala motif that is replaced by Gly-Val-Glu-Gly in SARS-CoV-2 (residues 482–485), yielding a more compact loop able to engage more interactions with proximal ACE2 residues (e.g., Ser19 and Gln24) (Shang et al., 2020b). Additionally, Phe486 of SARS-CoV-2 RBM (which replaces Ile of SARS) inserts into a hydrophobic pocket on the receptor surface, establishing strong aromatic interactions with Tyr83 of ACE2 (Wang et al., 2020). Asn501 in loop 2 further engages recognized hotspots on the ACE2 surface (Shang et al., 2020b). Consistently, MD studies confirmed that loop 1 and 2 are much more rigid in RBM-ACE2 complex of SARS-CoV-2 with respect to SARS (Brielle et al., 2020). These subtle structural differences probably account for the higher affinity of SARS-CoV-2 for ACE2 (Wang et al., 2020). Interestingly, MD simulations suggest that the difference in affinity is largely due to the solvation energy, emphasizing the relevant role of hydrophobic patches in RBM/ACE2 binding surface (He et al., 2020)."}

LitCovid-sample-Pubtator

LitCovid-sample-UniProt

LitCovid-sample-PD-FMA

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T389","span":{"begin":426,"end":433},"obj":"Body_part"},{"id":"T390","span":{"begin":657,"end":664},"obj":"Body_part"},{"id":"T391","span":{"begin":1042,"end":1047},"obj":"Body_part"},{"id":"T392","span":{"begin":1180,"end":1185},"obj":"Body_part"},{"id":"T393","span":{"begin":1619,"end":1624},"obj":"Body_part"}],"attributes":[{"id":"A389","pred":"fma_id","subj":"T389","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A390","pred":"fma_id","subj":"T390","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A391","pred":"fma_id","subj":"T391","obj":"http://purl.org/sig/ont/fma/fma75035"},{"id":"A392","pred":"fma_id","subj":"T392","obj":"http://purl.org/sig/ont/fma/fma75035"},{"id":"A393","pred":"fma_id","subj":"T393","obj":"http://purl.org/sig/ont/fma/fma75035"}],"text":"In spite of the recent emergence of SARS-CoV-2, multiple authors have already highlighted the structure of ACE2/SARS-CoV-2 RBD complex by either X-ray (Lan et al., 2020; Shang et al., 2020b; Wang et al., 2020) or cryo-EM (Walls et al., 2020; Wrapp et al., 2020; Yan et al., 2020). Pleasantly, all data converged to a consistent tridimensional arrangement of the receptor (Wang et al., 2020). In the “closed” conformation of S protein, the RBD is buried at the interface between protomers (Walls et al., 2020). Only in the “open” S conformation, RBD engages PD of ACE2 (Wrapp et al., 2020), and the complex may involve a dimeric ACE2 that accommodates two S protein trimers (Yan et al., 2020). In keeping with their sequence similarity, strong structural homology was found between ACE2/SARS-CoV RBD and ACE2/SARS-CoV-2 RBD (Lan et al., 2020; Shang et al., 2020b; Wang et al., 2020). SARS-CoV-2 RBM spans from residue 438–506 of S sequence and, likewise SARS-CoV RBM, it approaches the outer surface of ACE2 by a gently concave surface with a ridge on one side (Figure 8). The concave surface is made up by the two short β5 and β6 sheets of the external RBD subdomain, whereas the ridge contains the β5/β6 loop (loop 1: residues 474–489). A second smaller loop (loop 2: residues 498–505) is visible on the other side of the concave surface. Inspection of the complex structure and molecular dynamics (MD) highlighted that the motifs 453–456 (in β5), 484–489 (in the loop 1), and 500–505 (in the loop 2) are at the basis of the largest differences between SARS-CoV-2 and SARS-CoV RBM interactions with ACE2. SARS-CoV RBM ridge contains a Pro-Pro-Ala motif that is replaced by Gly-Val-Glu-Gly in SARS-CoV-2 (residues 482–485), yielding a more compact loop able to engage more interactions with proximal ACE2 residues (e.g., Ser19 and Gln24) (Shang et al., 2020b). Additionally, Phe486 of SARS-CoV-2 RBM (which replaces Ile of SARS) inserts into a hydrophobic pocket on the receptor surface, establishing strong aromatic interactions with Tyr83 of ACE2 (Wang et al., 2020). Asn501 in loop 2 further engages recognized hotspots on the ACE2 surface (Shang et al., 2020b). Consistently, MD studies confirmed that loop 1 and 2 are much more rigid in RBM-ACE2 complex of SARS-CoV-2 with respect to SARS (Brielle et al., 2020). These subtle structural differences probably account for the higher affinity of SARS-CoV-2 for ACE2 (Wang et al., 2020). Interestingly, MD simulations suggest that the difference in affinity is largely due to the solvation energy, emphasizing the relevant role of hydrophobic patches in RBM/ACE2 binding surface (He et al., 2020)."}

LitCovid-sample-PD-MONDO

LitCovid-sample-PD-MAT

{"project":"LitCovid-sample-PD-MAT","denotations":[{"id":"T127","span":{"begin":1791,"end":1799},"obj":"http://purl.obolibrary.org/obo/MAT_0000491"}],"text":"In spite of the recent emergence of SARS-CoV-2, multiple authors have already highlighted the structure of ACE2/SARS-CoV-2 RBD complex by either X-ray (Lan et al., 2020; Shang et al., 2020b; Wang et al., 2020) or cryo-EM (Walls et al., 2020; Wrapp et al., 2020; Yan et al., 2020). Pleasantly, all data converged to a consistent tridimensional arrangement of the receptor (Wang et al., 2020). In the “closed” conformation of S protein, the RBD is buried at the interface between protomers (Walls et al., 2020). Only in the “open” S conformation, RBD engages PD of ACE2 (Wrapp et al., 2020), and the complex may involve a dimeric ACE2 that accommodates two S protein trimers (Yan et al., 2020). In keeping with their sequence similarity, strong structural homology was found between ACE2/SARS-CoV RBD and ACE2/SARS-CoV-2 RBD (Lan et al., 2020; Shang et al., 2020b; Wang et al., 2020). SARS-CoV-2 RBM spans from residue 438–506 of S sequence and, likewise SARS-CoV RBM, it approaches the outer surface of ACE2 by a gently concave surface with a ridge on one side (Figure 8). The concave surface is made up by the two short β5 and β6 sheets of the external RBD subdomain, whereas the ridge contains the β5/β6 loop (loop 1: residues 474–489). A second smaller loop (loop 2: residues 498–505) is visible on the other side of the concave surface. Inspection of the complex structure and molecular dynamics (MD) highlighted that the motifs 453–456 (in β5), 484–489 (in the loop 1), and 500–505 (in the loop 2) are at the basis of the largest differences between SARS-CoV-2 and SARS-CoV RBM interactions with ACE2. SARS-CoV RBM ridge contains a Pro-Pro-Ala motif that is replaced by Gly-Val-Glu-Gly in SARS-CoV-2 (residues 482–485), yielding a more compact loop able to engage more interactions with proximal ACE2 residues (e.g., Ser19 and Gln24) (Shang et al., 2020b). Additionally, Phe486 of SARS-CoV-2 RBM (which replaces Ile of SARS) inserts into a hydrophobic pocket on the receptor surface, establishing strong aromatic interactions with Tyr83 of ACE2 (Wang et al., 2020). Asn501 in loop 2 further engages recognized hotspots on the ACE2 surface (Shang et al., 2020b). Consistently, MD studies confirmed that loop 1 and 2 are much more rigid in RBM-ACE2 complex of SARS-CoV-2 with respect to SARS (Brielle et al., 2020). These subtle structural differences probably account for the higher affinity of SARS-CoV-2 for ACE2 (Wang et al., 2020). Interestingly, MD simulations suggest that the difference in affinity is largely due to the solvation energy, emphasizing the relevant role of hydrophobic patches in RBM/ACE2 binding surface (He et al., 2020)."}

LitCovid-PubTator

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T312","span":{"begin":0,"end":280},"obj":"Sentence"},{"id":"T313","span":{"begin":281,"end":391},"obj":"Sentence"},{"id":"T314","span":{"begin":392,"end":509},"obj":"Sentence"},{"id":"T315","span":{"begin":510,"end":692},"obj":"Sentence"},{"id":"T316","span":{"begin":693,"end":882},"obj":"Sentence"},{"id":"T317","span":{"begin":883,"end":1071},"obj":"Sentence"},{"id":"T318","span":{"begin":1072,"end":1237},"obj":"Sentence"},{"id":"T319","span":{"begin":1238,"end":1339},"obj":"Sentence"},{"id":"T320","span":{"begin":1340,"end":1605},"obj":"Sentence"},{"id":"T321","span":{"begin":1606,"end":1860},"obj":"Sentence"},{"id":"T322","span":{"begin":1861,"end":2069},"obj":"Sentence"},{"id":"T323","span":{"begin":2070,"end":2165},"obj":"Sentence"},{"id":"T324","span":{"begin":2166,"end":2317},"obj":"Sentence"},{"id":"T325","span":{"begin":2318,"end":2438},"obj":"Sentence"},{"id":"T326","span":{"begin":2439,"end":2648},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"In spite of the recent emergence of SARS-CoV-2, multiple authors have already highlighted the structure of ACE2/SARS-CoV-2 RBD complex by either X-ray (Lan et al., 2020; Shang et al., 2020b; Wang et al., 2020) or cryo-EM (Walls et al., 2020; Wrapp et al., 2020; Yan et al., 2020). Pleasantly, all data converged to a consistent tridimensional arrangement of the receptor (Wang et al., 2020). In the “closed” conformation of S protein, the RBD is buried at the interface between protomers (Walls et al., 2020). Only in the “open” S conformation, RBD engages PD of ACE2 (Wrapp et al., 2020), and the complex may involve a dimeric ACE2 that accommodates two S protein trimers (Yan et al., 2020). In keeping with their sequence similarity, strong structural homology was found between ACE2/SARS-CoV RBD and ACE2/SARS-CoV-2 RBD (Lan et al., 2020; Shang et al., 2020b; Wang et al., 2020). SARS-CoV-2 RBM spans from residue 438–506 of S sequence and, likewise SARS-CoV RBM, it approaches the outer surface of ACE2 by a gently concave surface with a ridge on one side (Figure 8). The concave surface is made up by the two short β5 and β6 sheets of the external RBD subdomain, whereas the ridge contains the β5/β6 loop (loop 1: residues 474–489). A second smaller loop (loop 2: residues 498–505) is visible on the other side of the concave surface. Inspection of the complex structure and molecular dynamics (MD) highlighted that the motifs 453–456 (in β5), 484–489 (in the loop 1), and 500–505 (in the loop 2) are at the basis of the largest differences between SARS-CoV-2 and SARS-CoV RBM interactions with ACE2. SARS-CoV RBM ridge contains a Pro-Pro-Ala motif that is replaced by Gly-Val-Glu-Gly in SARS-CoV-2 (residues 482–485), yielding a more compact loop able to engage more interactions with proximal ACE2 residues (e.g., Ser19 and Gln24) (Shang et al., 2020b). Additionally, Phe486 of SARS-CoV-2 RBM (which replaces Ile of SARS) inserts into a hydrophobic pocket on the receptor surface, establishing strong aromatic interactions with Tyr83 of ACE2 (Wang et al., 2020). Asn501 in loop 2 further engages recognized hotspots on the ACE2 surface (Shang et al., 2020b). Consistently, MD studies confirmed that loop 1 and 2 are much more rigid in RBM-ACE2 complex of SARS-CoV-2 with respect to SARS (Brielle et al., 2020). These subtle structural differences probably account for the higher affinity of SARS-CoV-2 for ACE2 (Wang et al., 2020). Interestingly, MD simulations suggest that the difference in affinity is largely due to the solvation energy, emphasizing the relevant role of hydrophobic patches in RBM/ACE2 binding surface (He et al., 2020)."}

PMC:7556165 / 49779-52427 JSONTXT

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PMC:7556165 / 49779-52427 JSON TXT