PMC:7605337 / 39117-40490 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T57","span":{"begin":151,"end":158},"obj":"Body_part"},{"id":"T58","span":{"begin":778,"end":785},"obj":"Body_part"}],"attributes":[{"id":"A57","pred":"fma_id","subj":"T57","obj":"http://purl.org/sig/ont/fma/fma82749"},{"id":"A58","pred":"fma_id","subj":"T58","obj":"http://purl.org/sig/ont/fma/fma82749"}],"text":"H-bond analysis was also performed for the mutant systems and the results for H-bonds with more than 40% consistency are shown in Table S3. Few of the alanine substitutions increase the number of interfacial H-bonds between nCOV-2019 RBD and ACE2. Interestingly, the ala-substitution at Y489A increased the number of H-bonds in the wild-type complex. Mutation in some of the residues having consistent H-bonds in the wild type complex such as Q498A and Q493A, stunningly maintain the number of H-bonds in the wild-type complex. This indicates that the plasticity in the network of H-bonds in RBM of nCOV-2019 can reshape the network and strengthen other H-bonds upon mutation in these locations. However, few mutations decrease the number of H-bonds from the wild-type complex. Alanine substitution at residue G502 has a significant effect on the network of H-bonds between nCOV-2019 and SARS-COV. This residue locates at the end of L4 loop near two other important residues Q498 and T500. This mutation breaks the H-bonds at these residues. Mutation K417A decreases the number of H-bonds to only 5 where the H-bond at residue Q498 is broken. This indicates the delicate nature of the H-bond from residue Q498 which can easily be broken upon ala-substitution at other residues. Furthermore, mutation N487 also decreases the number of H-bonds by breaking the H-bond at Q498."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T270","span":{"begin":224,"end":233},"obj":"Disease"},{"id":"T271","span":{"begin":599,"end":608},"obj":"Disease"},{"id":"T272","span":{"begin":874,"end":883},"obj":"Disease"},{"id":"T273","span":{"begin":888,"end":892},"obj":"Disease"}],"attributes":[{"id":"A270","pred":"mondo_id","subj":"T270","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A271","pred":"mondo_id","subj":"T271","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A272","pred":"mondo_id","subj":"T272","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A273","pred":"mondo_id","subj":"T273","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"H-bond analysis was also performed for the mutant systems and the results for H-bonds with more than 40% consistency are shown in Table S3. Few of the alanine substitutions increase the number of interfacial H-bonds between nCOV-2019 RBD and ACE2. Interestingly, the ala-substitution at Y489A increased the number of H-bonds in the wild-type complex. Mutation in some of the residues having consistent H-bonds in the wild type complex such as Q498A and Q493A, stunningly maintain the number of H-bonds in the wild-type complex. This indicates that the plasticity in the network of H-bonds in RBM of nCOV-2019 can reshape the network and strengthen other H-bonds upon mutation in these locations. However, few mutations decrease the number of H-bonds from the wild-type complex. Alanine substitution at residue G502 has a significant effect on the network of H-bonds between nCOV-2019 and SARS-COV. This residue locates at the end of L4 loop near two other important residues Q498 and T500. This mutation breaks the H-bonds at these residues. Mutation K417A decreases the number of H-bonds to only 5 where the H-bond at residue Q498 is broken. This indicates the delicate nature of the H-bond from residue Q498 which can easily be broken upon ala-substitution at other residues. Furthermore, mutation N487 also decreases the number of H-bonds by breaking the H-bond at Q498."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T246","span":{"begin":815,"end":818},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T247","span":{"begin":819,"end":820},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"H-bond analysis was also performed for the mutant systems and the results for H-bonds with more than 40% consistency are shown in Table S3. Few of the alanine substitutions increase the number of interfacial H-bonds between nCOV-2019 RBD and ACE2. Interestingly, the ala-substitution at Y489A increased the number of H-bonds in the wild-type complex. Mutation in some of the residues having consistent H-bonds in the wild type complex such as Q498A and Q493A, stunningly maintain the number of H-bonds in the wild-type complex. This indicates that the plasticity in the network of H-bonds in RBM of nCOV-2019 can reshape the network and strengthen other H-bonds upon mutation in these locations. However, few mutations decrease the number of H-bonds from the wild-type complex. Alanine substitution at residue G502 has a significant effect on the network of H-bonds between nCOV-2019 and SARS-COV. This residue locates at the end of L4 loop near two other important residues Q498 and T500. This mutation breaks the H-bonds at these residues. Mutation K417A decreases the number of H-bonds to only 5 where the H-bond at residue Q498 is broken. This indicates the delicate nature of the H-bond from residue Q498 which can easily be broken upon ala-substitution at other residues. Furthermore, mutation N487 also decreases the number of H-bonds by breaking the H-bond at Q498."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T122","span":{"begin":136,"end":138},"obj":"Chemical"},{"id":"T123","span":{"begin":151,"end":158},"obj":"Chemical"},{"id":"T124","span":{"begin":778,"end":785},"obj":"Chemical"}],"attributes":[{"id":"A122","pred":"chebi_id","subj":"T122","obj":"http://purl.obolibrary.org/obo/CHEBI_29388"},{"id":"A123","pred":"chebi_id","subj":"T123","obj":"http://purl.obolibrary.org/obo/CHEBI_16449"},{"id":"A124","pred":"chebi_id","subj":"T124","obj":"http://purl.obolibrary.org/obo/CHEBI_16449"}],"text":"H-bond analysis was also performed for the mutant systems and the results for H-bonds with more than 40% consistency are shown in Table S3. Few of the alanine substitutions increase the number of interfacial H-bonds between nCOV-2019 RBD and ACE2. Interestingly, the ala-substitution at Y489A increased the number of H-bonds in the wild-type complex. Mutation in some of the residues having consistent H-bonds in the wild type complex such as Q498A and Q493A, stunningly maintain the number of H-bonds in the wild-type complex. This indicates that the plasticity in the network of H-bonds in RBM of nCOV-2019 can reshape the network and strengthen other H-bonds upon mutation in these locations. However, few mutations decrease the number of H-bonds from the wild-type complex. Alanine substitution at residue G502 has a significant effect on the network of H-bonds between nCOV-2019 and SARS-COV. This residue locates at the end of L4 loop near two other important residues Q498 and T500. This mutation breaks the H-bonds at these residues. Mutation K417A decreases the number of H-bonds to only 5 where the H-bond at residue Q498 is broken. This indicates the delicate nature of the H-bond from residue Q498 which can easily be broken upon ala-substitution at other residues. Furthermore, mutation N487 also decreases the number of H-bonds by breaking the H-bond at Q498."}

{"project":"LitCovid-sentences","denotations":[{"id":"T265","span":{"begin":0,"end":139},"obj":"Sentence"},{"id":"T266","span":{"begin":140,"end":247},"obj":"Sentence"},{"id":"T267","span":{"begin":248,"end":350},"obj":"Sentence"},{"id":"T268","span":{"begin":351,"end":527},"obj":"Sentence"},{"id":"T269","span":{"begin":528,"end":695},"obj":"Sentence"},{"id":"T270","span":{"begin":696,"end":777},"obj":"Sentence"},{"id":"T271","span":{"begin":778,"end":897},"obj":"Sentence"},{"id":"T272","span":{"begin":898,"end":989},"obj":"Sentence"},{"id":"T273","span":{"begin":990,"end":1041},"obj":"Sentence"},{"id":"T274","span":{"begin":1042,"end":1142},"obj":"Sentence"},{"id":"T275","span":{"begin":1143,"end":1277},"obj":"Sentence"},{"id":"T276","span":{"begin":1278,"end":1373},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"H-bond analysis was also performed for the mutant systems and the results for H-bonds with more than 40% consistency are shown in Table S3. Few of the alanine substitutions increase the number of interfacial H-bonds between nCOV-2019 RBD and ACE2. Interestingly, the ala-substitution at Y489A increased the number of H-bonds in the wild-type complex. Mutation in some of the residues having consistent H-bonds in the wild type complex such as Q498A and Q493A, stunningly maintain the number of H-bonds in the wild-type complex. This indicates that the plasticity in the network of H-bonds in RBM of nCOV-2019 can reshape the network and strengthen other H-bonds upon mutation in these locations. However, few mutations decrease the number of H-bonds from the wild-type complex. Alanine substitution at residue G502 has a significant effect on the network of H-bonds between nCOV-2019 and SARS-COV. This residue locates at the end of L4 loop near two other important residues Q498 and T500. This mutation breaks the H-bonds at these residues. Mutation K417A decreases the number of H-bonds to only 5 where the H-bond at residue Q498 is broken. This indicates the delicate nature of the H-bond from residue Q498 which can easily be broken upon ala-substitution at other residues. Furthermore, mutation N487 also decreases the number of H-bonds by breaking the H-bond at Q498."}

{"project":"LitCovid-PubTator","denotations":[{"id":"976","span":{"begin":242,"end":246},"obj":"Gene"},{"id":"977","span":{"begin":224,"end":228},"obj":"Species"},{"id":"978","span":{"begin":599,"end":603},"obj":"Species"},{"id":"979","span":{"begin":874,"end":878},"obj":"Species"},{"id":"980","span":{"begin":888,"end":896},"obj":"Species"},{"id":"981","span":{"begin":151,"end":158},"obj":"Chemical"},{"id":"982","span":{"begin":267,"end":270},"obj":"Chemical"},{"id":"983","span":{"begin":778,"end":785},"obj":"Chemical"},{"id":"984","span":{"begin":810,"end":814},"obj":"Chemical"},{"id":"985","span":{"begin":1127,"end":1131},"obj":"Chemical"},{"id":"986","span":{"begin":1205,"end":1209},"obj":"Chemical"},{"id":"987","span":{"begin":1242,"end":1245},"obj":"Chemical"}],"attributes":[{"id":"A976","pred":"tao:has_database_id","subj":"976","obj":"Gene:59272"},{"id":"A977","pred":"tao:has_database_id","subj":"977","obj":"Tax:2697049"},{"id":"A978","pred":"tao:has_database_id","subj":"978","obj":"Tax:2697049"},{"id":"A979","pred":"tao:has_database_id","subj":"979","obj":"Tax:2697049"},{"id":"A980","pred":"tao:has_database_id","subj":"980","obj":"Tax:694009"},{"id":"A981","pred":"tao:has_database_id","subj":"981","obj":"MESH:D000409"},{"id":"A982","pred":"tao:has_database_id","subj":"982","obj":"MESH:D000409"},{"id":"A983","pred":"tao:has_database_id","subj":"983","obj":"MESH:D000409"},{"id":"A987","pred":"tao:has_database_id","subj":"987","obj":"MESH:D000409"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"H-bond analysis was also performed for the mutant systems and the results for H-bonds with more than 40% consistency are shown in Table S3. Few of the alanine substitutions increase the number of interfacial H-bonds between nCOV-2019 RBD and ACE2. Interestingly, the ala-substitution at Y489A increased the number of H-bonds in the wild-type complex. Mutation in some of the residues having consistent H-bonds in the wild type complex such as Q498A and Q493A, stunningly maintain the number of H-bonds in the wild-type complex. This indicates that the plasticity in the network of H-bonds in RBM of nCOV-2019 can reshape the network and strengthen other H-bonds upon mutation in these locations. However, few mutations decrease the number of H-bonds from the wild-type complex. Alanine substitution at residue G502 has a significant effect on the network of H-bonds between nCOV-2019 and SARS-COV. This residue locates at the end of L4 loop near two other important residues Q498 and T500. This mutation breaks the H-bonds at these residues. Mutation K417A decreases the number of H-bonds to only 5 where the H-bond at residue Q498 is broken. This indicates the delicate nature of the H-bond from residue Q498 which can easily be broken upon ala-substitution at other residues. Furthermore, mutation N487 also decreases the number of H-bonds by breaking the H-bond at Q498."}