PMC:7219429 / 16057-16795 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T87","span":{"begin":77,"end":84},"obj":"Body_part"},{"id":"T88","span":{"begin":118,"end":125},"obj":"Body_part"},{"id":"T89","span":{"begin":172,"end":179},"obj":"Body_part"},{"id":"T90","span":{"begin":399,"end":406},"obj":"Body_part"},{"id":"T91","span":{"begin":605,"end":615},"obj":"Body_part"}],"attributes":[{"id":"A87","pred":"fma_id","subj":"T87","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A88","pred":"fma_id","subj":"T88","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A89","pred":"fma_id","subj":"T89","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A90","pred":"fma_id","subj":"T90","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A91","pred":"fma_id","subj":"T91","obj":"http://purl.org/sig/ont/fma/fma82739"}],"text":"Induced-fit conformational rearrangements during binding of ATM on the spike protein. (a) Docking of ATM on the spike protein (time = 0). ATM is in yellow spheres, and the protein segment 134-137 is in balls and sticks rendition. Three parts of the ATM molecule are marked with asterisks. The orientation of the side chains of residues 134-137 is shown under the complex. (b) ATM bound to the spike protein after MD simulations (time = 50 ns). Note that the complex has evolved according to a typical induced-fit mechanism. The asterisks on ATM help visualize its conformational changes. Reorientation of amino acid side chains is also clearly visible in the ATM-spike complex and in the isolated 134-137 fragment shown under the complex."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T161","span":{"begin":87,"end":88},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T162","span":{"begin":373,"end":374},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T163","span":{"begin":413,"end":415},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T164","span":{"begin":466,"end":469},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T165","span":{"begin":491,"end":492},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Induced-fit conformational rearrangements during binding of ATM on the spike protein. (a) Docking of ATM on the spike protein (time = 0). ATM is in yellow spheres, and the protein segment 134-137 is in balls and sticks rendition. Three parts of the ATM molecule are marked with asterisks. The orientation of the side chains of residues 134-137 is shown under the complex. (b) ATM bound to the spike protein after MD simulations (time = 50 ns). Note that the complex has evolved according to a typical induced-fit mechanism. The asterisks on ATM help visualize its conformational changes. Reorientation of amino acid side chains is also clearly visible in the ATM-spike complex and in the isolated 134-137 fragment shown under the complex."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T261","span":{"begin":60,"end":63},"obj":"Chemical"},{"id":"T262","span":{"begin":77,"end":84},"obj":"Chemical"},{"id":"T263","span":{"begin":101,"end":104},"obj":"Chemical"},{"id":"T264","span":{"begin":118,"end":125},"obj":"Chemical"},{"id":"T265","span":{"begin":138,"end":141},"obj":"Chemical"},{"id":"T266","span":{"begin":172,"end":179},"obj":"Chemical"},{"id":"T267","span":{"begin":249,"end":252},"obj":"Chemical"},{"id":"T268","span":{"begin":253,"end":261},"obj":"Chemical"},{"id":"T269","span":{"begin":376,"end":379},"obj":"Chemical"},{"id":"T270","span":{"begin":399,"end":406},"obj":"Chemical"},{"id":"T271","span":{"begin":413,"end":415},"obj":"Chemical"},{"id":"T272","span":{"begin":541,"end":544},"obj":"Chemical"},{"id":"T273","span":{"begin":605,"end":615},"obj":"Chemical"},{"id":"T274","span":{"begin":605,"end":610},"obj":"Chemical"},{"id":"T275","span":{"begin":611,"end":615},"obj":"Chemical"},{"id":"T276","span":{"begin":659,"end":662},"obj":"Chemical"}],"attributes":[{"id":"A261","pred":"chebi_id","subj":"T261","obj":"http://purl.obolibrary.org/obo/CHEBI_2955"},{"id":"A262","pred":"chebi_id","subj":"T262","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A263","pred":"chebi_id","subj":"T263","obj":"http://purl.obolibrary.org/obo/CHEBI_2955"},{"id":"A264","pred":"chebi_id","subj":"T264","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A265","pred":"chebi_id","subj":"T265","obj":"http://purl.obolibrary.org/obo/CHEBI_2955"},{"id":"A266","pred":"chebi_id","subj":"T266","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A267","pred":"chebi_id","subj":"T267","obj":"http://purl.obolibrary.org/obo/CHEBI_2955"},{"id":"A268","pred":"chebi_id","subj":"T268","obj":"http://purl.obolibrary.org/obo/CHEBI_25367"},{"id":"A269","pred":"chebi_id","subj":"T269","obj":"http://purl.obolibrary.org/obo/CHEBI_2955"},{"id":"A270","pred":"chebi_id","subj":"T270","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A271","pred":"chebi_id","subj":"T271","obj":"http://purl.obolibrary.org/obo/CHEBI_74699"},{"id":"A272","pred":"chebi_id","subj":"T272","obj":"http://purl.obolibrary.org/obo/CHEBI_2955"},{"id":"A273","pred":"chebi_id","subj":"T273","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A274","pred":"chebi_id","subj":"T274","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A275","pred":"chebi_id","subj":"T275","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A276","pred":"chebi_id","subj":"T276","obj":"http://purl.obolibrary.org/obo/CHEBI_2955"}],"text":"Induced-fit conformational rearrangements during binding of ATM on the spike protein. (a) Docking of ATM on the spike protein (time = 0). ATM is in yellow spheres, and the protein segment 134-137 is in balls and sticks rendition. Three parts of the ATM molecule are marked with asterisks. The orientation of the side chains of residues 134-137 is shown under the complex. (b) ATM bound to the spike protein after MD simulations (time = 50 ns). Note that the complex has evolved according to a typical induced-fit mechanism. The asterisks on ATM help visualize its conformational changes. Reorientation of amino acid side chains is also clearly visible in the ATM-spike complex and in the isolated 134-137 fragment shown under the complex."}

{"project":"LitCovid-sentences","denotations":[{"id":"T116","span":{"begin":138,"end":229},"obj":"Sentence"},{"id":"T117","span":{"begin":230,"end":288},"obj":"Sentence"},{"id":"T118","span":{"begin":289,"end":443},"obj":"Sentence"},{"id":"T119","span":{"begin":444,"end":523},"obj":"Sentence"},{"id":"T120","span":{"begin":524,"end":587},"obj":"Sentence"},{"id":"T121","span":{"begin":588,"end":738},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Induced-fit conformational rearrangements during binding of ATM on the spike protein. (a) Docking of ATM on the spike protein (time = 0). ATM is in yellow spheres, and the protein segment 134-137 is in balls and sticks rendition. Three parts of the ATM molecule are marked with asterisks. The orientation of the side chains of residues 134-137 is shown under the complex. (b) ATM bound to the spike protein after MD simulations (time = 50 ns). Note that the complex has evolved according to a typical induced-fit mechanism. The asterisks on ATM help visualize its conformational changes. Reorientation of amino acid side chains is also clearly visible in the ATM-spike complex and in the isolated 134-137 fragment shown under the complex."}

{"project":"LitCovid-PubTator","denotations":[{"id":"392","span":{"begin":71,"end":76},"obj":"Gene"},{"id":"393","span":{"begin":112,"end":117},"obj":"Gene"},{"id":"394","span":{"begin":393,"end":398},"obj":"Gene"},{"id":"395","span":{"begin":663,"end":668},"obj":"Gene"}],"attributes":[{"id":"A392","pred":"tao:has_database_id","subj":"392","obj":"Gene:43740568"},{"id":"A393","pred":"tao:has_database_id","subj":"393","obj":"Gene:43740568"},{"id":"A394","pred":"tao:has_database_id","subj":"394","obj":"Gene:43740568"},{"id":"A395","pred":"tao:has_database_id","subj":"395","obj":"Gene:43740568"}],"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":"Induced-fit conformational rearrangements during binding of ATM on the spike protein. (a) Docking of ATM on the spike protein (time = 0). ATM is in yellow spheres, and the protein segment 134-137 is in balls and sticks rendition. Three parts of the ATM molecule are marked with asterisks. The orientation of the side chains of residues 134-137 is shown under the complex. (b) ATM bound to the spike protein after MD simulations (time = 50 ns). Note that the complex has evolved according to a typical induced-fit mechanism. The asterisks on ATM help visualize its conformational changes. Reorientation of amino acid side chains is also clearly visible in the ATM-spike complex and in the isolated 134-137 fragment shown under the complex."}