PMC:7219429 / 16050-16795 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T87","span":{"begin":84,"end":91},"obj":"Body_part"},{"id":"T88","span":{"begin":125,"end":132},"obj":"Body_part"},{"id":"T89","span":{"begin":179,"end":186},"obj":"Body_part"},{"id":"T90","span":{"begin":406,"end":413},"obj":"Body_part"},{"id":"T91","span":{"begin":612,"end":622},"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":"Fig. 3 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":94,"end":95},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T162","span":{"begin":380,"end":381},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T163","span":{"begin":420,"end":422},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T164","span":{"begin":473,"end":476},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T165","span":{"begin":498,"end":499},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Fig. 3 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":67,"end":70},"obj":"Chemical"},{"id":"T262","span":{"begin":84,"end":91},"obj":"Chemical"},{"id":"T263","span":{"begin":108,"end":111},"obj":"Chemical"},{"id":"T264","span":{"begin":125,"end":132},"obj":"Chemical"},{"id":"T265","span":{"begin":145,"end":148},"obj":"Chemical"},{"id":"T266","span":{"begin":179,"end":186},"obj":"Chemical"},{"id":"T267","span":{"begin":256,"end":259},"obj":"Chemical"},{"id":"T268","span":{"begin":260,"end":268},"obj":"Chemical"},{"id":"T269","span":{"begin":383,"end":386},"obj":"Chemical"},{"id":"T270","span":{"begin":406,"end":413},"obj":"Chemical"},{"id":"T271","span":{"begin":420,"end":422},"obj":"Chemical"},{"id":"T272","span":{"begin":548,"end":551},"obj":"Chemical"},{"id":"T273","span":{"begin":612,"end":622},"obj":"Chemical"},{"id":"T274","span":{"begin":612,"end":617},"obj":"Chemical"},{"id":"T275","span":{"begin":618,"end":622},"obj":"Chemical"},{"id":"T276","span":{"begin":666,"end":669},"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":"Fig. 3 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":"T115","span":{"begin":0,"end":144},"obj":"Sentence"},{"id":"T116","span":{"begin":145,"end":236},"obj":"Sentence"},{"id":"T117","span":{"begin":237,"end":295},"obj":"Sentence"},{"id":"T118","span":{"begin":296,"end":450},"obj":"Sentence"},{"id":"T119","span":{"begin":451,"end":530},"obj":"Sentence"},{"id":"T120","span":{"begin":531,"end":594},"obj":"Sentence"},{"id":"T121","span":{"begin":595,"end":745},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Fig. 3 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":78,"end":83},"obj":"Gene"},{"id":"393","span":{"begin":119,"end":124},"obj":"Gene"},{"id":"394","span":{"begin":400,"end":405},"obj":"Gene"},{"id":"395","span":{"begin":670,"end":675},"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":"Fig. 3 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."}