PMC:7544934 / 20175-21614 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"472","span":{"begin":34,"end":38},"obj":"Gene"},{"id":"473","span":{"begin":317,"end":321},"obj":"Gene"},{"id":"474","span":{"begin":984,"end":988},"obj":"Gene"},{"id":"475","span":{"begin":1109,"end":1113},"obj":"Gene"},{"id":"476","span":{"begin":989,"end":999},"obj":"Chemical"},{"id":"477","span":{"begin":89,"end":97},"obj":"Disease"}],"attributes":[{"id":"A472","pred":"tao:has_database_id","subj":"472","obj":"Gene:59272"},{"id":"A473","pred":"tao:has_database_id","subj":"473","obj":"Gene:59272"},{"id":"A474","pred":"tao:has_database_id","subj":"474","obj":"Gene:59272"},{"id":"A475","pred":"tao:has_database_id","subj":"475","obj":"Gene:59272"},{"id":"A476","pred":"tao:has_database_id","subj":"476","obj":"MESH:D009271"},{"id":"A477","pred":"tao:has_database_id","subj":"477","obj":"MESH:D009436"}],"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":"The dynamics stability of the RBD-ACE2-naltrexone complex was analyzed by performing all-atoms MD simulations of 100 ns in GROMACS. The backbone RMSD analysis provides important information on the stability of protein and protein-ligand complexes and the time when simulation reached equilibrium. The RMSD of the RBD-ACE2-naltrexone complex displayed an average RMSD ∼2.46 Å throughout the entire simulation (Figure 3(A)). Besides, the RMSD of ligand was also found to be stable (red line in Figure 3(A)) with very minimal deviation as compared to the starting conformation. Overall, the complex system displayed the least backbone deviation, indicates that docked conformation is accurate and remained stable over the 100 ns timescale. Radiuses of gyration assess the compactness of the system, where a compact gyradius of ∼3.24 nm for the complex indicates the consistent shape and size of the system during the simulation (Figure 3(B)). The residue flexibility of protease and RBD-ACE2/Naltrexone complex was examined by performing Cα RMSF analysis of both the sub-units (Figure 3(C)). The average RMSF of ACE2 was found to be 0.14 nm, while for the RBD it was reported to be 0.17 nm (for the receptor-binding motif ∼0.16 nm). The receptor-binding motif of RBD displayed a high degree of flexibility and the residues participated in the ligand interaction also portrayed higher RMSF indicating their participation in ligand recognition."}

{"project":"LitCovid-sentences","denotations":[{"id":"T149","span":{"begin":0,"end":131},"obj":"Sentence"},{"id":"T150","span":{"begin":132,"end":296},"obj":"Sentence"},{"id":"T151","span":{"begin":297,"end":422},"obj":"Sentence"},{"id":"T152","span":{"begin":423,"end":574},"obj":"Sentence"},{"id":"T153","span":{"begin":575,"end":736},"obj":"Sentence"},{"id":"T154","span":{"begin":737,"end":939},"obj":"Sentence"},{"id":"T155","span":{"begin":940,"end":1088},"obj":"Sentence"},{"id":"T156","span":{"begin":1089,"end":1229},"obj":"Sentence"},{"id":"T157","span":{"begin":1230,"end":1439},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The dynamics stability of the RBD-ACE2-naltrexone complex was analyzed by performing all-atoms MD simulations of 100 ns in GROMACS. The backbone RMSD analysis provides important information on the stability of protein and protein-ligand complexes and the time when simulation reached equilibrium. The RMSD of the RBD-ACE2-naltrexone complex displayed an average RMSD ∼2.46 Å throughout the entire simulation (Figure 3(A)). Besides, the RMSD of ligand was also found to be stable (red line in Figure 3(A)) with very minimal deviation as compared to the starting conformation. Overall, the complex system displayed the least backbone deviation, indicates that docked conformation is accurate and remained stable over the 100 ns timescale. Radiuses of gyration assess the compactness of the system, where a compact gyradius of ∼3.24 nm for the complex indicates the consistent shape and size of the system during the simulation (Figure 3(B)). The residue flexibility of protease and RBD-ACE2/Naltrexone complex was examined by performing Cα RMSF analysis of both the sub-units (Figure 3(C)). The average RMSF of ACE2 was found to be 0.14 nm, while for the RBD it was reported to be 0.17 nm (for the receptor-binding motif ∼0.16 nm). The receptor-binding motif of RBD displayed a high degree of flexibility and the residues participated in the ligand interaction also portrayed higher RMSF indicating their participation in ligand recognition."}