PMC:7784834 / 29012-30299 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"391","span":{"begin":157,"end":162},"obj":"Gene"},{"id":"392","span":{"begin":321,"end":326},"obj":"Gene"},{"id":"393","span":{"begin":495,"end":500},"obj":"Gene"},{"id":"394","span":{"begin":991,"end":992},"obj":"Gene"},{"id":"395","span":{"begin":994,"end":999},"obj":"Gene"},{"id":"396","span":{"begin":1015,"end":1020},"obj":"Gene"},{"id":"397","span":{"begin":1072,"end":1073},"obj":"Gene"},{"id":"398","span":{"begin":1039,"end":1040},"obj":"Gene"},{"id":"399","span":{"begin":1012,"end":1013},"obj":"Gene"}],"attributes":[{"id":"A391","pred":"tao:has_database_id","subj":"391","obj":"Gene:43740568"},{"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:43740575"},{"id":"A395","pred":"tao:has_database_id","subj":"395","obj":"Gene:43740568"},{"id":"A396","pred":"tao:has_database_id","subj":"396","obj":"Gene:43740568"},{"id":"A397","pred":"tao:has_database_id","subj":"397","obj":"Gene:43740575"},{"id":"A398","pred":"tao:has_database_id","subj":"398","obj":"Gene:43740575"},{"id":"A399","pred":"tao:has_database_id","subj":"399","obj":"Gene:43740575"}],"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 radius of gyration analysis was evaluated to determine the change in compactness of protein systems used throughout the MD simulations. The Rg plots for spike, main protease and its complex with rutin show slight fluctuations at the initial frame and attain compactness after 30 ns with Rg score of 3.85 nm and 4 nm (spike and spike-rutin) and after 20 ns with Rg score of 2.27 nm and 2.23 nm (main protease and main protease-rutin), respectively (Figures 2(C) and 3(C)). When compared with spike protein, Rg value for spike-rutin is stabilized and remains constant, suggesting strong binding interaction of the inhibitor, and the same is observed in case of main protease and rutin. Similar observations were determined through SASA analysis representing the solvent defined protein surface and its orientation through folding, making the alterations in the exposed and buried regions of the surface area of proteins. The SASA values for all the simulation systems were about 460 nm/S2/N (spike), 485 nm/S2/N (spike-rutin), 154 nm/S2/N (main-protease), and 152 nm/S2/N (main protease-rutin) (Figures 2(D) and 3(D)). Here, spike-rutin and main protease-rutin solvation profile shows a convincing SASA value suggesting a stable structure and strong binding interaction with the rutin."}

{"project":"LitCovid-sentences","denotations":[{"id":"T204","span":{"begin":0,"end":139},"obj":"Sentence"},{"id":"T205","span":{"begin":140,"end":475},"obj":"Sentence"},{"id":"T206","span":{"begin":476,"end":687},"obj":"Sentence"},{"id":"T207","span":{"begin":688,"end":922},"obj":"Sentence"},{"id":"T208","span":{"begin":923,"end":1120},"obj":"Sentence"},{"id":"T209","span":{"begin":1121,"end":1287},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The radius of gyration analysis was evaluated to determine the change in compactness of protein systems used throughout the MD simulations. The Rg plots for spike, main protease and its complex with rutin show slight fluctuations at the initial frame and attain compactness after 30 ns with Rg score of 3.85 nm and 4 nm (spike and spike-rutin) and after 20 ns with Rg score of 2.27 nm and 2.23 nm (main protease and main protease-rutin), respectively (Figures 2(C) and 3(C)). When compared with spike protein, Rg value for spike-rutin is stabilized and remains constant, suggesting strong binding interaction of the inhibitor, and the same is observed in case of main protease and rutin. Similar observations were determined through SASA analysis representing the solvent defined protein surface and its orientation through folding, making the alterations in the exposed and buried regions of the surface area of proteins. The SASA values for all the simulation systems were about 460 nm/S2/N (spike), 485 nm/S2/N (spike-rutin), 154 nm/S2/N (main-protease), and 152 nm/S2/N (main protease-rutin) (Figures 2(D) and 3(D)). Here, spike-rutin and main protease-rutin solvation profile shows a convincing SASA value suggesting a stable structure and strong binding interaction with the rutin."}