PMC:7571312 / 125484-126966 JSON TXT

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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T33","span":{"begin":389,"end":394},"obj":"Body_part"},{"id":"T34","span":{"begin":525,"end":529},"obj":"Body_part"},{"id":"T35","span":{"begin":580,"end":584},"obj":"Body_part"},{"id":"T36","span":{"begin":1056,"end":1064},"obj":"Body_part"},{"id":"T37","span":{"begin":1335,"end":1343},"obj":"Body_part"}],"attributes":[{"id":"A33","pred":"fma_id","subj":"T33","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A34","pred":"fma_id","subj":"T34","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A35","pred":"fma_id","subj":"T35","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A36","pred":"fma_id","subj":"T36","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A37","pred":"fma_id","subj":"T37","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"The expression and purification strategy followed previous studies on SARS CoV-1 3CLpro.58 Genes encoding SARS CoV-1 3CLpro and SARS CoV-2 Mpro MN908947.3 were synthesized with codon usage optimized for Escherichia coli expression (Genscript and IDT). Genes were cloned into a modified pET24a vector to produce a TEV-cleavable N-terminal 6xHis tag under the T7 promoter control. BL21(DE3) cells (LifeTech) were grown in Terrific Broth (Teknova) at 37 °C until an OD600 = 0.6–0.8 and induced with 0.4 M IPTG for 5 h at 30 °C. Cell pellets were stored at −80 °C until purification. Cell pellets were resuspended and lysed by microfluidization in Buffer A (20 mM Tris pH 8.0 + 150 mM NaCl). Lysates were clarified at 25,000 × g for 1 h at 4 °C. The soluble lysate was loaded onto a nickel affinity column (Probond) and washed sequentially with Buffer A + 5 mM and 20 mM imidazole. The proteases were eluted with Buffer A + 300 mM imidazole. The His-tag was removed by TEV protease (1:40) during an overnight dialysis step in Buffer A + 1 mM DTT. The CoV Mpro proteins were further purified on a HiTrap Q hp (GE Healthcare), and the Q-flow-through material was concentrated and loaded onto a 26/60 Superdex-75 (GE Healthcare) gel filtration column equilibrated with Buffer B (20 mM Tris pH 7.8 + 150 mM NaCl + 1 mM EDTA + 1 mM DTT). Final proteins were concentrated from 5 to 25 mg/mL and were directly moved to crystallization experiments or snap-frozen in liquid nitrogen for storage."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T107","span":{"begin":70,"end":74},"obj":"Disease"},{"id":"T108","span":{"begin":106,"end":110},"obj":"Disease"},{"id":"T109","span":{"begin":128,"end":132},"obj":"Disease"}],"attributes":[{"id":"A107","pred":"mondo_id","subj":"T107","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A108","pred":"mondo_id","subj":"T108","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A109","pred":"mondo_id","subj":"T109","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"The expression and purification strategy followed previous studies on SARS CoV-1 3CLpro.58 Genes encoding SARS CoV-1 3CLpro and SARS CoV-2 Mpro MN908947.3 were synthesized with codon usage optimized for Escherichia coli expression (Genscript and IDT). Genes were cloned into a modified pET24a vector to produce a TEV-cleavable N-terminal 6xHis tag under the T7 promoter control. BL21(DE3) cells (LifeTech) were grown in Terrific Broth (Teknova) at 37 °C until an OD600 = 0.6–0.8 and induced with 0.4 M IPTG for 5 h at 30 °C. Cell pellets were stored at −80 °C until purification. Cell pellets were resuspended and lysed by microfluidization in Buffer A (20 mM Tris pH 8.0 + 150 mM NaCl). Lysates were clarified at 25,000 × g for 1 h at 4 °C. The soluble lysate was loaded onto a nickel affinity column (Probond) and washed sequentially with Buffer A + 5 mM and 20 mM imidazole. The proteases were eluted with Buffer A + 300 mM imidazole. The His-tag was removed by TEV protease (1:40) during an overnight dialysis step in Buffer A + 1 mM DTT. The CoV Mpro proteins were further purified on a HiTrap Q hp (GE Healthcare), and the Q-flow-through material was concentrated and loaded onto a 26/60 Superdex-75 (GE Healthcare) gel filtration column equilibrated with Buffer B (20 mM Tris pH 7.8 + 150 mM NaCl + 1 mM EDTA + 1 mM DTT). Final proteins were concentrated from 5 to 25 mg/mL and were directly moved to crystallization experiments or snap-frozen in liquid nitrogen for storage."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T154","span":{"begin":91,"end":96},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T155","span":{"begin":252,"end":257},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T156","span":{"begin":275,"end":276},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T157","span":{"begin":311,"end":312},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T158","span":{"begin":389,"end":394},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T159","span":{"begin":525,"end":529},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T160","span":{"begin":580,"end":584},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T161","span":{"begin":651,"end":652},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T162","span":{"begin":736,"end":740},"obj":"http://purl.obolibrary.org/obo/CLO_0001387"},{"id":"T163","span":{"begin":777,"end":778},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T164","span":{"begin":848,"end":849},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T165","span":{"begin":916,"end":917},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T166","span":{"begin":1029,"end":1030},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T167","span":{"begin":1090,"end":1091},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T168","span":{"begin":1101,"end":1103},"obj":"http://purl.obolibrary.org/obo/CLO_0003797"},{"id":"T169","span":{"begin":1101,"end":1103},"obj":"http://purl.obolibrary.org/obo/PR_000008725"},{"id":"T170","span":{"begin":1101,"end":1103},"obj":"http://purl.obolibrary.org/obo/UBERON_0000007"},{"id":"T171","span":{"begin":1186,"end":1187},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T172","span":{"begin":1269,"end":1270},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"}],"text":"The expression and purification strategy followed previous studies on SARS CoV-1 3CLpro.58 Genes encoding SARS CoV-1 3CLpro and SARS CoV-2 Mpro MN908947.3 were synthesized with codon usage optimized for Escherichia coli expression (Genscript and IDT). Genes were cloned into a modified pET24a vector to produce a TEV-cleavable N-terminal 6xHis tag under the T7 promoter control. BL21(DE3) cells (LifeTech) were grown in Terrific Broth (Teknova) at 37 °C until an OD600 = 0.6–0.8 and induced with 0.4 M IPTG for 5 h at 30 °C. Cell pellets were stored at −80 °C until purification. Cell pellets were resuspended and lysed by microfluidization in Buffer A (20 mM Tris pH 8.0 + 150 mM NaCl). Lysates were clarified at 25,000 × g for 1 h at 4 °C. The soluble lysate was loaded onto a nickel affinity column (Probond) and washed sequentially with Buffer A + 5 mM and 20 mM imidazole. The proteases were eluted with Buffer A + 300 mM imidazole. The His-tag was removed by TEV protease (1:40) during an overnight dialysis step in Buffer A + 1 mM DTT. The CoV Mpro proteins were further purified on a HiTrap Q hp (GE Healthcare), and the Q-flow-through material was concentrated and loaded onto a 26/60 Superdex-75 (GE Healthcare) gel filtration column equilibrated with Buffer B (20 mM Tris pH 7.8 + 150 mM NaCl + 1 mM EDTA + 1 mM DTT). Final proteins were concentrated from 5 to 25 mg/mL and were directly moved to crystallization experiments or snap-frozen in liquid nitrogen for storage."}

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T2","span":{"begin":1474,"end":1481},"obj":"http://purl.obolibrary.org/obo/GO_0051235"}],"text":"The expression and purification strategy followed previous studies on SARS CoV-1 3CLpro.58 Genes encoding SARS CoV-1 3CLpro and SARS CoV-2 Mpro MN908947.3 were synthesized with codon usage optimized for Escherichia coli expression (Genscript and IDT). Genes were cloned into a modified pET24a vector to produce a TEV-cleavable N-terminal 6xHis tag under the T7 promoter control. BL21(DE3) cells (LifeTech) were grown in Terrific Broth (Teknova) at 37 °C until an OD600 = 0.6–0.8 and induced with 0.4 M IPTG for 5 h at 30 °C. Cell pellets were stored at −80 °C until purification. Cell pellets were resuspended and lysed by microfluidization in Buffer A (20 mM Tris pH 8.0 + 150 mM NaCl). Lysates were clarified at 25,000 × g for 1 h at 4 °C. The soluble lysate was loaded onto a nickel affinity column (Probond) and washed sequentially with Buffer A + 5 mM and 20 mM imidazole. The proteases were eluted with Buffer A + 300 mM imidazole. The His-tag was removed by TEV protease (1:40) during an overnight dialysis step in Buffer A + 1 mM DTT. The CoV Mpro proteins were further purified on a HiTrap Q hp (GE Healthcare), and the Q-flow-through material was concentrated and loaded onto a 26/60 Superdex-75 (GE Healthcare) gel filtration column equilibrated with Buffer B (20 mM Tris pH 7.8 + 150 mM NaCl + 1 mM EDTA + 1 mM DTT). Final proteins were concentrated from 5 to 25 mg/mL and were directly moved to crystallization experiments or snap-frozen in liquid nitrogen for storage."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T679","span":{"begin":0,"end":251},"obj":"Sentence"},{"id":"T680","span":{"begin":252,"end":378},"obj":"Sentence"},{"id":"T681","span":{"begin":379,"end":524},"obj":"Sentence"},{"id":"T682","span":{"begin":525,"end":579},"obj":"Sentence"},{"id":"T683","span":{"begin":580,"end":687},"obj":"Sentence"},{"id":"T684","span":{"begin":688,"end":741},"obj":"Sentence"},{"id":"T685","span":{"begin":742,"end":877},"obj":"Sentence"},{"id":"T686","span":{"begin":878,"end":937},"obj":"Sentence"},{"id":"T687","span":{"begin":938,"end":1042},"obj":"Sentence"},{"id":"T688","span":{"begin":1043,"end":1328},"obj":"Sentence"},{"id":"T689","span":{"begin":1329,"end":1482},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The expression and purification strategy followed previous studies on SARS CoV-1 3CLpro.58 Genes encoding SARS CoV-1 3CLpro and SARS CoV-2 Mpro MN908947.3 were synthesized with codon usage optimized for Escherichia coli expression (Genscript and IDT). Genes were cloned into a modified pET24a vector to produce a TEV-cleavable N-terminal 6xHis tag under the T7 promoter control. BL21(DE3) cells (LifeTech) were grown in Terrific Broth (Teknova) at 37 °C until an OD600 = 0.6–0.8 and induced with 0.4 M IPTG for 5 h at 30 °C. Cell pellets were stored at −80 °C until purification. Cell pellets were resuspended and lysed by microfluidization in Buffer A (20 mM Tris pH 8.0 + 150 mM NaCl). Lysates were clarified at 25,000 × g for 1 h at 4 °C. The soluble lysate was loaded onto a nickel affinity column (Probond) and washed sequentially with Buffer A + 5 mM and 20 mM imidazole. The proteases were eluted with Buffer A + 300 mM imidazole. The His-tag was removed by TEV protease (1:40) during an overnight dialysis step in Buffer A + 1 mM DTT. The CoV Mpro proteins were further purified on a HiTrap Q hp (GE Healthcare), and the Q-flow-through material was concentrated and loaded onto a 26/60 Superdex-75 (GE Healthcare) gel filtration column equilibrated with Buffer B (20 mM Tris pH 7.8 + 150 mM NaCl + 1 mM EDTA + 1 mM DTT). Final proteins were concentrated from 5 to 25 mg/mL and were directly moved to crystallization experiments or snap-frozen in liquid nitrogen for storage."}

LitCovid-PubTator

2_test

{"project":"2_test","denotations":[{"id":"33054210-18237196-61913470","span":{"begin":88,"end":90},"obj":"18237196"}],"text":"The expression and purification strategy followed previous studies on SARS CoV-1 3CLpro.58 Genes encoding SARS CoV-1 3CLpro and SARS CoV-2 Mpro MN908947.3 were synthesized with codon usage optimized for Escherichia coli expression (Genscript and IDT). Genes were cloned into a modified pET24a vector to produce a TEV-cleavable N-terminal 6xHis tag under the T7 promoter control. BL21(DE3) cells (LifeTech) were grown in Terrific Broth (Teknova) at 37 °C until an OD600 = 0.6–0.8 and induced with 0.4 M IPTG for 5 h at 30 °C. Cell pellets were stored at −80 °C until purification. Cell pellets were resuspended and lysed by microfluidization in Buffer A (20 mM Tris pH 8.0 + 150 mM NaCl). Lysates were clarified at 25,000 × g for 1 h at 4 °C. The soluble lysate was loaded onto a nickel affinity column (Probond) and washed sequentially with Buffer A + 5 mM and 20 mM imidazole. The proteases were eluted with Buffer A + 300 mM imidazole. The His-tag was removed by TEV protease (1:40) during an overnight dialysis step in Buffer A + 1 mM DTT. The CoV Mpro proteins were further purified on a HiTrap Q hp (GE Healthcare), and the Q-flow-through material was concentrated and loaded onto a 26/60 Superdex-75 (GE Healthcare) gel filtration column equilibrated with Buffer B (20 mM Tris pH 7.8 + 150 mM NaCl + 1 mM EDTA + 1 mM DTT). Final proteins were concentrated from 5 to 25 mg/mL and were directly moved to crystallization experiments or snap-frozen in liquid nitrogen for storage."}

PMC:7571312 / 125484-126966 JSONTXT

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PMC:7571312 / 125484-126966 JSON TXT