PMC:3333881 / 22496-26457 JSON TXT

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2_test

{"project":"2_test","denotations":[{"id":"22187158-17942396-77584449","span":{"begin":598,"end":600},"obj":"17942396"},{"id":"22187158-21664225-77584450","span":{"begin":601,"end":603},"obj":"21664225"}],"text":"Tat counteracts the IκB-α inhibition of p65 by competing the repressor binding\nWe further investigated the physical interaction of Tat with IκB-α using in vitro translated proteins in coimmunoprecipitation assays. For mapping the interaction domains, we used the following Tat mutants: Tat T,N(23,24)A, Tat C(22,25,27)A, Tat K(50,51)A and Tat R(49–57)A (Figure 3A). IκB-α coimmunoprecipitated with all Tat proteins, except Tat R(49–57)A (Figure 3B). These results indicated that the arginine-rich domain of Tat was involved in the binding to IκB-α, which was consistent with previous observations (50,51). Moreover, Tat associating with IκB-α competed the binding of IκB-α to p65 in a dose-dependent manner (Figure 3C, lanes 3–5), while Tat R(49–57)A, which lacked the binding site for IκB-α, did not associate with IκB-α and did not compete the binding of IκB-α to p65 (Figure 3C, lanes 6–8).\nFigure 3. Tat relieves p65 from the IκB-α inhibition. (A) Schematic representation of wild-type and mutant Tat proteins. (B) HA-IκB-α (5 µl) was incubated in presence or absence of FLAG-Tat, FLAG-Tat T,N(23,24)A, FLAG-Tat K(50,51)A, FLAG-Tat R(49–57)A or FLAG-Tat C(22,25,27)A (10 µl) using in vitro translated proteins. Wild-type and mutant Tat proteins were immunoprecipitated with anti-FLAG antibody; immunocomplexes were separated by 12% SDS–PAGE and analysed by western blotting with anti-HA and anti-FLAG antibodies. (C) 35S-methionine-labeled p65 (5 µl) was incubated with in vitro translated HA-IκB-α (5 µl) in presence or absence of FLAG-Tat or FLAG-Tat R(49–57)A (5, 10 or 20 µl). HA-IκB-α was immunoprecipitated with anti-HA antibody; immunocomplexes were separated by 12% SDS–PAGE and analysed by western blotting with anti-HA and anti-FLAG antibodies, or autoradiography (35S-Met-p65). Densitometry values (D) of the bands were expressed as fold increase above the control (lane 1). (D) The p65 DNA binding activity was analysed by EMSA using in vitro translated proteins. 32P-labeled-NF-κB double-stranded oligonucleotide was incubated with p65 (0.5 µl) in presence or absence of HA-IκB-α (1 µl), FLAG-Tat or FLAG-Tat R(49–57)A (5 and 10 µl); competition of DNA binding was performed with 10 - up to 100-fold molar excess of unlabeled NF-κB double-stranded oligonucleotide. DNA/protein complexes were run on 6% PAGE–TBE and analysed by autoradiography. (E) p50−/−p65−/−MEFs (3 × 105 cells) were transfected with pκBLuc (0.5 µg) and pSV-β-Gal (0.1 µg) with or without pRc/CMV-p65 (0.5 µg), pCMV4-HA-IκB-α (0.5 µg), p3xFLAG-Tat or p3xFLAG-Tat R(49–57)A (0.5, 1 and 2 µg). The luciferase activity was measured in cell extracts 48-h post-transfection and normalized to β-galactosidase activity. Fold activation was calculated relative to transfection of the pκBLuc plasmid alone. Values (mean ± SE, n = 3) are shown. As control of protein expression, aliquots of cell extracts (20 µg) were analysed by western blotting with anti-p65, anti-HA, anti-FLAG and anti-γ-tubulin antibodies.\nNext, we evaluated whether Tat counteracted the IκB-α-mediated inhibition of p65 binding to DNA by incubating in vitro translated p65 and IκB-α proteins with the NF-κB probe in presence or absence of Tat followed by EMSA. The p65 DNA binding activity was inhibited by IκB-α and restored in a dose-dependent manner by wild-type Tat, and not by Tat R(49–57) (Figure 3D). Further, we analysed the Tat effect on the IκB-α repression of p65 transcriptional activity by transfecting p50−/−p65−/−MEFs with the NF-κB-Luc reporter together with expression vectors of p65 and IκB-α, in presence or absence of Tat. IκB-α inhibited the p65-dependent expression of the luciferase gene, which was restored in a dose-dependent manner by wild-type Tat, and not by Tat R(49–57)A (Figure 3E). Altogether these results indicated that Tat counteracts the IκB-α repression of the p65 DNA-binding and transcriptional activity by associating with IκB-α and competing the repressor binding to p65."}

pmc-enju-pas

bionlp-st-ge-2016-coref

{"project":"bionlp-st-ge-2016-coref","denotations":[{"id":"T11963","span":{"begin":57,"end":70},"obj":"Anaphor"},{"id":"T11964","span":{"begin":20,"end":25},"obj":"Antecedent"},{"id":"T11965","span":{"begin":3932,"end":3945},"obj":"Anaphor"},{"id":"T11966","span":{"begin":3912,"end":3917},"obj":"Antecedent"}],"relations":[{"id":"R9815","pred":"boundBy","subj":"T11963","obj":"T11964"},{"id":"R9816","pred":"boundBy","subj":"T11965","obj":"T11966"}],"namespaces":[{"prefix":"_base","uri":"https://bionlp.dbcls.jp/ontology/ge.owl#"}],"text":"Tat counteracts the IκB-α inhibition of p65 by competing the repressor binding\nWe further investigated the physical interaction of Tat with IκB-α using in vitro translated proteins in coimmunoprecipitation assays. For mapping the interaction domains, we used the following Tat mutants: Tat T,N(23,24)A, Tat C(22,25,27)A, Tat K(50,51)A and Tat R(49–57)A (Figure 3A). IκB-α coimmunoprecipitated with all Tat proteins, except Tat R(49–57)A (Figure 3B). These results indicated that the arginine-rich domain of Tat was involved in the binding to IκB-α, which was consistent with previous observations (50,51). Moreover, Tat associating with IκB-α competed the binding of IκB-α to p65 in a dose-dependent manner (Figure 3C, lanes 3–5), while Tat R(49–57)A, which lacked the binding site for IκB-α, did not associate with IκB-α and did not compete the binding of IκB-α to p65 (Figure 3C, lanes 6–8).\nFigure 3. Tat relieves p65 from the IκB-α inhibition. (A) Schematic representation of wild-type and mutant Tat proteins. (B) HA-IκB-α (5 µl) was incubated in presence or absence of FLAG-Tat, FLAG-Tat T,N(23,24)A, FLAG-Tat K(50,51)A, FLAG-Tat R(49–57)A or FLAG-Tat C(22,25,27)A (10 µl) using in vitro translated proteins. Wild-type and mutant Tat proteins were immunoprecipitated with anti-FLAG antibody; immunocomplexes were separated by 12% SDS–PAGE and analysed by western blotting with anti-HA and anti-FLAG antibodies. (C) 35S-methionine-labeled p65 (5 µl) was incubated with in vitro translated HA-IκB-α (5 µl) in presence or absence of FLAG-Tat or FLAG-Tat R(49–57)A (5, 10 or 20 µl). HA-IκB-α was immunoprecipitated with anti-HA antibody; immunocomplexes were separated by 12% SDS–PAGE and analysed by western blotting with anti-HA and anti-FLAG antibodies, or autoradiography (35S-Met-p65). Densitometry values (D) of the bands were expressed as fold increase above the control (lane 1). (D) The p65 DNA binding activity was analysed by EMSA using in vitro translated proteins. 32P-labeled-NF-κB double-stranded oligonucleotide was incubated with p65 (0.5 µl) in presence or absence of HA-IκB-α (1 µl), FLAG-Tat or FLAG-Tat R(49–57)A (5 and 10 µl); competition of DNA binding was performed with 10 - up to 100-fold molar excess of unlabeled NF-κB double-stranded oligonucleotide. DNA/protein complexes were run on 6% PAGE–TBE and analysed by autoradiography. (E) p50−/−p65−/−MEFs (3 × 105 cells) were transfected with pκBLuc (0.5 µg) and pSV-β-Gal (0.1 µg) with or without pRc/CMV-p65 (0.5 µg), pCMV4-HA-IκB-α (0.5 µg), p3xFLAG-Tat or p3xFLAG-Tat R(49–57)A (0.5, 1 and 2 µg). The luciferase activity was measured in cell extracts 48-h post-transfection and normalized to β-galactosidase activity. Fold activation was calculated relative to transfection of the pκBLuc plasmid alone. Values (mean ± SE, n = 3) are shown. As control of protein expression, aliquots of cell extracts (20 µg) were analysed by western blotting with anti-p65, anti-HA, anti-FLAG and anti-γ-tubulin antibodies.\nNext, we evaluated whether Tat counteracted the IκB-α-mediated inhibition of p65 binding to DNA by incubating in vitro translated p65 and IκB-α proteins with the NF-κB probe in presence or absence of Tat followed by EMSA. The p65 DNA binding activity was inhibited by IκB-α and restored in a dose-dependent manner by wild-type Tat, and not by Tat R(49–57) (Figure 3D). Further, we analysed the Tat effect on the IκB-α repression of p65 transcriptional activity by transfecting p50−/−p65−/−MEFs with the NF-κB-Luc reporter together with expression vectors of p65 and IκB-α, in presence or absence of Tat. IκB-α inhibited the p65-dependent expression of the luciferase gene, which was restored in a dose-dependent manner by wild-type Tat, and not by Tat R(49–57)A (Figure 3E). Altogether these results indicated that Tat counteracts the IκB-α repression of the p65 DNA-binding and transcriptional activity by associating with IκB-α and competing the repressor binding to p65."}

bionlp-st-ge-2016-spacy-parsed

GO-BP

GO-MF

GO-CC

{"project":"GO-CC","denotations":[{"id":"T26141","span":{"begin":1288,"end":1296},"obj":"http://purl.obolibrary.org/obo/GO_0019815"},{"id":"T26142","span":{"begin":1630,"end":1638},"obj":"http://purl.obolibrary.org/obo/GO_0019815"},{"id":"T26143","span":{"begin":1747,"end":1757},"obj":"http://purl.obolibrary.org/obo/GO_0019815"},{"id":"T26144","span":{"begin":2976,"end":2986},"obj":"http://purl.obolibrary.org/obo/GO_0019815"},{"id":"T26145","span":{"begin":1288,"end":1296},"obj":"http://purl.obolibrary.org/obo/GO_0042571"},{"id":"T26146","span":{"begin":1630,"end":1638},"obj":"http://purl.obolibrary.org/obo/GO_0042571"},{"id":"T26147","span":{"begin":1747,"end":1757},"obj":"http://purl.obolibrary.org/obo/GO_0042571"},{"id":"T26148","span":{"begin":2976,"end":2986},"obj":"http://purl.obolibrary.org/obo/GO_0042571"},{"id":"T26149","span":{"begin":2282,"end":2303},"obj":"http://purl.obolibrary.org/obo/GO_0001114"},{"id":"T26150","span":{"begin":2282,"end":2303},"obj":"http://purl.obolibrary.org/obo/GO_0032993"},{"id":"T26151","span":{"begin":2282,"end":2303},"obj":"http://purl.obolibrary.org/obo/GO_0097522"},{"id":"T26152","span":{"begin":2286,"end":2303},"obj":"http://purl.obolibrary.org/obo/GO_0043234"},{"id":"T26153","span":{"begin":2391,"end":2396},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T26154","span":{"begin":2618,"end":2622},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T26155","span":{"begin":2867,"end":2871},"obj":"http://purl.obolibrary.org/obo/GO_0005623"}],"text":"Tat counteracts the IκB-α inhibition of p65 by competing the repressor binding\nWe further investigated the physical interaction of Tat with IκB-α using in vitro translated proteins in coimmunoprecipitation assays. For mapping the interaction domains, we used the following Tat mutants: Tat T,N(23,24)A, Tat C(22,25,27)A, Tat K(50,51)A and Tat R(49–57)A (Figure 3A). IκB-α coimmunoprecipitated with all Tat proteins, except Tat R(49–57)A (Figure 3B). These results indicated that the arginine-rich domain of Tat was involved in the binding to IκB-α, which was consistent with previous observations (50,51). Moreover, Tat associating with IκB-α competed the binding of IκB-α to p65 in a dose-dependent manner (Figure 3C, lanes 3–5), while Tat R(49–57)A, which lacked the binding site for IκB-α, did not associate with IκB-α and did not compete the binding of IκB-α to p65 (Figure 3C, lanes 6–8).\nFigure 3. Tat relieves p65 from the IκB-α inhibition. (A) Schematic representation of wild-type and mutant Tat proteins. (B) HA-IκB-α (5 µl) was incubated in presence or absence of FLAG-Tat, FLAG-Tat T,N(23,24)A, FLAG-Tat K(50,51)A, FLAG-Tat R(49–57)A or FLAG-Tat C(22,25,27)A (10 µl) using in vitro translated proteins. Wild-type and mutant Tat proteins were immunoprecipitated with anti-FLAG antibody; immunocomplexes were separated by 12% SDS–PAGE and analysed by western blotting with anti-HA and anti-FLAG antibodies. (C) 35S-methionine-labeled p65 (5 µl) was incubated with in vitro translated HA-IκB-α (5 µl) in presence or absence of FLAG-Tat or FLAG-Tat R(49–57)A (5, 10 or 20 µl). HA-IκB-α was immunoprecipitated with anti-HA antibody; immunocomplexes were separated by 12% SDS–PAGE and analysed by western blotting with anti-HA and anti-FLAG antibodies, or autoradiography (35S-Met-p65). Densitometry values (D) of the bands were expressed as fold increase above the control (lane 1). (D) The p65 DNA binding activity was analysed by EMSA using in vitro translated proteins. 32P-labeled-NF-κB double-stranded oligonucleotide was incubated with p65 (0.5 µl) in presence or absence of HA-IκB-α (1 µl), FLAG-Tat or FLAG-Tat R(49–57)A (5 and 10 µl); competition of DNA binding was performed with 10 - up to 100-fold molar excess of unlabeled NF-κB double-stranded oligonucleotide. DNA/protein complexes were run on 6% PAGE–TBE and analysed by autoradiography. (E) p50−/−p65−/−MEFs (3 × 105 cells) were transfected with pκBLuc (0.5 µg) and pSV-β-Gal (0.1 µg) with or without pRc/CMV-p65 (0.5 µg), pCMV4-HA-IκB-α (0.5 µg), p3xFLAG-Tat or p3xFLAG-Tat R(49–57)A (0.5, 1 and 2 µg). The luciferase activity was measured in cell extracts 48-h post-transfection and normalized to β-galactosidase activity. Fold activation was calculated relative to transfection of the pκBLuc plasmid alone. Values (mean ± SE, n = 3) are shown. As control of protein expression, aliquots of cell extracts (20 µg) were analysed by western blotting with anti-p65, anti-HA, anti-FLAG and anti-γ-tubulin antibodies.\nNext, we evaluated whether Tat counteracted the IκB-α-mediated inhibition of p65 binding to DNA by incubating in vitro translated p65 and IκB-α proteins with the NF-κB probe in presence or absence of Tat followed by EMSA. The p65 DNA binding activity was inhibited by IκB-α and restored in a dose-dependent manner by wild-type Tat, and not by Tat R(49–57) (Figure 3D). Further, we analysed the Tat effect on the IκB-α repression of p65 transcriptional activity by transfecting p50−/−p65−/−MEFs with the NF-κB-Luc reporter together with expression vectors of p65 and IκB-α, in presence or absence of Tat. IκB-α inhibited the p65-dependent expression of the luciferase gene, which was restored in a dose-dependent manner by wild-type Tat, and not by Tat R(49–57)A (Figure 3E). Altogether these results indicated that Tat counteracts the IκB-α repression of the p65 DNA-binding and transcriptional activity by associating with IκB-α and competing the repressor binding to p65."}

sentences

events-check-again

bionlp-st-ge-2016-reference-tees

test2

bionlp-st-ge-2016-reference

bionlp-st-ge-2016-uniprot

PMC:3333881 / 22496-26457 JSONTXT

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PMC:3333881 / 22496-26457 JSON TXT