Biorthogonal noncanonical amino acid tagging (BONCAT) was performed by treating 20 μg of proteins with 75 μM Acetylene-PEG4-Biotin (Jena Bioscience), 5.6 mM CuSO4, 70 mM sodium ascorbate, 1 mM tris(3-hydroxypropyltriazolylmethyl)amine (THPTA; Sigma-Aldrich; ref. 762342). Biotinylated proteins were then separated by electrophoresis and immunoblotted on nitrocellulose. The resulting blot was blocked in 5% nonfat dry milk and incubated overnight with HRP-conjugated streptavidin (1:10000) or anti-GFP antibody (1:2000) in a solution of 5% nonfat dry milk. Chemiluminescence was detected using an Immobilon Classico or Crescendo western HRP substrate. Images were acquired using the ImageQuant LAS system.
Phosphatase inhibitor cocktail
Phosphatase inhibitor cocktail is a laboratory reagent used to prevent the activity of phosphatases, which are enzymes that remove phosphate groups from proteins. This product is designed to maintain the phosphorylation state of proteins during sample preparation and analysis.
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PhosSTOP™ is a phosphatase inhibitor cocktail product manufactured by Roche. It is currently available for purchase through authorized distributors. The product is commercialized by the manufacturer, Roche.
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1 293 protocols using «phosphatase inhibitor cocktail»
Western Blot Characterization of Cellular Signaling
Biorthogonal noncanonical amino acid tagging (BONCAT) was performed by treating 20 μg of proteins with 75 μM Acetylene-PEG4-Biotin (Jena Bioscience), 5.6 mM CuSO4, 70 mM sodium ascorbate, 1 mM tris(3-hydroxypropyltriazolylmethyl)amine (THPTA; Sigma-Aldrich; ref. 762342). Biotinylated proteins were then separated by electrophoresis and immunoblotted on nitrocellulose. The resulting blot was blocked in 5% nonfat dry milk and incubated overnight with HRP-conjugated streptavidin (1:10000) or anti-GFP antibody (1:2000) in a solution of 5% nonfat dry milk. Chemiluminescence was detected using an Immobilon Classico or Crescendo western HRP substrate. Images were acquired using the ImageQuant LAS system.
Liver Protein Extraction and Western Blot
Protein Extraction and Western Blot Analysis
Western blot analysis was used with the SDS-polyacrylamide gel electrophoresis system and afterwards transferred onto PVDF membranes of 0.45-µm pore size. Then, membranes were blocked with 5% milk or Bovine Serum Albumin (Sigma-Aldrich) in 1× TBST buffer for 30-60 min. Primary antibodies including rabbit polyclonal antibodies against NLRP3, caspase-1, GSDME, interleukin-1, ASC, GAPDH (1:1,000 dilution; ABclonal, Woburn, MA, USA), and β-actin (1:3,000 dilution; Cell Signaling, Danvers, MA, USA) were incubated with the membranes overnight at 4°C for probing. On alternate days, membranes were washed with 1× TBST buffer for 10 min, repeating the process 3 times. They were then incubated with a secondary antibody conjugated to horseradish peroxidase for 60 min at 25 °C. The membranes were washed with 1× TBST buffer for 10 min, repeating the process 3 times. All cell protein levels were analyzed by Cytiva Amersham™ ECL™ Prime Western Blotting Detection Reagent (Thermo Fisher Scientific) and a ChemiDocTMXRS+ System (Bio-Rad Laboratories, Hercules, CA, USA). The intensities of the protein bands were analyzed using Image J software.
Quantifying Mitochondrial Protein Levels in Cell Lysates
HAP1 WT and HAP1 CLPB KO cells were washed two times with PBS and then harvested with 0.05% trypsin-EDTA (Gibco, #25300054). Immediately, the cells were lysed with RIPA buffer supplemented with protease inhibitors (leupeptin, antipain, pepstatin, 1 μg/ml of each) and PMSF 1 mM. Lysates were centrifuged at 12,000 rpm for 10 min at 4 °C to remove debris, aggregates, and insoluble proteins. The resulting supernatants, containing the extracted proteins and indicated as whole cell lysates were quantified using the DC protein assay kit (Bio-Rad, #5000113), and 25 μg of protein was loaded in a NuPAGE 10% and 4–12% Bis-Tris gels (Invitrogen, #NP0322BOX) and then separated electrophoretically in reducing and non-reducing conditions. After electrophoretic separation, proteins were transferred onto LF PVDF membranes (Bio-Rad, #1704275) and those were blocked for 1 h at room temperature, following the incubation overnight at 4 °C with the primary antibodies. The following antibodies were used: anti-CLPB (Proteintech, #15743-1-AP, 1:1000), anti-MCU (Sigma, #HPA016480, 1:500), anti-MICU1 (Sigma, #HPA037480, 1:500), anti-MICU2 (Abcam, #ab101465, 1:1000), anti-EMRE (Bethyl, #A300-BL19208, 1:1000), anti-TOM20 (Proteintech, #667771, 1: 1000), anti-HSP70 (Thermo Scientific, #MA3-028, 1:1000), and anti-OPA1 (BD Lab, #612606, 1:1000). After antibodies incubation, membranes were washed three times with TBS-Tween for 10 min and then incubated with fluorescence secondary antibodies (Licor, 1:5000) for 1 h in shaking at room temperature in the dark. Proteins were detected with chemiluminescence using the Azura Biosystems software. Proteins of interest as well as loading control bands were quantified by densitometry using ImageJ software (NIH, Bethesda, USA). Western blots shown throughout the paper are representative of at least three independent experiments.
Western Blot Analysis of ABCG2 Protein
Top 5 most cited protocols using «phosphatase inhibitor cocktail»
Affinity Purification of SMG-9 Protein Complexes
A 293T cells were transfected using HEKfectin (Biorad), and lysed with a loose-fit Potter–Elvehjem homogenizer in T-buffer [20 mM HEPES–NaOH at pH 7.5, 50 mM NaCl, 0.05% Tween-20, 2.5 mM MgCl2, 0.5 mM DTT, protease inhibitor cocktail (Roche), phosphatase inhibitor cocktail (Roche) and 100 μg/ml RNaseA (Qiagen)]. The soluble fractions were pre-cleared with sepharose 4B (Sigma) and then incubated with streptavidin–sepharose (GE Biotech) for 2 h at 4°C with gentle rotation. Pre-cleared lysates were incubated with streptavidin–sepharose or anti-V5 antibodies for 2 h or 1 h at 4°C with gentle rotation. For antibodies, subsequently, the soluble fractions were incubated with 30 μl of protein G sepharose (GE Biotech) for an additional 1 h at 4°C with gentle rotation. After washing with RNase(−) T-lysis buffer, the affinity-purified protein complexes were eluted by incubation at 4°C for 30 min with RNase(−) lysis buffer containing 2 mM biotin (Sigma) or SDS sample buffer, respectively. All proteins in western blot experiments were detected with an ECL western blot detection kit (GE Biotech) or Lumi-Light (Roche). All experiments were performed two to three times, and typical results are shown.
Corresponding organizations : Consejo Superior de Investigaciones Científicas, Unidades Centrales Científico-Técnicas
SILAC-Based Proteomic Analysis of HeLa Cells
Corresponding organizations : Scripps Research Institute, Dana-Farber Cancer Institute, Harvard University, Torrey Pines Institute For Molecular Studies
Proteomic Analysis of Xenograft Tumor Tissue
Corresponding organizations : Baylor College of Medicine, The University of Texas MD Anderson Cancer Center
Purification of Dynein, Nudel, and Lis1 Proteins
Lis1 constructs were purified via His8 and ZZ tags. Lysed cells were resuspended in Buffer A (final concentrations: 50 mM potassium phosphate [pH 8.0], 150 mM potassium acetate, 150 mM NaCl, 2 mM magnesium acetate, 5 mM β-mercaptoethanol, 10% glycerol, 0.2% Triton X-100, 0.5 mM Pefabloc, and 1 mM PMSF) supplemented with 10 mM imidazole (pH 7.5). Subsequent steps were at 4°C unless indicated. The lysate was clarified by centrifugation at 264,900 g for 1 hr. The supernatant was incubated with Ni-NTA agarose (QIAGEN) for 1 hr, transferred into a column, washed three times with Buffer A + 20 mM imidazole, and eluted with Buffer A + 250 mM imidazole. Eluted protein was then incubated with IgG sepharose beads (Amersham Pharmacia) for 1 hr, transferred into a column, and washed twice with Buffer A + 20 mM imidazole and once with TEV buffer (10 mM Tris-HCl [pH 8.0], 150 mM KCl, 10% glycerol, 0.2% Triton X-100, 1 mM PMSF, and 1 mM DTT). Lis1 was released from beads via incubation with TEV protease for 1 hr at 16°C, resulting in cleavage from the His8-ZZ tag.
Corresponding organizations : Harvard University, University of Leeds
Phosphoproteomics of Hyper-Virulent M. tuberculosis
Corresponding organizations : South African Tuberculosis Vaccine Initiative, Stellenbosch University, South African Medical Research Council, University of Bergen, Max Planck Society, University of Cape Town, University of Oslo
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