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6 protocols using α flag m2 hrp

1

Comprehensive Antibody Detection Protocol

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Antibodies used were α-GFP (Roche; from mouse, catalog no. 11814460001) 1:1,000; α-myc (Covance; 9E10 from mouse, catalog no. MMS-150R) 1:1,000; α-PGK 1:10,000 (Invitrogen; from mouse, catalog no. 459250); α-Flag M2-HRP (Sigma; from mouse, catalog no. A 8592) 1:10,000; α-tubulin-HRP 1:1,000 (Santa Cruz; from rat, catalog no. sc-53030); and HRP-coupled α-mouse (GE Healthcare; catalog no. NA931) 1:10,000. All antibodies were diluted in 5% (wt/vol) milk in Tris-buffered saline containing 0.01% (vol/vol) Tween-20.
For visualization Amersham ECL Prime Western Blotting Detection Reagent (GE Healthcare) was used. Images were acquired by Amersham Imager 600 (GE Healthcare).
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2

Quantitative Analysis of MeV Proteins

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BSR-T7/5 cells were transfected in a 12-well plate format (4 × 105 per well) with 2 μg of N-encoding plasmid DNA, and 40 hours after transfection, cells were washed once with phosphate-buffered saline (PBS) and lysed in radioimmunoprecipitation assay buffer [1% sodium deoxycholate, 1% NP-40, 150 mM NaCl, 50 mM tris-Cl (pH 7.2), 10 mM EDTA, 50 mM NaF, 0.05% SDS, protease inhibitors (Roche), 1 mM phenylmethylsulfonyl fluoride]. Cleared lysates (20,000g, 10 min, 4°C) were mixed with 5× urea buffer [200 mM tris (pH 6.8), 8 M urea, 5% SDS, 0.1 mM EDTA, 0.03% bromphenol blue, 1.5% dithiothreitol]. Samples were denatured for 30 min at 50°C, fractionated on 8% SDS–polyacrylamide gel electrophoresis (PAGE) gels, blotted on polyvinylidene difluoride membranes (Millipore), and subjected to enhanced chemiluminescence detection (Pierce) using specific antibodies directed against MeV-N (83KKKII, Millipore), MeV-P (9H4, Abcam), GAPDH (6C5, Ambion), α-FLAG-M2-HRP (Sigma-Aldrich), or HA (16B12, Sigma-Aldrich), as specified. Immunoblots were developed using a ChemiDoc digital imaging system (Bio-Rad). Only nonsaturated images were used for densitometry and carried out using the Image Lab package (Bio-Rad) and global background correction.
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3

Identification of ORMM1 Interacting Proteins

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1% of the IP samples were loaded onto an Any kD MINI-PROTEAN TGX precast gel (Bio-Rad, Hercules, CA) followed by standard procedures of immunoblotting. α-FLAG-M2-HRP (Sigma-Aldrich, St. Louis, MO) was used to detect FLAG-tagged proteins. 10% of the IP samples were separated on a 10% polyacrylamide gel before being subjected to silver staining compatible to mass spectrometry. Co-purifying proteins with FLAG-tagged ORMM1 were identified by tandem mass spectrometry using a nanoLC-LTQ-Orbitrap instrument, followed by database searching with MASCOT against TAIR10 [36 (link)].
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4

Western Blot Protein Analysis

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15 to 30 µg of total protein samples were resolved on ExpressPlus™ PAGE 4-20% gels (GenScript), in MOPS running buffer, or 8% Tris-glycine polyacrylamide gels in SDS/Tris-glycine running buffer, according to the size-resolution required. The resolved proteins were transferred to polyvinylidenedifluoride (PVDF) membranes (Bio-Rad), through a Trans-Blot® Turbo™ Transfer System (Bio-Rad). PVDF membranes were subsequently blocked in Tris-buffered saline plus 0.1% Tween (TBS-T) and 5% non-fat milk for 1 hour at 4°C and then incubated over-night at 4°C with primary antibodies in TBS-T plus 5% non-fat milk. Membranes were then washed in TBS-T (3x10 minutes) at room temperature (RT) and subsequently incubated for 1 hour at RT with horseradish peroxidase (HRP)-conjugated α-mouse or α-rabbit IgG. Blots were then washed in TBS-T (4x10 min) at RT and rinsed in TBS-T, and immunoreactive proteins were visualised using Immobilon® Forte Western HRP Substrate (Merck Millipore). Densitometric analysis was carried out using the ImageJ software. The antibodies used for Western Blot are as follows: mouse α-β-actin (A1978, Sigma-Aldrich, 1:20000), mouse α-pan 14-3-3 (sc-1657, Santa Cruz Biotechnology, 1:1000 to 1:10000), α-Flag® M2-HRP (A8592, Sigma-Aldrich, 1:20000), mouse α-His-HRP (A7058, Sigma-Aldrich, 1:10000).
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5

Immunoprecipitation and Western Blot Protocol

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Cells were harvested and washed twice in PBS before lysing them in 150 mM KAc pH 7.4, 30 mM HEPES pH 7.4, 5 mM MgAc, 1 mM DTT, 15% glycerol, 1% tergitol and 1 tablet of protease inhibitor per 10 ml (complete mini EDTA-free, Roche). Lysis was further facilitated using a Bioruptor (Diagenode, 20 cyles: 20 s ON, 20 s OFF). The lysate was cleared by centrifugation before it was incubated with Protein G Dynabeads (Invitrogen) that had been coated with 1 μl of anti-FLAG M2 (Sigma) per 10 μl beads. The beads were washed twice with 150 mM KAc pH 7.4, 30 mmM HEPES pH 7.4, 5 mM MgAc, 0.1% tergitol and twice with 150 mM KAc pH 7.4, 30 mmM HEPES pH 7.4, 5 mM MgAc. The beads were boiled in SDS loading dye for analysis on a SDS-PAGE and subsequent Western Blot performed as previously described (36 (link)). Antibodies used for the Western Blot were α-FLAG-HRP M2 (Sigma), α-Strep-tag II-HRP (IBA) or anti-Dcr2 (a kind gift of M. Siomi).
Details on our immunoprecipitations for mass spectrometry are given in the supplementary information.
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6

Western Blot Protein Detection

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Samples were resolved on 8% Tris/glycine polyacrylamide gels and transferred to a PDVF membrane (Millipore Immobilon, Merck, pore size 0.45 μm). The membranes were blocked by 5% non‐fat dry milk powder (NFDM) in TBS‐T (20 mM Tris–HCl pH 7.4, 150 mM NaCl and 0.1% (v/v) Tween‐20) for at least 1 h at RT. Primary antibodies were diluted in 5 % NFDM in TBS‐T as follows: α‐HA‐4D2 (Roche) 1:2,000; α‐PTH1R 4D2 (Thermo Fisher Scientific) 1:2,000; α‐FLAG‐HRP M2 (Sigma‐Aldrich) 1:5,000; α‐1D4‐HRP (Santa Cruz Biotechnology, sc‐57432) 1:2,000. Membranes were incubated for either 1 h at RT (α‐FLAG‐HRP) or overnight at 4°C with the primary antibody (α‐HA, α‐PTH1R and α‐1D4‐HRP), followed by 3 × 10 min washes in TBS‐T. Secondary antibodies, either α‐rat‐HRP (Cell Signaling) or α‐mouse‐HRP (Santa Cruz Biotechnology, sc‐516102), were used at 1:10,000 in 5% NFDM in TBS‐T for 1 h at RT followed by 3 × 10 min wash cycles in TBS‐T. Membranes were soaked in homemade ECL reagent (10 parts 0.1 M Tris–HCl pH 8.6 with 250 mg/l luminol, one part DMSO with 1,100 mg/l p‐hydroxycoumarin acid, and 0.003 parts 30% H2O2). After 1 min, signals were detected for 5 min in the dark (Gbox, Syngene).
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