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8 protocols using g7781

1

Immunoblotting and Immunofluorescence Protocols

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Primary antibodies for immunoblotting: mouse anti-Ub (FK2; BML-PW8810 and UBCJ2; AB_2935893, Enzo Life Science), mouse anti-DnaK (8E2/2, ADI-SPA- 880, Enzo Life Science), goat anti-GroEL (ABIN6292975, antibodies-online), mouse anti-tubulin (E7, DSHB), rabbit anti-GST (G7781, Sigma) and rat anti-GFP (3H9, Proteintech).
Primary antibodies used for immunofluorescence microscopy: α-Ub (1:400, FK2; BML-PW8810 and UBCJ2; AB_2935893, Enzo Life Science) α-M1 (1:400, 1E3, ZRB2114, Merck) α-K63 (1:400, Apu3, 05–1308, Millipore) and α-LC3 (1:300, CTB-LC3–2-IC, Cosmo Bio,). Anti-Burkholderia antibody was provided by the United States Army Medical Research Institute of Infectious Diseases, an agency of the U.S. Government (“USAMRIID”).
Secondary antibodies used: Thermo Fisher Scientific (1:500, Alexa-conjugated anti-mouse, anti-goat and anti-rabbit antisera) and Dabco (1:5000, HRP-conjugated reagents).
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2

Immunofluorescence Assay for p65, FLAG, and GST

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MCF10A cells seeded on glass coverslips in 24-well plates (5.0 × 104 cells per well) were transfected as described above. Twenty-four hours after transfection, or after TNFα addition when stated, cells were fixed for 10 min in 4% paraformaldehyde (PFA). Coverslips were then sequentially incubated with PBS-Triton X-100 for 5 min, and with antibodies against p65 (SantaCruz Biotechnology #sc-372), FLAG (Sigma-Aldrich #F1804) or GST (Sigma-Aldrich #G7781) diluted in PBS–BSA 3% for 1 h. Secondary antibodies anti-rabbit-AlexaFluor-555 (Cell Signaling #4413) and anti-mouse-AlexaFluor-488 (Cell Signaling #4408) were next incubated in PBS–BSA 3% for 1 h. Nuclei were stained with DAPI and coverslips were mounted with Vectashield medium (Vector Laboratories, Cambridgeshire, UK). Results are presented as a representative example of three biologically independent repetitions of the experiment.
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3

In Vitro Phosphorylation of GST-GluA2

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Example 4

The purified GST-GluA2 was submitted to in vitro phosphorylation in the presence of the active Src protein (14-326, Merck™) and ATP, for 1 h at 25° C. All reactions were carried out in kinase assay buffer (20 mM MES pH 6.5, 150 mM NaCl, 10 mM MgCl2, 1mMDTT). A reaction containing GST-GluA2 but without Src kinase was carried out as a negative control. Tyrosine phosphorylation of GST-GluA2 was checked by western blotting using anti-pTyr antibody (PY99) HRP (sc-7020 HRP, Santa Cruz Biotechnology™). Then, the membranes were reprobed with anti-GST antibodies (G7781, Sigma-Aldrich™)

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4

Antibody sources and applications

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The antibodies listed in the Key Resources Table were used as follows: rabbit polyclonal antibody to actin (A2066, Sigma-Aldrich, WB 1:2,000), mouse monoclonal to cytochrome c (6H2.B4, 612302, BioLegend, IF 1:200), rabbit polyclonal to DsRed (632496, Clontech Laboratories, IF 1:500, WB 1:1,000), mouse monoclonal to GFP (9F9.F9, ab1218, abcam, IF 1:400–1,000), rabbit polyclonal to GFP (A11122, Thermo Fischer Scientific, IF 1:400), rabbit polyclonal to GFP (ab6556, abcam, WB 1:1,000), rabbit polyclonal to GST (G7781, Sigma-Aldrich, WB 1:20,000), mouse monoclonal to HA (HA-7, H9658, Sigma-Aldrich, IP), rat monoclonal to HA (3F10, 11867423001, Roche, IF 1:100, IP), rabbit polyclonal to optineurin (Ab2, HPA003360, Sigma-Aldrich, IF 1:100), mouse monoclonal to parkin (PRK8, sc-32282, Santa Cruz Biotechnology, WB 1:500), rabbit polyclonal to Tom20 (FL-145, sc-11415, Santa Cruz Biotechnology, IF 1:100), mouse monoclonal to α-tubulin (DM1A, T9025, WB 1:2,000), mouse monoclonal to ubiquitin (P4D1, sc-8017, Santa Cruz Biotechnology, WB 1:1,000), mouse monoclonal to ubiquitin (FK2, ST1200, Millipore, WB 1:1,000). Affinity-purified rabbit polyclonal antibodies against MYO6, TAX1BP1, NDP52, and OPTN (IF 1:100, WB 1:1,000) were generated as previously described (Buss et al., 1998 (link), Morriswood et al., 2007 (link), Sahlender et al., 2005 (link)).
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5

Quantifying γTuSC-Spc110p Interaction

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Our purification method selects for γTuSC that is competent to interact with Spc110p. To quantify the fraction of γTuSC within baculovirus-infected insect cells that is capable of interacting with Spc110p, we performed a series of γTuSC purifications with varying amounts of glutathione-Sepharose resin. The high-speed supernatant and flowthrough fractions were analyzed by Western blotting for each condition. γTuSCCFP/YFP and GST-Spc110p1‑220 were detected by α-GFP (1:4000; A-11122; Life Technologies) and α-GST (1:8000; G7781, Sigma-Aldrich), respectively, imaged by fluorophore-conjugated goat α-rabbit secondary antibody (1:2000; 926-68021; Licor Biosciences, Lincoln, NE). Blots were scanned using a Licor Odyssey scanner. Band intensities were quantified using Fiji (Schindelin et al., 2012 (link)).
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6

GST Pull-Down Assay for Protein-Protein Interactions

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In vitro translated (IVT) proteins were generated with pCS2-N-terminal 6xMYC vectors previously described using TnT® SP6 High-Yield Wheat Germ Extract (L3260, Promega) and by following manufacturer’s recommendations. For each pull-down reaction, 2.5 μg of GST or GST-tagged protein was added along with 1–10 μL IVT protein and 5 μL of washed Glutathione Sepharose 4B beads in 300 uL binding buffer (25 mM HEPES-NaOH [pH 7.4], 500 mM NaCl, 5 mM MgCl2, and 0.1% Triton X-100) and mixed for 1 hr at 4°C. The beads were washed five times with the same buffer and eluted with LDS sample buffer. The eluates were then resolved by SDS-PAGE and analyzed by immunoblotting with anti-GST (G7781, Sigma-Aldrich) and anti-C-MYC (CBL430, EMD Millipore) antibodies. For pull-down assays using nucleotide-loaded IVT RABL2B, IVT RABL2B proteins were first generated as described above, then incubated at room temperature in the presence of 5 mM MgCl2 and 1 mM GTP or GDP. The pull-down assays were performed as described with the loaded IVT proteins, with the exception that the binding buffer contained 1 mM GTP or GDP.
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7

GST Pull-Down Assay with Detailed Antibodies

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GST pull-down was performed with Glutathione Sepharose beads (GE healthcare, Chalffint, UK) and carried out in low-salt EBC lysis buffer (150 mM NaCl; 50 mM Tris, pH 7.5; 1 mM EDTA; 0.5% NP40). Antibodies included in this study: CEP131 (A301-425A, Bethyl, WB 1:1000; ab84864, Abcam, Cambridge, UK, IF 1:300), PCM1 (sc-50164, Santa Cruz, IF 1:200), SSX2IP (HPA027306, Sigma-Aldrich, WB 1:1000), MK2 (3042S, Cell Signalling, Danvers, MA, USA, WB 1:1000), HSP27 pS82 (9709, Cell Signalling, WB 1:5000), GST (G7781, Sigma-Aldrich, WB 1:1000), Pericentrin (ab4448, Abcam, IF 1:1000), p38 MAPK (9212S, Cell Signalling, WB 1:1000), p38 MAPK phospho-Thr180/Tyr182 (9216S, Cell Signalling, WB 1:1000), γ-tubulin (T5326, Sigma-Aldrich, IF 1:250), p150 (610473, BD Biosciences, WB 1:10,000), NOGO-B (previously described by Rousseau et al. [66 (link)] WB 1:1000), SRF phospho-Ser103 (4261, Cell Signalling, WB 1:1000), and α-tubulin (T9026, Sigma-Aldrich, IF 1:500).
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8

Antibody Immunoblotting Protocol

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GFP antibody (1:5,000; G1544), GST antibody (1:5,000; G7781), and beta-actin (1:10,000; A5441) were purchased from Sigma Aldrich (Sant Luis, USA). Secondary antibodies coupled to horseradish peroxidase used for immunoblotting were obtained from Sigma (A4914 Goat anti-Rabbit IgG).
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