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14 protocols using fusion sl system

1

Immunoblot Analysis of Protein Markers

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Immunoblot analysis was performed as described before [13 (link),49 (link)] using primary antibodies to desmoplakin, E-cadherin, β-catenin, plakoglobin, keratin 14, keratin 17, keratin 6, keratin 16, IKBα and phosphorylated- IKBα, ERK and phosphorylated-ERK, and tubulin to control loading (see Supplemental Table 2). For the analysis of IL-1β and Tnf-α, dot blots were performed. Blots were developed using ECL substrate (Thermo Scientific, Rockford, IL) and the Fusion SL system (Peqlab, Erlangen, Germany). The signals obtained from Western blot analyses were densitometrically quantified with ImageJ's gel analysis program, values were expressed as percentage of expression levels seen in untreated cells after normalization to loading control.
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2

Quantitative Western Blot Analysis

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Wild-type HEK293 cells or HEK293 cells stably expressing either nNOS or eNOS were harvested and homogenized by sonication (3 × 5 s) in ice-cold RIPA lysis buffer (Sigma, Vienna, Austria) containing 2 mM EDTA, protease and phosphatase inhibitors (Complete™, PhosSTOP™, Roche, Vienna, Austria). Protein concentration was determined with the Pierce™ BCA Protein Assay Kit (Fisher Scientific Austria GmbH, Vienna, Austria) using bovine serum albumin as standard. Denatured samples (30 μg) were separated by SDS-PAGE on 10% gels and transferred electrophoretically to nitrocellulose membranes. After blocking with 5% nonfat dry milk in Tris-buffered saline containing 0.1% (v/v) TWEEN-20 for 1 h, membranes were incubated overnight at 4 °C with a primary antibody against eNOS (1:2000; BD Transduction Laboratories), nNOS (1:1000; BD Transduction Laboratories) or β-actin (1:200,000; Sigma-Aldrich). Thereafter, membranes were washed 3 times and incubated for 1 h with a horseradish peroxidase-conjugated anti-mouse IgG secondary antibody (1:5000). Immunoreactive bands were visualized by chemiluminescence using ECL detection reagent (Biozym, Germany) and quantified densitometrically by the Fusion SL system (Peqlab, Erlangen, Germany).
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3

Immunoblotting of ASYN Variants

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Purified protein stocks (ASYN variants and GFP) were stored in H2O, because of a lower tendency to form covalent ASYN di- and multimers compared with storage in buffers. Samples were directly subjected to separation by a 15% SDS gel (2 μg/lane), transferred onto nitrocellulose membranes (Amersham Biosciences) and blocked with 5% milk powder in PBS-Tween (0.1%) for 1 h. Monoclonal antibodies (anti-ASYN, 1:3000, BD Bioscience; anti-3-NT, 1:250, Hycult Biotech; anti-3-NT Sigma, 1:250; anti-C-terminal amino acid sequence EPEA antibody fragment (CaptureSelect™ Biotin Anti-C-tag Conjugate, 1:1000, Thermo Fisher) were incubated over night at 4 °C. The horseradish peroxidase-conjugated secondary antibody (goat anti mouse IgG, Jackson ImmunoResearch, 1:2500), or Streptavidin-HRP (1:5000; Invitrogen) was incubated for 1 h. Protein bands were detected by a FUSION SL™ system (Peqlab, Erlangen, Germany) and quantified by ImaEva.
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4

Protein Extraction and Western Blot Analysis

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After harvest, 2x106 cells were washed twice with PBS and lysed in CelLytic MT buffer (Sigma-Aldrich) supplemented with Mini Complete protease inhibitor (Roche), 1% phosphatase inhibitor cocktail (Calbiochem), and 1mM PMSF. After 10 min incubation on ice and centrifugation at 11,000g for 10 min at 4°C, the protein concentration was determined by BCA Assay (Thermo Scientific). Protein samples were loaded on 10% Bis-Tris gels and transferred on a PVDF membrane (BioRad). For protein detection of MTSS1 or GAPDH primary antibodies from Cell Signaling (#4386, clone N747, 1:1000 dilution) or Santa Cruz (sc-32233, clone 6C5, 1:2000 dilution) were used followed by a secondary goat anti-rabbit HRP conjugated antibody (Dako, 1:10000) and light emission analysis using Fusion SL system (PeqLab).
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5

Affinity Purification of Tagged Yeast Proteins

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All yeast strains were grown to log phase (2–3 × 107 cells/ml). Afterwards, the cells were harvested and lysed in IP buffer (1 × PBS, 3 mM KCl, 2.5 mM MgCl2, 0,5% Triton X-100 and protease inhibitors from Roche). 35 µl of this lysate was loaded onto an SDS-gel (lysate lanes). The supernatant was incubated for 1 h at 4 °C with GFP-Selector beads (NanoTag) (Fig. 5A,B,D, Supplementary Fig. S5.1A, 5.2A, 5.3B) or with Myc-trap beads (Chromotek) (Fig. 5C, Supplementary Fig. S5.3A). The beads were washed five times with IP buffer, and finally resuspended in 35 µl SDS-sample buffer. The entire eluate sample was loaded onto the SDS-gels.
Subsequently, the proteins were detected by Western blot analyses with the indicated antibodies (GFP (Chromotek) 1:4,000; c-myc (9E10) (Santa Cruz) 1:1,000; Hem15 and Grx4 each 1:5,000 and Aco1 1:2,000 (U. Mühlenhoff); Nop1 (Santa Cruz) 1:4,000; Hdf1 (Yku70) (Santa Cruz) 1:4,000). Signals were detected with the Fusion SL system (PeqLab) and FusionFX7 Edge (Fusion FX Vilber). To be able to detect several proteins in one experiment, the western blots were cut horizontally according to the size of the desired proteins to be able to detect each stripe with individual antibodies.
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6

Western Blot Protein Detection Protocol

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Western Blot experiments were performed as previously described (Troschel et al. 2020 (link)). About 107 cells were trypsinized and lysed. Subsequently, 30 µg of whole protein was electrophoresed and transferred to nitrocellulose and thus used for immuno-detection. Antibody binding was visualized using ECL peroxidase blotting substrate (Thermo Fisher Scientific). Then, quantification of luminescence was performed with a Fusion SL System (Peqlab, Erlangen, Germany). Primary and secondary antibody details are shown in Supplementary Table S3.
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7

ALDH2 Mutant Expression Analysis

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Expression of C301S/C303S-ALDH2 in the absence and presence of cycloheximide was determined by immunoblotting. Cells were harvested and homogenized by sonication (3x5s) in 10 mM Tris buffer, pH 7.4, containing 125 mM KCl, 5 mM EGTA, 2 mM MgCl2, and Complete Protease Inhibitor Cocktail. Protein concentrations were determined with the Pierce BCA Protein Assay Kit using bovine serum albumin as standard. Denatured samples (10 μg) were separated by SDS-PAGE on 10% gels and transferred electrophoretically to nitrocellulose membranes. After blocking with 5% nonfat dry milk in phosphate-buffered saline containing 0.1% (v/v) Tween-20 for 1 hour, membranes were incubated overnight at 4°C with a primary polyclonal antibody to human ALDH2 (1:20 000; kindly provided by Dr. Henry Weiner) or to β-actin (1:200 000; Sigma). Thereafter, membranes were washed three times and incubated for 1 hour with a horseradish peroxidase-conjugated anti-rabbit (ALDH2) or anti-mouse (β-actin) IgG secondary antibody (1:5000). Immunoreactive bands were visualized by chemiluminescence using ECL detection reagent (Biozym Scientific, Hessisch Oldendorf, Germany) and quantified densitometrically using the Fusion SL system (Peqlab, Erlangen, Germany).
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8

Quantitative Western Blot Analysis

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Wild-type HEK293 cells or HEK293 cells stably expressing either nNOS or eNOS were harvested and homogenized by sonication (3 × 5 s) in ice-cold RIPA lysis buffer (Sigma, Vienna, Austria) containing 2 mM EDTA, protease and phosphatase inhibitors (Complete™, PhosSTOP™, Roche, Vienna, Austria). Protein concentration was determined with the Pierce™ BCA Protein Assay Kit (Fisher Scientific Austria GmbH, Vienna, Austria) using bovine serum albumin as standard. Denatured samples (30 μg) were separated by SDS-PAGE on 10% gels and transferred electrophoretically to nitrocellulose membranes. After blocking with 5% nonfat dry milk in Tris-buffered saline containing 0.1% (v/v) TWEEN-20 for 1 h, membranes were incubated overnight at 4 °C with a primary antibody against eNOS (1:2000; BD Transduction Laboratories), nNOS (1:1000; BD Transduction Laboratories) or β-actin (1:200,000; Sigma-Aldrich). Thereafter, membranes were washed 3 times and incubated for 1 h with a horseradish peroxidase-conjugated anti-mouse IgG secondary antibody (1:5000). Immunoreactive bands were visualized by chemiluminescence using ECL detection reagent (Biozym, Germany) and quantified densitometrically by the Fusion SL system (Peqlab, Erlangen, Germany).
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9

Immunoprecipitation of GFP-tagged Proteins

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IPs were essentially done as described previously (Zander et al., 2016). Briefly, late log phase cells (2–3 × 107 cells/mL) were harvested and lysed in IP buffer (1 × PBS, 3 mm KCl, 2.5 mm MgCl2, 0.5% Triton X‐100, vanadyl phosphatase inhibitors and protease inhibitors from Roche). The resulting lysate was incubated with GFP‐Trap®_A beads (Chromotek) and if applicable 200 μg/mL RNase A for 3–4 h at 4°C. Afterwards beads were washed five times with IP buffer and proteins were detected by Western blot analyses with the indicated antibodies [GFP (Pierce) 1:5000; c‐myc (9E10, Santa Cruz) 1:1000; Rps3 (rabbit, own serum) 1:700]. Signals were detected with the Fusion SL system (PeqLab). Intensities were quantified using the Bio1D software.
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10

ATP-induced eNOS Phosphorylation in Transfected EA.hy926 Cells

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Transfected EA.hy926 cells (siControl, siMCU/EMRE or siMICU1) were incubated with vehicle (water) or 100 μM ATP at 37 °C for 3 or 5 min. Cells were then harvested and homogenized by sonication (3×5 s) in ice-cold RIPA lysis buffer (Sigma, Vienna, Austria) containing 2 mM EDTA, protease and phosphatase inhibitors (CompleteTM, PhosSTOPTM, Roche, Vienna, Austria). Protein concentration was determined with the PierceTM BCA Protein Assay Kit using bovine serum albumin as standard (Fisher Scientific Austria GmbH, Vienna, Austria). Denatured samples (30 μg) were separated by SDS-PAGE on 10% gels and transferred electrophoretically to nitrocellulose membranes. After blocking with 5% non- fat dry milk in Tris-buffered saline containing 0.1% (v/v) TWEEN-20 for 1 h, membranes were incubated overnight at 4 °C with a primary antibody against eNOS (1:2000; BD Transduction Laboratories), Ser1177 phospho-eNOS (1:1000; BD Transduction Laboratories) or β-actin (1:200,000; Sigma). Thereafter, membranes were washed 3 times and incubated for 1 h with a horseradish peroxidase-conjugated anti-mouse IgG secondary antibody (1:5000). Immunoreactive bands were visualized by chemiluminescence using ECL detection reagent (Biozym, Germany) and quantified densitometrically using the Fusion SL system (Peqlab, Erlangen, Germany).
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