Publication protocol
Briefly, cell lysates prepared using ice-cold radioimmunoprecipitation assay (RIPA) buffer (Millipore) was applied to IP or IB assays, with the appropriate antibodies. For the ubiquitinayltion assay in cells, 10 mM N-ethylmaleimide (NEM; Sigma-Aldrich) was subsequently added to the RIPA buffer. The cell lysates were subjected to IP with the indicated antibodies. The ubiquitin-conjugated proteins were detected by IB. For the ubiquitination assays under denaturing conditions, denatured cell extracts were prepared by resuspending cell pellets in 1 ml of denaturing buffer [50 mM tris (pH 7.5), 150 mM NaCl, 1% SDS, and 10 mM NEM] and boiled for 10 min. IPs were performed with an antibody recognizing Myc after addition of 9 ml of tris-buffered saline (TBS) buffer [50 mM tris (pH 7.5) and 150 mM NaCl] together with 0.5% NP-40 and 10 mM NEM. To detect the ubiquitinated RAS proteins, we captured the ubiquitinated proteins using an UbiQapture-Q Kit50 (Enzo Life Sciences, Switzerland) according to the manufacturer’s instructions. Cells were collected and lysed with RIPA buffer. We then added 50 μl of UbiQapture-Q matrix to the cell lysate. The sample was resuspended gently by inversion at 4 °C overnight to allow the ubiquitinated protein conjugates to bind to the affinity matrix. After centrifugation at 5000 × g for 30 s, the matrix was washed twice in phosphate-buffered saline (PBS). Extracted ubiquitinated proteins were then subjected to immunoblotting using anti-RAS (Millipore, 05-516, 1:3000) antibody. For the GST pull-down assay, bacterially expressed GST-H, K, or NRAS were purified using glutathione agarose beads (BD Biosciences). The cell lysates were incubated with the purified soluble GST fusion proteins and the pull-down samples were subjected to IB analyseis. Following primary antibodies were used for IB; anti-Ras (Millipore, 05-516, 1:3000), anti-HRas (Santa Cruz Biotechnology, sc-520, 1:500), anti-KRas (Santa Cruz Biotechnology, sc-30, 1:500), anti-NRas (Santa Cruz Biotechnology, sc-31, 1:500), anti-p-ERK (Cell Signaling Technology, #9101S, 1:1000), anti-ERK (Santa Cruz Biotechnology, sc-514302, 1:5000), anti-PCNA (Santa Cruz Biotechnology, sc-56, 1:3000), anti-N-cadherin (BD Bioscience, #610920, 1:3000), anti-αSMA (Abcam, ab7817, 1:3000), anti-Myc (Cell Signaling Technology, #2276S, 1:3000), anti-FLAG (Sigma-Aldrich, F7425, 1:3000), anti-HA (Santa Cruz Biotechnology, sc-7392, 1:3000), anti-V5 (MBL International., M167-3, 1:3000), anti-GFP (Santa Cruz Biotechnology, sc-8334, 1:3000), anti-GST (Santa Cruz Biotechnology, sc-374171, 1:3000) and anti-β-actin (Santa Cruz Biotechnology, sc-47778, 1:3000). WDR76 polyclonal antibody was generated from immunization of rabbits with partially purified WDR76 proteins (GST-WDR76 1-300; Abfrontier, Korea). The antibody was purified using ProteinA-Sepharose and a standard procedure. Secondary antibodies, horseradish peroxidase-conjugated anti-mouse antibody (Cell Signaling Technology, #7076, 1:5000) or anti-rabbit antibody (Bio-Rad, #1706515, 1:5000) were used in this study. The band signals were acquired with a LAS-4000 LCD camera coupled to MultiGauge software (Fuji).
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