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4 protocols using m lysis buffer

1

Profiling Lamin A and Progerin Interactomes

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Lamin A and progerin were N-terminally tagged with the myc-BirA* biotinylation enzyme and cloned into the pTRIPZ lentiviral vector. Primary and TERT+ fibroblasts stably expressing either construct were generated by lentiviral transduction and selected with 1.0 μg/ml puromycin. The myc-BirA*-fusion constructs were expressed upon induction with doxycycline for at least 6 days prior to analysis. Induction was verified by western blotting and by immunofluorescence microscopy using an anti-myc antibody (Santa Cruz, sc40). 50 µM biotin was added to the medium for 24 hr prior to lysing cells under denaturing conditions (M-lysis buffer; Roche). Control cells not induced with doxycycline, or without addition of biotin were processed in parallel. Biotinylated proteins were purified using streptavidin-coupled magnetic beads (Invitrogen). After reduction and alkhylation, purified proteins were separated by SDS-PAGE electrophoresis and analyzed by mass spectrometry. Proteins were quantified using the Exponentially Modified Protein Abundance Index (emPAI), which is directly proportional to the abundance of a protein in a mixture (Ishihama et al., 2005 (link)).
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2

Proteomic Analysis of ABCA8 Interactome

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Human glial (oligodendrocytic) hybrid cell line (MO3.13: Cedarlane, ON, Canada) stably expressing myc-BirA-ABCA8-v5 was generated by lentiviral transduction and selected with 1.0 μg/ml puromycin. The myc-BirA∗-fusion construct was expressed upon induction with doxycycline for at least 6 days prior to analysis. Induction was verified by Western blotting using an anti-myc antibody (sc40; Santa Cruz, Dallas, TX). 50 μM biotin was added to the medium for 24 h prior to cell lysis under denaturing conditions (M-lysis buffer; Roche, Basel, Switzerland). Control cells not induced with doxycycline or without addition of biotin were processed in parallel. Biotinylated proteins were purified using streptavidin-coupled magnetic beads (Invitrogen). After reduction and alkylation, purified proteins were separated by 4–12% NuPage Novex Bis-Tris gels (Invitrogen), stained with Colloidal Blue (Invitrogen), and digested in-gel using trypsin (27 (link)).
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3

Western Blot Protein Detection Protocol

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Whole cell lysates and homogenized tissue lysates were prepared in ice-cold Lysis-M buffer (Roche, Mannheim, Germany), supplemented with cOmplete Mini protease inhibitor and PhosSTOP phosphatase inhibitor tablets (Roche). The whole process after protein separation was performed as previously described [56 (link)]. We used 10% or 15% sodium dodecyl sulfate-polyacrylamide gel electrophoresis for protein separation. The primary antibodies and the dilutions used were: CTGF (Santa Cruz Biotechnology, Santa Cruz, CA; 14939, 1:200), X-linked inhibitor of apoptosis (Abcam, Cambridge, UK; 21278, 1:1,000), β-actin (Sigma-Aldrich, St. Louis; A1978, 1:1,000). Secondary antibodies were immunoglobulins conjugated to horseradish peroxidase (Dako, Glostrup, Denmark; 1:1,000). Immunodetection was performed using Amersham ECL Western Blotting Detection Reagent (GE Healthcare, Little Chalfont, Buckinghamshire, UK). Densitometric analysis was performed using the ImageJ software (http://rsb.info.nih.gov/ij/).
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4

Afatinib and HAD-B1 Inhibition in H1975 Cells

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H1975 cells were incubated with HAD-B1 and with afatinib in RPMI1640 (2% fetal bovine serum, 1× antibiotics) for 72 hours, after which the cells were harvested to extract the proteins. The cell lysates were prepared in Lysis-M buffer (Roche) containing protease and phosphatase inhibitor cocktails (both from Roche). The cell lysates were clarified by centrifugation. Lysates containing 30 µg of protein were loaded into each well and separated through 12% sodium dodecyl sulfate–gel electrophoresis. Gels were soaked in transfer buffer (16 mM Tris-HCl, 30-mM glycine, and 20% methanol), and proteins were then transferred to polyvinylidene difluoride membranes. Nonspecific binding sites were blocked by incubation with 5% nonfat dry milk in PBST (137 mM NaCl, 27 mM KCl, 100 mM Na2HPO4, 20 mM KH2PO4, 0.05% Tween20, and pH 7.4). The polyvinylidene difluoride membranes were then incubated with primary antibodies against p-ERK1/2 (1:1000), ERK1/2 (1:1000), p-EGFR (1:1000), EGFR (1:1000), p16 (1:1000), and β-actin (1:10000) in PBST containing 5% bovine serum albumin and 5% nonfat dry milk at 4°C overnight. Membranes were washed with PBST and incubated with secondary antibodies (anti-mouse at 1:16 000, anti-rabbit at 1:16 000). Signals were then developed by using an enhanced chemiluminescence Western blotting detection kit and were exposed to X-ray films.
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