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7 protocols using phosphoserine

1

Phosphoproteomic Profiling of Hepatocytes

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Proteins (10 μg) were separated by SDS-PAGE using 12% tris-glycine polyacrylamide gel electrophoresis and then transferred to a PVDF membrane using a wet blotting system (Roche, Basel, Switzerland) to profile phosphoproteins in hepatocytes. Membranes were blocked with 5% BSA in TBST (20 mM tris, 500 mM sodium chloride, 0.1% Tween-20, pH 7.5) for 4 h at room temperature (RT) and then incubated with primary antibodies at 4 °C for 18 h. The membranes were washed thrice with TBST for 10 min and then incubated with secondary antibodies for 1 h at RT. Signals were detected using iBright 1500 (Thermo Fisher Scientific) and ECL Prime Immunoblotting Detection Reagent (Cytiva, Marlborough, MA, USA).
To verify the phosphoproteomics results, primary antibodies specific to p53 (Cell Signaling Technology, Danvers, MA, USA; P/N 2524S), histone H3 (Cell Signaling Technology; P/N 9715S), α-tubulin (Abcam, UK; P/N ab52866), phospho-serine (Abcam, P/N ab9332), phospho-threonine (Cell Signaling Technology, P/N 9381S), phospho-tyrosine (Cell Signaling Technology, P/N 9411S), phospho-c-Raf (Cell Signaling Technology, P/N 9421S), phospho-MEK1/2 (Cell Signaling Technology, P/N 9154S), phospho-ERK1/2 (Cell Signaling Technology, P/N 9101S), and ERK1/2 (Cell Signaling Technology, P/N 9102S) were used.
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2

Immunoprecipitation and Western Blot Analysis

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Cells were lysed in RIPA lysis buffer (50 mmol/L Tris pH 7.4, 120 mmol/L NaCl, 1% Triton X‐100, 1% sodium deoxycholate, .1% SDS, Beyotime, Shanghai, China) supplemented with protease inhibitors (Complete Mini, Roche, Basel, Switzerland) and phosphatase inhibitors (PhosSTOP, Roche). Equal amounts of protein were analyzed by western blot assays with indicated antibodies.
For immunoprecipitations analysis, 1000 μg of total cell lysates was incubated with the 1 μg primary antibody or control rabbit IgG at 4°C overnight; 20 μL of Protein A+G agarose (Bioworld Technology, St. Louis Park, MN, USA) was then added for 2 hours at 4°C with rocking. The precipitates were washed 4 times with RIPA washing buffer (50 mmol/L Tris pH 7.4, 150 mmol/L NaCl, 1% NP‐40, .5% sodium deoxycholate, .1% SDS, Beyotime) and boiled for 15 minutes with SDS sample buffer.
Primary antibodies: CDK2 (ab32147; Abcam, Cambridge, UK), SEPT2 (ab88657, ab179436; Abcam), Flag (ab002‐100; Multi Sciences, HangZhou, China), HA (ab003‐100; Multi Sciences), Phospho‐Threonine (#9381; CST, Boston, MA, USA), phosphoserine (ab9332; Abcam), cyclin A (sc‐239; Santa Cruz, Dallas, TX, USA), cyclin B1 (sc‐245, Santa Cruz), PCNA (sc‐56, Santa Cruz), p44/42 MAPK(Erk1/2) (#9102; CST), Phospho‐p44/42 MAPK (Erk1/2) (#4370; CST) and GAPDH (60004‐1‐Ig; Proteintech, Rosemont, IL, USA).
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3

Protein Expression of GPBAR1 and CSE in LSEC

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To investigate protein expression of GPBAR1 and CSE, LSEC were serum starved overnight and then stimulated with 10 μM BAR501 for 18 h. In another experimental setting serum starved LSEC were incubated 5, 15, 30 and 60 minutes with 10 μM BAR501. Total lysates were prepared by solubilization of endothelial cells in E1A lysis buffer containing protease and phosphatase inhibitors. The proteins were separated by SDS-PAGE, transferred to nitrocellulose membranes (Bio-Rad) and probed with primary antibodies CSE (Santa Cruz), GPBAR1/TGR5 (Abcam), tubulin (Sigma), phospho-Akt (Thr308—Santa Cruz), Akt (Santa Cruz), phospho-Serine (Abcam), phosphoeNOS (ser1177 –Cell Signaling), eNOS (Cell Signaling), phosphoFOXO1 (Thr24 –Santa Cruz) and FOXO1 (Santa Cruz). nitrocellulose membranes from immunoprecipitation (IP) experiments were first probed with a phospho-Serine antibody, stripped and then re-probed with the CSE antibody. Similarly, nitrocellulose membranes from IP experiments were first probed with the phospho-Akt antibody, stripped and then re-probed with the Akt antibody. The anti-immunoglobulin G horseradish peroxidase conjugate (Bio-Rad) was used as the secondary antibody, and specific protein bands were visualized using Super Signal West Dura (Pierce), following the manufacturer’s suggested protocol.
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4

Immunoprecipitation of TGF-β Receptor

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PAFs were seeded in 100‐mm dishes for immunoprecipitation. When the cells had grown to 70% to 80% confluence, they were starved in serum‐free medium for 24 hours. The cells were pretreated with or without 100 μmol/L Na2SO3/NaHSO3 for 60 minutes and then stimulated with or without TGF‐β1 (10 ng/mL). After 60 minutes, the cells were harvested and lysed, spun at 13 000 g for 10 minutes, and preincubated with protein A/G agarose beads (Thermo Fisher Scientific) for 1 hour at 4°C. Equal amounts of cell lysates subsequently incubated with the antibody against type I TGF‐β receptor (TβRI; Santa Cruz Biotechnology, CA) overnight at 4°C. The antibody–antigen complex was immunoprecipited with protein A/G agarose beads for 4 hours at 4°C. The precipitated proteins were resolved by 10% SDS‐PAGE and then immunoblotted with antibodies against phosphoserine (Abcam).19
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5

Mitochondrial Dynamics in LPS-Induced Inflammation

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Ultra Pure LPS (Escherichia coli 0111:B4) was obtained from List Biologicals (Campbell, CA, USA). Antibodies for CaMKIV, Parkin, Mfn1, phospho-serine, ATP5a, and actin were obtained from Abcam (Cambridge, MA, USA). Antibodies for OPA-1, Drp-1, p-Ser616-DRP1, p-Ser637-DRP1, Parkin and tubulin were obtained from Cell Signaling Technology (Danvers, MA, USA). p-Ser65-Parkin was obtained from Biorbyte Ltd (St. Louis MO, USA). Rabbit anti-PINK1 antibody was purchased from Novus Biologicals (Littleton, CO, USA). Anti-Flag antibody was purchased from Sigma Aldrich (St. Louis, MO, USA). Total mitochondrial complex (I-V) expression was analyzed using the total OXPHOS rodent antibody cocktail from Abcam. Total oxidatively modified proteins was analyzed using the OxyBlot Protein Oxidation Detection Kit from Millipore (Burlington, MA, USA).
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6

Immunoblot Analysis of Protein Expression

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Proteins were extracted from cells or lung tissues using RIPA buffer (Beyotime Biotechnology), and the protein concentrations were determined with a BCA Protein Assay Kit (Beyotime Biotechnology). Protein samples were separated using SDS PAGE, transferred to a PVDF membrane, and subjected to immunoblot analysis using specific antibodies, including those against ZNF451 (Cat# 25228-1-AP, Proteintech), acetylated-lysine (Cat# 9441, Cell Signaling Technology), GAPDH (Cat# TA-08, ZSGB-BIO, China), SLUG (Cat# 9585S, Cell Signaling Technology), phosphoserine (Cat# ab9332, Abcam), Myc (Cat# 562, MBL BIOTECH, Beijing, China), DDK (Cat# PM020, MBL BIOTECH), GFP (Cat# M048-3, MBL BIOTECH) and HA (Cat# 561, MBL BIOTECH). Binding of the primary antibody was detected by peroxidaseconjugated secondary antibodies and enhanced chemiluminescence. The signaling was visualized using a ChemiDocTM XRS+ with Image LabTM Software (Bio-Rad, Hercules, California, USA) and chemiluminescence detection reagent (Tanon).
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7

Immunoblot Analysis of Ileum Samples

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Ileum samples were resolved on SDS-polyacrylamide slab gels (precast 10% gel; Invitrogene, Carlsbad, CA). Protein was blotted onto a nitrocellulose membrane (type NC, 0.45 lm; Schleicher & Schuell Bioscience GmbH, Dassel, Germany) using a Novext blotting apparatus and the manufacturer's protocol. The nitrocellulose membrane was blocked by incubation for 90 min at room temperature in phosphate buffered saline (PBS) containing 5% nonfat dried milk. The blot was then incubated overnight with specific antibodies primary antibodies to actin, HSP-70, HSP-90 (Santa Cruz Biotechnologyt Inc., Dallas, TX); PDH (BD Transduction Laboratories, San Diego, CA); phosphoserine (Abcam, Cambridge, MA); and pyruvate dehydrogenase kinase 1 (PDK-1; Cell Signaling Technologyt, Danvers, MA) in PBS-5% bovine serum albumin (BSA). The blot was washed three times (10 min each) in Tris-buffered saline (TBS), 0.1% Tweent 20 before it was incubated for 60 min at room temperature with a 1,0003 dilution of species-specific IgG peroxidase conjugate (Santa Cruz Biotechnology) in 1% gelatin in PBS. The blot was washed six times (5 min each) in TBS, 0.1% Tween 20 before detection of the peroxidase activity using the Enhanced Chemiluminescence Kit (Amersham Life Science Products, GE Healthcare Bio-Sciences Corp., Piscataway, NJ).
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