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9 protocols using anti pak2

1

Quantification of Phosphorylated Proteins

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Cells were resuspended to a concentration of 2 million/ml in RPMI with 0.2% FBS. We stimulated cells with 10 nM fMLP and quenched the reaction at the indicated time points by adding aliquots of the cell mixture to ice-cold 20% trichloroacetic acid (TCA) containing the phosphatase inhibitors 40 mM NaF and 20 mM β-glycerol phosphate (50020; Fluka, St. Gallen, Switzerland). The samples were spun at 20,000 × g for 15 min to pellet. The sample pellets were washed with 0.5% TCA and resuspended in Laemmli protein sample buffer (161-0737; Bio-Rad) containing 5% β-mercaptoethanol. Protein bands were separated by SDS–PAGE gel electrophoresis, transferred to nitrocellulose, blocked with Odyssey block, and incubated at 4°C overnight with 1:1000 dilutions of anti–phospho-PAK (2605S; Cell Signaling, Danvers, MA) and anti-Pak2 (4825S; Cell Signaling) or anti–phospho-Akt (4060S; Cell Signaling) and anti-Akt (40D4; Cell Signaling). The blot was developed with the fluorescent secondary antibodies, and protein bands were imaged using an Odyssey Infrared Imaging System (LI-COR Biosciences, Lincoln, NE).
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2

Analyzing Protein Expression in Cellular Compartments

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Cytoplasmic and nuclear fractions were separated by using a Qproteome cell compartment kit (Qiagen). Standard Western blot assays were used to analyze protein expression in cells. The following antibodies were used for assays: anti-p53 (1:2000 dilution; Santa Cruz Biotechnology, FL393), anti-Flag (1:40,000 dilution; Sigma, F7425), anti-Rac1 (1:4000 dilution; Millipore, 05-389), anti-HA (1:2000 dilution; Roche, 12013819001), anti-Myc (1:2000 dilution; Santa Cruz Biotechnology, SC-40 HRP), anti-SENP1 (1:2000 dilution; Cell Signaling Technology, 11929), anti-α-tubulin (1:2000 dilution; Santa Cruz Biotechnology, sc8035), anti-Histone H3 (1:1000 dilution; Cell Signaling Technology, 9715), anti-SUMO-1 (1:2000 dilution; Cell Signaling Technology, 4930), anti-p-PAK1/2 (1:1000 dilution; Cell Signaling Technology, 2606), anti-PAK1 (1:2000 dilution; Cell Signaling Technology, 2602), and anti-PAK2 (1:2000 dilution; Cell Signaling Technology, 2615).
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3

Molecular Profiling of Mitochondrial Dynamics

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Primary antibodies used for western blot were anti-choline kinase α, anti-Mfn2 (Abcam); anti-Drp1, anti-Opa1 (BD Biosciences); anti-Pak1, anti-Pak2, anti-phospho-Pak1(S144)/Pak2(S141), anti-pDrp1(S637), anti-Tom20 (Cell Signaling Technology); anti-choline kinase β, anti-Vdac1, anti-Mfn2 (Santa Cruz); and anti-Gapdh (Ambion). Secondary antibodies used were anti-mouse HRP IgG and anti-rabbit HRP (Cell Signaling Technology). For immunofluorescence, primary antibodies used were dystrophin and Ki67 (Abcam), Pax7 (DSHB), and laminin (Sigma). Alexafluor-488-conjugated wheat germ agglutinin and secondary antibodies (anti-mouse IgG1 Alexafluor-647 and anti-rabbit Alexafluor-488) were from Invitrogen. For references on use of selected antibodies, see [18 ] (Pak1, Pak2, pPak1/2, GAPDH); [27 (link)] (DRP1, pDRP1(S637), Opa1, Mfn1, Mfn2,); [28 (link)] (laminin); [29 (link)] (Ki67); and [30 (link)] (choline kinase α).
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4

Comprehensive Antibody Panel for PAK Family

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Anti-PAK1, anti-PAK2 and anti-GEFH-1 were purchased from Cell Signalling Technology. Anti-c-Myc and anti-PAK5 were acquired from Santa Cruz. Anti-Cortactin from Upstate. Anti-GAPDH from Millipore. Anti-p-GEFH-1 (Ser885) from Abcam. Anti-PAK3 from New England Biolabs and anti-PAK6 from Calbiochem. Anti-GFP from Roche Life Science. Anti-β-Actin and anti-β-Tubulin from Sigma Aldrich. Anti-HMWMAA and anti-human IgG kind gift from Sophia Karagiannis, King's College London (KCL). Anti-PAK4 was previously described [17 (link)]. Horseradish peroxidase (HRP) conjugated secondary antibodies were purchased from DAKO. The Alexa Fluor 488 conjugated antibodies and Phalloidin from Invitrogen. GFP-PAK1r, GFP-PAK4r, HA-PAK4r and HA-PAK4K350/351Mr were constructed by site-directed mutagenesis, according to the manufacturer's instructions, using the QuikChange Multisuite II kit (Stratagene). The Myc-PDZ-RhoGEF and Myc-PDZ-RhoGEFΔDH were kind gifts from John Masters, University College London (UCL). The RhoA Biosensor was generously provided by Maddy Parsons, (KCL). IPA-3 was purchased from Sigma.
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5

Total Protein Extraction and Western Blotting

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For total protein extraction, the tissue and cell samples were lysed in Radio Immunoprecipitation assay (RIPA) lysis solution (CWBIO) with protease and phosphatase inhibitors (Roche, Madison, WI, USA), followed by denaturation at 95 °C for 10 min. The denatured supernatant was separated using sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (12%) and transferred to polyvinylidene difluoride membranes at 4 °C for 90 min. The membranes were blocked with BSA (5%) or defatted milk (5%) and incubated with primary antibody in BSA (5%) at 4 °C overnight. The primary antibodies were obtained from Cell Signaling Technology, including anti‐PAK2 (1:1000; Cat# 2608), anti‐p‐Smad1/5/9 (D5B10) (1:1000; Cat# 13820), anti‐p‐Smad1/5(41D10) (1:1000; Cat# 9516), and anti‐p‐PAK1 (Ser144)/PAK2 (Ser141) (1:1000; Cat# 2606); and from Abcam, including Smad1/5/9 (1:1000; Cat# ab66737). The secondary antibodies used were anti‐rabbit IgG conjugated to horse radish peroxidase (HRP) (Cat# 7074, Cell Signaling Technology) and anti‐mouse IgG conjugated to HRP (Cat# 7076, Cell Signaling Technology). Signals were detected using the FluorChem E imaging system (Cell Biosciences, San Jose, CA, USA) and analyzed using ImageJ software (version 1.4.3.67). The relative levels of these proteins were normalized to that of GAPDH (1:5000; Cat# 60004, Proteintech, Rosemont, IL, USA).
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6

Protein Expression Analysis in Cell Lysates

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Embryo or cell lysates were prepared using standard lysis buffer containing 50 mM Tris (pH 7.5), 150 mM NaCl, 0.5% (v/v) NP-40, 1 mM Na3VO4, 10 mM NaF, and 1× protease inhibitor cocktail (Roche). Proteins were separated by 4%–12% NuPAGE Bis-Tris gels (Invitrigen) and analyzed using the following primary antibodies: polyclonal rabbit anti-β-Pix 07-1450 (1:2000; Millipore-Chemicon), mouse anti-β-actin AC-74 (1:10,000; Sigma), monoclonal rabbit anti-PAK-1 (1:1000; Cell Signaling), anti-PAK-2 (1:1000; Cell Signaling), rabbit anti-GIT (1:1000; Cell Signaling), rabbit anti-N-cadherin (1:1000; Zymed ), and mouse anti-E-cadherin (1:1000; BD Biosciences). HRP-conjugated secondary antibodies (Dako) were used at 1:5000 dilution.
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7

Western Blot Analysis of Cellular Proteins

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Proteins were separated by sodium dodecyl sulfate–polyacrylamide gel electrophoresis and transferred to polyvinylidene difluoride (PVDF) membrane (Millipore). The protein containing PVDF membranes were probed with different primary antibodies: anti-PAK2 (2615, Cell Signaling Technology, Beverly, MA, USA), anti-c-Myc (9402, Cell Signaling Technology, Beverly, MA, USA), anti-CCND1 (ab134175, Abcam, Melbourne Australia), anti-PKM2 (4053, Cell Signaling Technology, Beverly, MA, USA), anti-Active β-Catenin (05665, Millipore, Burlington, USA), anti-GAPDH (5174, Cell Signaling Technology, Beverly, MA, USA), anti-β-Catenin (9562, Cell Signaling Technology, Beverly, MA, USA) and anti-flag (NBP1-06712SS, Novus Biologicals, Littleton, CO, USA) in a 1:1000 dilution. After 2 h of primary antibody incubation at room temperature, membranes were washed with 1× TBST (tris-buffered saline and Tween-20) and incubated with secondary antibodies Alexa-Flour 680 anti-rabbit IgG (A21109, Thermo Fisher Scientific, Waltham, MA, USA) and Alexa-Flour 790 goat anti-mouse IgG (A28182, Thermo Fisher Scientific, Waltham, MA, USA) for 30 min at room temperature. The membrane was washed, and bands were visualized using an Odyssey membrane Scanning system (Li-Cor Biosciences, Bad Homburg, Germany).
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8

Efficient siRNA Knockdown Optimization

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The 24ST1NLESG cells were transfected by electroporation using the Neon Transfection System (Life Technologies, Carlsbad, CA, USA). Electroporation parameters were 1350 Pulse Voltage (V), 10 Pulse Width (ms), 3 Pulse Number, 2 × 107 cell/mL. Final concentrations were 1 × 107 cell/mL, 1 µM siRNA (siPAK1, Dharmacon, cat # L-003521-00-0020; siPAK2, Dharmacon, cat # L-003597-00-0020; siPAK4, Dharmacon, cat # L-003615-00-0020; siMAPK1, Thermofisher cat # 4390824; siPKA, Thermofisher cat # 4390825; Non-targeting Control, Dharmacon, cat # D-001810-10-20). The efficiency of siRNA knockdown was assessed by Western blot analysis. Anti-PAK1 (cat # 2602S), anti-PAK2 (cat #2608S), anti-PAK4 (cat # 62690), anti-PKA (cat # 4782), anti-MAPK (cat # 9108), and anti-GAPDH (cat # 97166S) antibodies were purchased from Cell Signaling. The efficiency of siRNA knockdown was quantified using ImageJ.
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9

Western Blot Analysis of Protein Expression

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Total protein was extracted from H9c2 cells or mouse left ventricle tissue by the radio immunoprecipitation assay (RIPA) Lysis Buffer (Solarbio, Beijing, China) according to the manufacturer’s instructions. Proteins were separated by electrophoresis on the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) (10–12% polyacrylamide gels) and then transferred to polyvinylidene fluoride (PVDF) membranes. Subsequently, the PVDF membranes were blocked in 5% non-fat milk for 2 h and then incubated overnight at 4°C with anti-PAK2 (1:1,000, Cell Signaling Technology, Danvers, MA, United States), or anti-XBP1s (1:1,000, Cell Signaling Technology, Danvers, MA, United States), or anti-β-actin (1:2,000, Santa Cruz Biotechnology, Dallas, TX, United States), or anti-GAPDH (1:100,000, ABclonal, Wuhan, China), or anti-cas-12 (1:2,000, Abcam, United States) primary antibodies after washing with TBS-Tween 20 (TBST) three times, 10 min each time. Horseradish peroxidase (HRP)-conjugated secondary antibodies were incubated at room temperature for 1 h, then washed with TBST three times, 10 min each time. Membranes were visualized using enhanced chemiluminescence. Protein expression was quantified using ImageJ, and β-actin or GAPDH was used as the internal control.
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