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Nupage sds page

Manufactured by Thermo Fisher Scientific

NuPage SDS-PAGE is a pre-cast polyacrylamide gel system designed for the separation and analysis of proteins. It provides a simple and consistent method for performing sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE).

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16 protocols using nupage sds page

1

Isolation and Cross-Linking of Yeast Nuclear Pore Complexes

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Intact S. cerevisiae NPCs were isolated following the method described (Kim et al., 2018 (link)). To minimize local domain movements, purified NPCs were mildly cross-linked by the addition of DSS (DiSuccinimidylSuberate, Creative Molecules) to yield a final concentration of 0.5 mM and incubated for 30 min at 25°C with gentle agitation in a shaker (900 rpm). The reaction was then quenched by addition of ammonium bicarbonate to a final concentration of 50 mM. After Cysteine reduction, cross-linked samples were separated by NuPage SDS-PAGE (4%–12%, Invitrogen) for quality control and concentration estimation. Gels were briefly stained by GelCode Blue Stain Reagent (Thermo Fisher Scientific) to enable the visualization of the protein complex. Aliquots of crosslinked NPCs (~0.3 mg/mL) were flash frozen and stored at −80°C in small aliquots in buffer: 20 mM HEPES (pH7.5), 50 mM Potassium acetate, 20 mM NaCl, 2 mM MgCl2, 1 mM DTT, 0.1% Tween 20) supplemented with 10% glycerol. Samples were thawed only once prior to making grids for data collection.
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2

Expression and Purification of Mouse Cadherin and Protocadherin Constructs

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Recombinant modified pcDNA3 vectors encoding the entire cytoplasmic regions of mouse cadherin-23, Pcdh15-CD2 and Pcdh15-CD3 (GenBank Accession Nos. Q99PF4, Q0ZM28, and Q0ZM20, respectively) coupled to an N-terminal Flag-tag were constructed for expression in HEK-293 cells. Cell lysates were prepared in Nupage Sample Buffer (Invitrogen).
A recombinant modified pFastbac vector encoding the cytoplasmic domain of mouse Pcdh15-CD1 (GenBank Accession No. NP_001165405) was constructed for expression in Sf9 insect cells. The N-terminally tagged fusion product, 6His-Flag-protein, was purified on a Ni-NTA column.
All samples were resolved by 4–8% Nupage SDSPAGE (Invitrogen). Proteins were transferred to PVDF membranes (Millipore) and immunoprobed, and bound antibody was detected by enhanced chemiluminescence (Pierce Biotechnology). A monoclonal anti-flag antibody was used to detect the four recombinant proteins (M2 Sigma-Aldrich, 1:500 dilution).
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3

Cytoplasmic Region Protein Expression

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The cDNAs encoding the cytoplasmic regions of mouse CDH23, PCDH15-CD1, PCDH15-CD2, and PCDH15-CD3 (Genbank accession no. AY563163, Q99PJ1-1; Q99PJ1-10, and Q99PJ1-18, respectively), were cloned in modified pcDNA3 vectors with a Flag-tag-encoding sequence at their 5′ end. The cDNAs encoding the short and long isoforms of whirlin were cloned in PCMV vectors. The various recombinant proteins were produced in transfected HEK-293 cells. Cells were collected 48 h after transfection by centrifugation. The pellets were dissolved in Nupage Sample Buffer (Invitrogen) and submitted to 4–12% Nupage SDS-PAGE (Invitrogen). The separated proteins were blotted onto PVDF membranes (Millipore), and were processed for immuno-chemiluminescence detection (Pierce Biotechnology). An anti-flag monoclonal antibody (M2 Sigma-Aldrich, 1:500 dilution) was used to detect Flag-CDH23 cyto, Flag-PCDH15-CD1 cyto, Flag-PCDH15-CD2 cyto and Flag-PCDH15-CD3 cyto.
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4

Isolation and Cross-Linking of Yeast Nuclear Pore Complexes

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Intact S. cerevisiae NPCs were isolated following the method described (Kim et al., 2018 (link)). To minimize local domain movements, purified NPCs were mildly cross-linked by the addition of DSS (DiSuccinimidylSuberate, Creative Molecules) to yield a final concentration of 0.5 mM and incubated for 30 min at 25°C with gentle agitation in a shaker (900 rpm). The reaction was then quenched by addition of ammonium bicarbonate to a final concentration of 50 mM. After Cysteine reduction, cross-linked samples were separated by NuPage SDS-PAGE (4%–12%, Invitrogen) for quality control and concentration estimation. Gels were briefly stained by GelCode Blue Stain Reagent (Thermo Fisher Scientific) to enable the visualization of the protein complex. Aliquots of crosslinked NPCs (~0.3 mg/mL) were flash frozen and stored at −80°C in small aliquots in buffer: 20 mM HEPES (pH7.5), 50 mM Potassium acetate, 20 mM NaCl, 2 mM MgCl2, 1 mM DTT, 0.1% Tween 20) supplemented with 10% glycerol. Samples were thawed only once prior to making grids for data collection.
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5

Assaying HAD2 Phosphatase Activity

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Recombinant HAD2aD262A and HAD2bD171A were purified in parallel with wild type proteins under identical conditions (see recombinant protein expression). Proteins were separated with 12% NuPage SDS-PAGE (Invitrogen) and stained with Coomassie Blue. Phosphatase activity was assessed by conversion of the phosphatase substrate para-Nitrophenyl Phosphate (p-NPP, Sigma), based on published methods (Zhuo et al., 1993 (link), Takai & Mieskes, 1991 (link)). 1 μg of recombinant protein (His6-HAD2a, His6-HAD2b and respective D->A mutants) was incubated with 27 mM p-NPP in 50 mM HEPES (pH 7.5), 1 mM DTT for 4 hrs at RT and OD405 nm of triplicate reactions was measured in a M5 SpectraMax spectrophotometer (Molecular Devices). Reactions were done in presence of either 5 mM MgCl2, 0.5 mM MnCl2 or a combination of both salts and background corrected values are depicted as percentage of control (in absence of cation).
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6

Immunoblotting of Protein Modifications

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Proteins were separated using 4–12% Nu-PAGE SDS-PAGE (Invitrogen) and stained with a silver stain kit (Thermo), or transferred onto PVDF membranes. Membranes were stained with 0.1% Ponceau S in 5% acetic acid to verify that equal amounts of proteins were loaded.18 (link) Western blots were performed with the following antibodies: monoclonal anti-K63 (Apub3, Millipore, Darmstadt, Germany), monoclonal anti-K48, (Apub2, Millipore), and polyclonal antiubiquitin (AB1690, Millipore), anti-S100A6 (H-55, Santa Cruz Biotech, Dallas, TX, USA, and Sigma-Aldrich), anti-MHC class I (Santa Cruz Biotech) and hnRNP K (H-300, Santa Cruz Biotech and Sigma-Aldrich). Blots were developed with ECL reagent (Pierce, Rockford, IL, USA) and visualized in a Fluor-Chem Q imaging system (Alpha Innotech, Santa Clara, CA, USA).
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7

Protein Extraction and Western Blot Analysis

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Whole-cell protein extracts were prepared from different types of cells using RIPA buffer. Western blot analyses were performed using NuPAGE SDS-PAGE (Invitrogen) or Mini-PROTEAN TGX (Bio-Rad) precast acrylamide gels according to the manufacturer’s instructions, and proteins were transferred to Amersham Protran 0.45 μm nitrocellulose membrane (GE Healthcare Life Sciences) in 1× Towbin Transfer Buffer (25 mM TRIS, 192 mM glycine, 20% methanol). Membranes were blocked with 5% non-fat dry milk (Difco skim milk) for 1 h and incubated overnight at 4°C with the following primary antibodies: anti-LHX1 (PA5-78394, Invitrogen); anti-PDIA3 (ab10287, Abcam); anti-GAPDH (6C5, sc-32233, Santa Cruz Biotechnology). The following secondary antibodies were used: goat anti-rabbit HRP (31460, Invitrogen) and goat anti-mouse HRP (32430, Invitrogen). Protein detection was carried out with WesternBright ECL (Advansta) using ChemiDocTM MP System.
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8

Cytosolic and Total Cell Protein Extraction

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Cytosolic protein extracts were obtained by re-suspending the cell pellet in 250 mM sucrose, 50 mM Tris-HCl pH 7.4, 5 mM MgCl2 and total cell extracts were obtained in RIPA buffer. Both were supplemented with cOmplete Mini Protease Inhibitor Cocktail (Roche Applied Science), followed by 20 strokes with a Dounce homogenizer and centrifugation at 3000 rpm for 10 min for cytosolic extracts or 14000 rpm for 30 min for total cell extracts. Western blot was performed in a NuPAGE SDS-PAGE (LifeTechnologies) system for the following primary antibodies: rabbit anti-AIF and mouse anti-RIP (1:2000 to 1:200, from BD Biosciences), cleaved PARP D-214 (Cell Signaling), mouse anti-cytochrome c (1:200) (clone 7H8.2C12, Abcam) and MFN1 (H-65) and MFN2 (H-68, Sta. Cruz Technologies). β-actin antibody coupled to peroxidase (1:5000, Sta. Cruz Technologies ) was used as a loading control.
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9

Dysferlin Protein Detection Protocol

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Detection of dysferlin was performed using the following protocol with primary anti-dysferlin antibodies (NCL-Hamlet 2, Cliniscience) diluted 1:300 or (NCL-Hamlet, Abcam) diluted 1:200 on untreated and treated patient cell protein extracts. Immunoblots were done using a whole protein extract sample prepared in lysis buffer (100 mM Tris buffer at pH 6.8, 4% SDS, 10% glycerol and 1% 2-mercaptoethanol). A 1% reducing agent (Life Technologies) was added and the samples were boiled for ten minutes. 20 μg of sample was loaded onto each lane of a 3–8% NuPage SDS–PAGE (Life Technologies). Proteins were then separated under electrophoresis at 80 volts at room temperature. Proteins were finally transferred onto nitrocellulose membranes (at 260 mA for 2 h at 4°C). Membranes were incubated with blocking buffer (1% non-fat milk powder in TBS-T) for one hour at room temperature. Primary antibodies were then diluted in blocking buffer and incubated with the membranes at room temperature for 1 h, with constant agitation. After washing in TBS-T, membranes were then incubated with the relevant secondary antibodies, which were diluted 1:10,000 in blocking buffer, for one hour at room temperature. The membranes were finally washed in TBS-T and developed using Pico Chemiluminescent Substrate (Pierce). GAPDH (Millipore) was detected using a dilution of 1:10,000.
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10

Protein Expression Analysis Protocol

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Protein extracts were made as described8 . 30 μg of protein was separated by 4–12% NuPAGE SDS-PAGE (Thermo). Proteins were detected using the following antibodies; anti-DNAJA1/HDJ2 (Thermo # MA5-12748), anti-Actin (CST # 9774), Anti-Hsc70 (Santa Cruz, # sc-7298), anti-Hsp70 (Enzo # C92F3A­5), anti-Hsp90 ⍺/ℬ (Santa Cruz # sc-13119), anti-Bag3 (Santa Cruz # sc-136467), anti-Hsp110 (Stress Marq, # SPC-195),) at 1:4,000 dilution in TBST + 1% BSA. The secondary antibody (StarBright Blue 700 Fluorescent Secondary Mouse) was used at 1:3,000 dilution in TBST + 1% BSA. Blots were imaged on a Chemi Doc MP imaging system (Bio-Rad).
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