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18 protocols using n dodecyl β d maltoside ddm

1

C2C12 Cell Fractionation and Immunoblotting

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To fractionate C2C12 cells into cytosolic and membrane fractions, we first washed a 10‐cm dish with cold PBS and lysed the cells by homogenization in hypotonic buffer (10 mM Tris pH 8.0, 1 mM ethylenediaminetetraacetic acid [EDTA]) supplemented with 1 mM phenylmethane sulfonyl fluoride (PMSF) and a protease inhibitor mix. The homogenate was centrifuged at 15,000 revolutions per minute (RPM) for 5 min to pellet nuclei and cell debris. The supernatant was centrifuged at 12,000 RPM for 20 min to pellet membrane structures. The supernatant from this step was the cytosolic fraction, and the membrane fraction was solubilized in an equal volume of hypotonic buffer + 1% n‐dodecyl β‐d‐maltoside (DDM; Sigma‐Aldrich, St. Louis, United States) for further analyses by immunoblotting.
For analysis of whole‐cell extracts, Radioimmunoprecipitation assay buffer (RIPA buffer) (10 mM Tris–Cl [pH 8.0], 1 mM EDTA, 0.5 mM egtazic acid (EGTA), 1% Triton X‐100, 0.1% sodium deoxycholate, 0.1% sodium dodecyl sulfate [SDS], 140 mM NaCl) supplemented with 1 mM PMSF and a protease inhibitor mix was used for cell lysate preparation.
For immunoblotting, equal protein amounts were separated by 12% SDS–polyacrylamide gel electrophoresis, transferred to a PVDF membrane (Millipore, MA), blocked in 5% milk in TBS‐tween, and incubated with primary antibodies.
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2

Antibody and Reagent Characterization for Protein Signaling

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Mouse anti-β-arrestin-1 polyclonal antibody was from Abmart. Rabbit anti-β-arrestin-1 (A1CT) antibody was a gift from Dr. Robert J. Lefkowitz. Rabbit anti-PPARα polyclonal antibody was purchased from Abcam. Rabbit anti-PPARγ polyclonal antibody was from Santa Cruz Biotechnology. Thrombin protease was obtained from GE Healthcare. 15NH4Cl was from Cambridge Isotope Laboratories. Inc. Rosiglitazone, GW7647, and n-Dodecyl β-D-maltoside (DDM) were from Sigma.
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3

Antimony-Based Leishmania Treatment Assay

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Trivalent antimony (SbIII), amphotericin B (AmB), paromomycin, Triton X-100, paraformaldehyde, 4′,6-diamidino-2-phenylindole dilactate (DAPI), n-dodecyl-β-D-maltoside (DDM), 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and phorbol 12-myristate 13-acetate (PMA) were obtained from Sigma-Aldrich (St. Louis, USA). Miltefosine was purchased from Æterna Zentaris (Frankfurt, Germany). Glucantime® was purchased from Sanofi-Aventis (Paris, France). L-glutamine and penicillin/streptomycin were obtained from Gibco. All chemicals were of the highest quality available.
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4

Protein Extraction and Solubilization Protocol

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Dithiothreitol (DTT), iodoacetamide (IAA), formic acid (LC-MS grade), Na2HPO4, and NaH2PO4 were purchased from Thermo Fisher Scientific (Waltham, MA). Ammonium bicarbonate (ABC) buffer (50 mM) was freshly prepared from a 500 mM stock solution. LC-MS grade water and acetonitrile were purchased from Honeywell (Charlotte, NC). Trypsin gold and rLys-C (MS grade) were from Promega (Madison, WI). Scott’s tap water substitute bluing reagent was from Ricca Chemical (Arlington, TX). Ethanol was purchased from Decon Laboratories, King of Prussia, PA, and paraffin wax was from Blended Waxes, Inc. (Oshkosh, WI). Other chemicals were from Sigma-Aldrich (St. Louis, MO). Neutral buffered formalin (pH 6.8–7.0) was prepared by combining 25 mL (37–40% w/w) of formaldehyde with 225 mL of purified water, 1.0 g of NaH2PO4, and 1.625 g of anhydrous Na2HPO4. Carboxymethylcellulose solution (CMC; 2.5% w/v in water) was prepared for embedding fresh samples prior to freezing. A stock solution of n-dodecyl-β-d-maltoside (DDM, Sigma-Aldrich), a nonionic surfactant used for protein extraction and solubilization,36 (link) was prepared at 1% (w/v) in water and further diluted for use, as described below. Nanowell chips were fabricated as described previously.17 (link)
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5

Biochemical Reagent Sourcing for Protein Analysis

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Sucrose and mannitol were purchased from BDH Chemicals and Mallickrodt Chemicals, respectively. Bis-Tris, tricine, and amino-caproic acid were purchased from MB Biochemicals (Irvine, CA). Pre-stained SDS-PAGE markers were purchased from Thermo Scientific (Pittsburgh, PA). Bradford protein assay solution and Coomassie brilliant blue (CBB) R-250 were from Bio-Rad laboratories (Richmond, CA). Silver nitrate, streptozotocin (STZ), sodium citrate, NADH, EDTA, n-dodecyl-β-D-maltoside (DDM), and nitro blue tetrazolium (NBT) chloride tablets were obtained from Sigma (St. Louis, MO, USA). Serva Blue G was purchased from Serva (Heidelberg, Germany). Rabbit anti-HNE polyclonal antibodies (IgG) and goat anti-rabbit IgG conjugated with horseradish peroxidase were purchased from US Biological (Salem, MA) and Invitrogen (San Diego, CA), respectively. Hybond-C membrane and a Western blot detection kit were obtained from GE Healthcare (Piscataway, NJ).
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6

Protein Preparation for Mass Spectrometry

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Dithiothreitol (DTT) and iodoacetamide (IAA) (ThermoFisher Scientific, Waltham, MA) were freshly prepared in 50 mM ammonium bicarbonate (ABC) buffer. n-Dodecyl β-D-maltoside (DDM) (Sigma-Aldrich, St. Louis, MO) was dissolved in 50 mM ABC buffer with a concentration of 1% (w/w), aliquoted, and stored at −20°C until use. MS-grade trypsin and Lys-C were products of Promega (Madison, WI, USA). Other unmentioned reagents were obtained from Sigma-Aldrich (St. Louis, MO, USA). Deionized water (18.2 MΩ) was purified using a Barnstead Nanopure Infinity system (Los Angeles, CA, USA).
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7

Mitochondrial Membrane Protein Extraction

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Cultured fibroblasts were harvested, resuspended in homogenisation buffer (HB) (0.6 M mannitol, 1 mM ethylene glycol tetraacetic acid, 10 mM Tris-HCl pH 7.4, 1 mM PMSF and 0.1% (v/v) bovine serum albumin (BSA)) and subjected to 3 × 15 passes of homogenisation using a Teflon glass Dounce homogeniser at 4 °C. Standard differential centrifugation (400 g for 10 min) was used to remove nuclei and cell debris and mitochondria were finally pelleted at 11 000 g for 10 min at 4 °C. Mitochondria were washed in HB without BSA and the final pellet was solubilised by n-Dodecyl β-D-maltoside (DDM) (Sigma) at 2 mg/mg protein on ice for 20 min. Following centrifugation (100 000 g for 15 min at 4 °C) the supernatant was collected and Coomassie Blue G-250 (AMS Biotechnology (Europe) Ltd, Abingdon, UK) was added. Mitochondrial membrane proteins (50 μg) were loaded on a NativePAGE 4–16% BisTris gel (Life Technologies), electrophoretically separated and transferred to a PVDF membrane. The membrane was subsequently immunoblotted with antibodies raised against OXPHOS complexes.
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8

Isolation and Analysis of Mitochondrial Complexes

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Mitochondria from cultured cells were isolated as previously described37 (link). Mitochondrial membrane proteins were isolated from whole cells or mitochondria with n-dodecyl-β-D-maltoside (DDM, Sigma, St. Louis, USA) at the required ratio38 (link). Protein (60 μg) containing 0.5% Blue G-250 (Sigma, St. Louis, USA) and 5% glycerol were separated by BN-PAGE (3–11% gel) as previously described38 (link). For complex I in-gel activity assays, gels were soaked in assay buffer [25 mg nitrotetrazolium blue (NTB) (Sigma, St. Louis, USA) and 10 μl 1 mg/ml reduced nicotinamide adenine dinucleotide (NADH) (Sigma, St. Louis, USA) in 10 ml 5 mM Tris/HCL (pH 7.4)] for approximately 1 h. For complex IV assays, gels were soaked in Assay buffer [50 mM NaH2PO4 (pH 7.4), 5 mg 3, 3’-Damiobenzidine tetra hydrochloride hydrate (DAB) (Sigma, St. Louis, USA) and 50 μM cytochrome C (Sigma, St. Louis, USA)].
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9

Blue Native Gel Electrophoresis of Plasmodium Proteins

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Protein samples (~150 μg) were resuspended in 500 mM 6-aminohexanoic acid, 1 mM EDTA and 50 mM imidazole/HCl (pH 7.0) and solubilized with either Triton X-100 (Sigma), Digitonin (SERVA) or n-dodecyl-β-D-maltoside (DDM) (Sigma) using detergent:protein (w/w) ratios of 10:1, 6:1 and 3:1, respectively. The solubilized samples were centrifuged at 22,000 × g for 20 min; 4 °C. The supernatants were recovered, supplemented with Coomassie-blue loading buffer and separated on either a 4–16% or 3–16% polyacrylamide gradient blue native gels as described previously17 (link). For mass calibration, purified bovine heart mitochondria (50–100 μg) solubilized under the same conditions were run alongside each set of Plasmodium samples.
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10

BN-PAGE Gel Shift Assay for Env Variants

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BN-PAGE gel mobility shift assays were performed using virions produced by transfection of the infectious molecular clone plasmid pLAI displaying the Env variant ADA.CM (Leaman and Zwick, 2013 (link)). Virions and a dilution series of Fab were incubated at RT for 30 min. The virion/Ab mixture was solubilized in 1% n-Dodecyl β-D-maltoside (DDM; Sigma) for 20 min on ice, and then run on a 3–8% gradient Tris-Acetate NuPAGE gel (ThermoFisher) in Tris-Glycine Native Sample Buffer (ThermoFisher), supplemented with 0.25% Coomassie G-250. Gels were run for 3 h at 150 V in Tris-Glycine Native Running Buffer (ThermoFisher) + 0.002% Coomassie G-250. Proteins were transferred onto PDVF membrane and Western blotted using a cocktail of primary antibodies to gp120 (F105, 2G12 and HGN194, 2 μg/mL each) and gp41 (10E8, 2F5, and 7B2, 1 μg/mL each) followed by a goat anti-human-Fcγ-HRP secondary antibody (Jackson). The blot was developed using ECL Plus Substrate (Pierce) and a ChemiDoc XRS + Imaging System (Bio-Rad).
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