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Ubiquitin from bovine erythrocytes

Manufactured by Merck Group
Sourced in United States

Ubiquitin from bovine erythrocytes is a purified protein that is commonly used in research applications. It is a small, highly conserved protein that plays a crucial role in the regulation of protein degradation and various cellular processes. This product provides a reliable source of ubiquitin for researchers studying the ubiquitin-proteasome system or other related areas of cellular biology.

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10 protocols using ubiquitin from bovine erythrocytes

1

Protein Mixture Preparation for Mass Spectrometry

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Ubiquitin from bovine erythrocytes, cytochrome c from equine heart, and myoglobin from equine heart were purchased from Sigma-Aldrich (St. Louis, MO, USA). Trimethylamine was purchased from EMD Chemicals (Gibbstown, NJ, USA). HPLC-grade methanol and Optima LC/MS-grade water were purchased from Fisher Scientific (Fair Lawn, NJ, USA), and acetic acid was purchased from Mallinckrodt (Phillipsburg, NJ, USA). Protein stock solutions were prepared at a concentration of approximately 1 mg/mL. Stocks were diluted to a concentration of 1 μM, 2 μM, and 2 μM for ubiquitin, cytochrome c, and myoglobin, respectively, in 49.5/49.5/1, by volume, water/methanol/acetic acid. A simple protein mixture of 1μM cytochrome c and 1 μM myoglobin was prepared in 49.5/49.5/1, by volume, water/methanol/acetic acid.
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2

ESI-MS Analysis of Proteins

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Ubiquitin from bovine erythrocytes, azurin, and equine heart cytochrome c were purchased from Sigma-Aldrich (St. Louis, MO, USA). β-2-microglobulin (β2m) was purchased from Fitzgerald Industries International, Inc. (Concord, MA, USA). The His-tagged R131Q mutant of the cellular retinoic acid binding protein I (CRABP I) was a gift from Professor Lila M. Gierasch's group at the University of Massachusetts Amherst. Ammonium acetate, water, methanol and acetic acid were obtained from Fisher Scientific (Fair Lawn, NJ, USA).
Protein solutions for ESI-MS analysis were prepared by diluting stock solutions in de-ionized water to a final concentration of 1-5 μM in 5 mM Ammonium acetate. The pH of the solution was then adjusted with acetic acid to the level used to obtain the NMR or X-ray crystal structures of the protein of interest.
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3

Protein Sample Preparation Protocol

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Methanol, N,N-dimethyl formamide (DMF), and formic acid were purchased from Fisher Scientific (Fairmont, NJ). Ubiquitin from bovine erythrocytes, myoglobin from horse heart, cytochrome c from equine heart, and ammonium acetate were purchased from Sigma-Aldrich (St. Louis, MO). 1-Hydroxy-7-azabenzonitrazole (HOAt) was purchased from TCI America (Portland, OR). 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) was purchased from Thermo Scientific (Rockford, IL). 3-Sulfobenzoic acid monosodium salt was purchased from Alfa Aesar (Ward Hill, MA).
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4

Optimizing Mass Spectrometry Experiments

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Ubiquitin from bovine erythrocytes
(≥98% purity) and ammonium acetate were purchased from Sigma
Chemical Co. (St. Louis, MO, USA). Acetic acid and HPLC-grade water
were obtained from Fisher Scientific (Leics, UK). All reagents were
used without further purification. Two 10 μM solutions were
prepared by dissolving ubiquitin in either aqueous 1% Acetic acid
or in 100 mM ammonium acetate aqueous solution, corresponding to the
partially unfolded (charge states 7+ and 8+) and the native protein
conformations (charge states 5+ and 6+), respectively. Papaverine
hydrocloride (99%) was purchased from ACROS Organics and a 0.1 mM
stock solution was prepared in ACN/H2O/AcOH 90:10:0.1 (v/v/v).
A series of dilutions were performed to final concentrations of 0.003,
0.03, 0.15, and 0.3 μM in order to map the stability diagram
of the Omnitrap under different space charge loads. Bradykinin acetate
salt (≥98%) was purchased from Sigma-Aldrich, and 1.2 μM
solution was prepared in H2O/MeOH/AcOH 60:39:1 (v/v/v)
in order to measure the secular frequency of the ions under variable
space charge loads and across a wide range of excitation amplitudes.
Oxidized insulin chain B from bovine pancreas (≥80%) and myoglobin
from equine heart were purchased from Sigma-Aldrich. Insulin chain
B 10 μM solution was prepared in ACN/H2O/AcOH 50:49.9:0.1
(v/v/v) and 10 μM myoglobin solution was prepared in H2O/MeOH/AcOH 49:49:2 (v/v/v).
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5

Peptide Synthesis and Characterization

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Methanol, ammonium hydroxide and glacial acetic acid were purchased from Mallinckrodt (Phillipsburg, NJ). The peptides ARAAARA, AKAAARA, AKAAAKA, AHARAHARA, ARAMAKA, HGAGGHGAGGHL, AAEAAEAA and AADAADAA were custom synthesized by NeoBioLab (Cambridge, MA). The peptides ARACAKA, ARAWAKA were synthesized by Pepnome Ltd. (Shenzhen, China). The peptides GRGDSPR, LKRApYLG, LKRApYGL-NH2 were custom synthesized by AnaSpec Inc. (San Jose, CA). The peptide GLSDGEWQQVLNVWGK was purchased from SynPep (Dublin, CA). Woodward’s reagent K, Angiotensin II (sequence: DRVYIHPF), ubiquitin from bovine erythrocytes, α-casein from bovine milk, TPCK-treated trypsin from bovine pancreas, peptide RPKPQQFFG, acetyl chloride and ethylamine were obtained from Sigma-Aldrich (St. Louis, MO). The reagent 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) was purchased from Thermo Fisher Scientific (Rockford, IL). All materials were used without further purification. All peptide solutions for positive electrospray were prepared in 49.5/49.5/1 (v/v/v) Methanol/water/acetic acid (~10 μM), and all peptide solutions for negative electrospray were prepared in 49.5/49.5/1 (v/v/v) Methanol/water/ammonium hydroxide (~10 μM). The wrk reagent was dissolved in water (~2 mM), and a new solution was made before each experiment.
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6

In vitro Ubiquitylation Assay for NQO1

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In vitro ubiquitylation was performed in 50 mM Tris HCl pH 7.5, 50 mM NaCl, 10 mM MgCl2, 2 mM DTT and 2 mM ATP. Reactions contained 100 nM UBE1 (Boston Biochem, Cambridge, MA), 2 µM either UbcH5a or Uev1A/Ubc13, 5 µM CHIP and 100 mM ubiquitin from bovine erythrocytes (Sigma-Aldrich). 2.5 µM NQO1 P187S mutant was added as substrate where indicated. Reactions proceeded at 37°C for 1 hr and then were stopped by adding reducing SDS sample buffer and boiling samples at 95°C for 5 min. Protein modification was analyzed by SDS-PAGE and immunoblotting using antibodies against NQO1, CHIP and ubiquitin. Where indicated, CHIP pelleted with 20% PA-containing liposomes was used instead of soluble protein.
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7

In vitro Autoubiquitination Assay of RNF183

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For in vitro autoubiquitination assays, HEK293T were transfected with
pCMV-HA-RNF183 or pCMV-HA-RNF183-CC/AA. Twenty-four hours after transfection,
cells were lysed on ice in NDLB, pH=8.0, clarified at 12,000gfor 10 min and then immunoprecipitated for 4 h with
anti-HA antibody (Covance) and Protein A/G beads (Life Technologies). Beads were
then washed three times in NDLB with 350 mM NaCl and two times in
ligase buffer: 50 mM Tris pH 7.5, 150 mM KCl,
1 mM MgCl2. After the final wash, beads were resuspended in ligase
buffer containing 100 nM recombinant E1 (Enzo Life Sciences),
1 μM recombinant UbcH5b (Enzo Life Sciences),
5 μM ubiquitin from bovine erythrocytes (Sigma), plus or minus
5 mM Mg2+ ATP and incubated for 1.5 h at
37 °C.
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8

Profiling Protein Oxidation by FPOP

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The protocol was performed as described by Hambly and Gross with minor
modifications.8 (link) Ubiquitin from bovine erythrocytes (Sigma Aldrich)
was prepared in 10 mM phosphate-buffered saline (PBS; Sigma Aldrich) at a final
concentration of 0.18 mg/mL in a 50 μL final volume. l-glutamine was added
to the protein sample as the hydroxyl radical scavenger at a final concentration of 40 mM.
The effect of five different CPEs (azone (AZ), dimethylacetamide (DMAC), dimethylformamide
(DMF), oleic acid (OA), or propylene glycol (PG); Sigma Aldrich) on the extent of FPOP
modification was tested at various concentrations (0, 0.1, 0.5, 1, and 2%). Immediately
prior to FPOP, hydrogen peroxide was added to a final concentration of 7.5 mM. The 50
μL sample was infused using a syringe pump through a 150 μm inner diameter
(i.d.) fused silica capillary (Polymicro Technologies) using a 34.19 μL/min flow
rate, 20% exclusion fraction, 2.58 mm spot width, and 10 Hz laser frequency. A 248 nm KrF
excimer laser (GAM Laser, Inc.) was used to irradiate the sample and photolyze hydrogen
peroxide at 161 mJ/pulse. Samples were collected in a vial containing a final
concentration of 30 mM methionine and 500 nM catalase to quench excess OH radicals and
hydrogen peroxide, respectively. A total of three laser-irradiated samples and three
controls (no laser irradiation) were prepared for each condition.
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9

Protein Standard Preparation Protocol

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Optima LC/MS grade formic acid, methanol, and water were obtained from Fisher Scientific (Waltham, MA). Ubiquitin from bovine erythrocytes, cytochrome C from equine heart, β-lactoglobulin from bovine milk, carbonic anhydrase from bovine erythrocytes, and bovine serum albumin were obtained from Sigma Aldrich (St. Louis, MO).
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10

MALDI-TOF Lipid Profiling Protocol

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Methanol (LC-MS grade), Fisher Scientific (Leicestershire, UK); purified water, ELGA Purelab Option (Marlow, UK); Lipid standard phosphatidylcholine (PC) 16:0/18:1, Avanti Polar Lipids (Delfzyl, The Netherlands); Trifluoroacetic acid (TFA), Acros Organics (Loughborough, UK); MALDI matrices and analytes 2,6-dihydroxyactophenone (2,6-DHAP), histidine, glutamic acid, amiodarone, insulin, probucol, choline chloride, fumaric acid, cysteine, ketoglutaric acid, glutamic acid, dopamine hydrochloride, l-histidine, tryptophan, ibuprofen, palmitic acid, glucose 6 phosphate, glutathione, clozapine, glycochenodeoxycholate, raffinose, probucol, amiodarone, co-enzyme Q10, ubiquitin (from bovine erythrocytes) were purchased from Sigma Aldrich (Dorset, UK) at 98% purity or above. Paclitaxel and rapamycin from Alfa Aesar (Lancashire, UK). Superfrost Plus (Thermo Scientific, Waltham, MA, USA) glass slides were used for all experiments.
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