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15 protocols using oleoyl coa

1

Chemoenzymatic Synthesis of Acyl-Carrier Protein

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The restriction enzymes, T4 DNA ligase, oligonucleotide
primers,
and the competent E. coli BL21(DE3) cells were purchased
from Invitrogen. Pfu Turbo and Deep Vent DNA polymerases were purchased from Strategene. The cloning vectors
were from Novagen. DNA sequencing was performed by the DNA Sequencing
Facility of the University of New Mexico. Acetyl-CoA, benzoyl-CoA,
propanoyl-CoA, hexanoyl-CoA, lauroyl-CoA, myristoyl-CoA, palmitoyl-CoA,
and oleoyl-CoA were purchased from Sigma. The thioester substrates
4-hydroxybenzyol-CoA, 3-hydroxybenzoyl-CoA, 1,4-dihydroxynapthoyl-CoA,
3-hydroxyphenylAcetyl-CoA, and coumaroyl-CoA were synthesized as previously
reported.18 (link),21 (link)E. coli strains JW1676
ydiI::kanr) and BW25113 (wild-type)
of the Keio collection were obtained from Yale University.22 (link) The engineered E. coli strain
DK574, carrying the plasmid pJT93 expressing the E. coli AcpS transferase gene, under tac-promoter control,
was a kind gift from Dr. John Cronan of the University of Illinois.
The holoACP (UniProt accession code P0A6A8) purified
from this strain was converted to benzoyl-holoACP by using the chemical
procedure reported in ref (23 (link)). The molecular mass and purity of the isolated adduct were
verified by ES-MS analysis.
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2

Cholesterol Esterification Assay for SOAT1 Inhibitor Screening

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2.8 mM cholesterol/11.2 mM PC/18.6 mM taurocholate were mixed to generate the cholesterol donor47 (link). The tetrameric or dimeric hSOAT1 enzyme was prepared in GDN detergent. First, 10 μl 2 M KCl, 5 μl 5% BSA, 1 μl SOAT1 protein (A280 = 0.5), 5 μl micelles, 40 μl TBS buffer with 40 μM GDN were mixed with TBS buffer with 0.5% CHAPS to reach the volume of 100 μl and incubated at 37 °C for 2 min. In order to measure the IC50 of inhibitors, different concentrations of given inhibitors were added, as indicated. Then, 1.0 μl 0.2 mg ml−1 NBD-cholesterol (Sigma, N2161) solubilized in 35% β-cyclodextrin (Sigma, HZB1102) was added and the mixture was incubated at 37 °C for 2 min. To start the enzymatic reaction, 1 μl 2.5 mM oleoyl-CoA (Sigma, O1012) was added and the reaction mixture was incubated at 37 °C for 15 min. The reaction was terminated by adding 2:1 chloroform/methanol, the extract was separated on an HPLC column at 0.2 ml/min (Agilent, Poroshell HPH-C18, 2.7 μm) running in 100% ethanol and detected via fluorescence detector on an HPLC (SHIMADZU). NBD-cholesterol eluted at 1.3 min and its ester eluted at 1.9 min. The peak areas of the NBD-cholesteryl ester products and remaining NBD-cholesterol were integrated separately to obtain the relative ratio of NBD-cholesterol that was converted into NBD-cholesteryl esters.
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3

Recombinant Protein Expression and Purification

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The
Ambion RETROscript Kit, ProBond nickel-chelating resin, and MicroPoly(A)
Purist were purchased from Invitrogen. NdeI, XhoI, Antarctic Phosphatase, and T4 DNA ligase were purchased
from New England Biolabs. BL21(DE3) E. coli cells,
XL10 E. coli cells, and the pET-28a(+) vector were purchased from Novagen. Kanamycin
monosulfate and isopropyl β-d-1-thiogalactopyranoside
were purchased from Gold Biotechnology. Oligonucleotides were purchased
from Eurofins MWG Operon, and PfuUltra High-Fidelity DNA polymerase
was purchased from Agilent. Benzoyl-CoA, acetyl-CoA, butyryl-CoA,
hexanoyl-CoA, octanoyl-CoA, decanoyl-CoA, oleoyl-CoA, and N-acetylserotonin were purchased from Sigma-Aldrich. All
other reagents were of the highest quality available from either Sigma-Aldrich
or Fisher Scientific.
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4

Triolein Metabolism Assay Protocol

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[9,10-3H]Triolein was obtained from PerkinElmer Life Sciences. Triolein, phosphatidylcholine, phosphatidylinositol, 1(rac)-oleoylglycerol, oleoyl-CoA, and free glycerol detection reagents were purchased from Sigma. 1-Oleoyl-2-hydroxy-sn-glycero-3-phosphocholine was purchased from Avanti Polar Lipids Inc., Alabaster, AL, and the NEFA kit was from WAKO Diagnostics, Neuss, Germany. Hi76-0079 obtained from Novo Nordisk, Denmark, Atglistatin was a generous gift from R. Breinbauer (Graz University of Technology, Austria). The protein assay kit was obtained from Bio-Rad; Thermo Scientific, Rockford, IL was the source for the Pierce® BCA protein assay kit. The synthetic peptides were synthesized by Peptide Specialty Laboratories GmbH, Heidelberg, Germany.
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5

Triolein Metabolism Analysis Protocol

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If not stated otherwise, chemicals, antibiotics, and buffers were obtained from Sigma-Aldrich (St. Louis, MO) or Carl Roth GmbH (Karlsruhe, Germany); columns for protein purification were from GE Healthcare Life Sciences (Chicago, IL). The [9,10-3H] Triolein was obtained from PerkinElmer Life Sciences (Waltham, MA). Triolein, phosphatidylcholine, phosphatidylinositol, 1(rac)-oleoylglycerol, oleoyl-CoA, and free glycerol detection reagents were purchased from Sigma-Aldrich.
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6

Isothermal Titration Calorimetry of RaaS

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RaaS protein and oleoyl-CoA (Sigma) were diluted in 50 mm Tris-HCl (pH 8.5) and 150 mm NaCl. RaaS (15 μm in a 1.4-ml cell) was then titrated at 25 °C by 5-μl injections of the ligand (250 μm in the syringe) using a VP-ITC calorimeter (MicroCal). Raw data were normalized and corrected for heats of dilution of the ligand. Binding stoichiometries, enthalpy values, and equilibrium dissociation constants were determined by fitting the corrected data to a bimolecular interaction model using Origin 7 software (OriginLab).
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7

Antibody-Based Analysis of Human L-FABP

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Antibody against Human L-FABP (H-120), a rabbit polyclonal antibody raised against amino acids 7–126 mapping within an internal region of L-FABP of human origin was purchased from Santa Cruz Biotechnology (Dallas, TX). Antibody against mouse L-FABP was developed in our laboratory as described [102 (link);103 (link)]. Mini-PROTEAN TGX Any kD precast polyacrylamide gels as well as Precision Plus Protein Dual Xtra Standards were purchased from Bio-Rad (Hercules, CA). SimplyBlue SafeStain was obtained from Invitrogen (Carlsbad, CA). ANS (1-anilinonaphthalene-8-sulfonic acid) was purchased from Life Technologies (Grand Island, NY). Stearic acid, palmitic acid, oleic acid, linoleic acid, arachidonic acid (AA), cis-5,8,11,14,17-eicosapentaenoic acid (EPA), cis-4,7,10,13,16,19-docosahexaenoic acid (DHA), Oleoyl CoA, and Oleoyl-L-α-lysophosphatidic acid sodium salt (LPA) were purchased from Sigma (St. Louis, MO). 2-oleoyl glycerol (2-OG), 1-palmitoyl-2-oleoyl-sn-glycerol (PODG), and 1-palmitoyl-2-Oleoyl-sn-Glycero-3-Phosphate monosodium salt (POPA) were obtained from Avanti Polar Lipids (Alabaster, Alabama). All reagents and solvents used were of the highest grade available.
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8

Purification and Characterization of Acyl-CoA Analogues

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Recombinant p300 (1195-1662) and Gcn5 (497-662) were obtained from Enzo. Acetyl-CoA, propionyl-CoA, butyryl-CoA, succinyl-CoA, crotonyl-CoA, malonyl-CoA, and palmitoyl-CoA were synthesized according to the literature procedure (Padmakumar et al., 1997 (link)). All synthesized CoA analogues were HPLC purified, with purity verified by LC-MS prior to use. Linoleoyl-CoA, myristoyl-CoA, oleoyl-CoA, and palmitoleoyl-CoA were purchased from Sigma with purity verified by LC-MS prior to use. H3K14-CoA and desulfo-CoA were synthesized according to previously reported procedures (Chase et al., 1966 (link); Montgomery et al., 2014 (link); Zheng et al., 2004 (link)). Qubit Protein Assay kit (Life Technologies) was used to determine cell lysate and histone extract concentrations. Pyruvate dehydrogenase, ketoglutarate dehydrogenase, and NAD+ were purchased from Sigma. Labchip EZ-Reader 12-sipper chip (#760404) and ProfilerPro Separation Buffer (#760367) were purchased from Perkin-Elmer. H3K9Ac (9649P), H3K14Ac (7627P), H3K27Ac (8173), H4K8Ac (2594P), acetylated tubulin (5225P), GAPDH (5174S), Gcn5 (3305S), and pCAF (3378S) antibodies were purchased from Cell Signaling Technologies, while Mof (A300-992A-T) antibody was purchased from Bethyl Laboratories.
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9

Cloning and Expression of Acyl-CoA Thioesterases

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ProBond nickel-chelating resin was purchased from Invitrogen. Polymerase chain reaction (PCR) primers were purchased from Eurofins MWG Operon. PfuUltra High-Fidelity DNA polymerase was purchased from Agilent. BL21(DE3) E. coli cells, E. coli XL10 competent cells, and the pET-28a(+) vector were purchased from Novagen. NdeI, XhoI, Antarctic Phosphatase, and T4 DNA ligase were purchased from New England Biolabs. Kanamycin monosulfate and isopropyl β-D-1-thiogalactopyranoside (IPTG) were purchased from Gold Biotechnology. Acetyl-CoA, butyryl-CoA, hexanoyl-CoA, octanoyl-CoA, oleoyl-CoA, coenzyme A, and Nω-acetylhistamine were purchased from Sigma-Aldrich. All other reagents were of the highest quality available from either Sigma-Aldrich or Fisher Scientific.
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10

Fatty Acid Biosynthesis Regulation

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Coenzyme A, palmitic acid, oleic acid, linoleic
acid, eicosapentaenoic acid, palmitoyl-CoA, oleoyl-CoA, linoleoyl-CoA,
and clofibrate were from Sigma (St. Louis, MO). Eicosapentaenoyl-CoA
was synthesized as previously described15 (link) and purified by high-performance liquid chromatography (HPLC).17 (link) All CoA thioesters, whether freshly synthesized
or obtained commercially, were >98% undegraded. The human glucocorticoid
receptor (hGR) was purchased from Pierce Thermo Scientific (Rockford,
IL). Monoclonal antibodies for PPARα and polyclonal antibodies
for LXRα (each specific for the α isotype) were purchased
from Pierce Thermo Scientific. Polyclonal antibodies for PPARα,
RXRα, and GR were purchased from Santa Cruz Biotechnology (Santa
Cruz, CA). Anti-rabbit IgG secondary antibodies were from Sigma.
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