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12 protocols using pyridoxal phosphate

1

Kinetic Assay for Tryptophan Inhibitors

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The assay was carried out in a cuvette (1 cm optical path length) in a BioSpectrometer Kinetic (Eppendorf, Hauppauge, NY) at 37 °C as previously reported70 (link), but with some modification. The reaction mixture contained 0.005% BSA (Sigma), 1 mM reduced glutathione (Sigma), 100 μM pyridoxal phosphate (Sigma), 100 μM NADH (Sigma), 3 U/mL lactate dehydrogenase (Sigma) and apotryptophanase (10 U/mL, Sigma) in 0.15 M potassium phosphate buffer (pH 8.0). Following a 3 min incubation with inhibitor, the enzymatic reaction was initiated by adding l-tryptophan (300 μM final, Sigma). The decrease in optical density at 340 nm was monitored for 5 min at 5 s intervals and used for calculating the TIL reaction velocity. The inhibitory effect of TPL inhibitors (2-aza-tyrosine and l-meta-tyrosine) on TIL enzymatic activity was measured. Homo-BZI-Ala was used as a positive control of TIL inhibitor.
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2

Purification and Characterization of Enzymes

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Sodium phosphate dibasic (N2HPO4), Tris(hydroxymethyl)aminomethane hydrochloride (Tris-HCl), 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), sodium chloride (NaCl), sodium dodecyl sulfate (SDS), dithiothreitol (DTT), L-cysteine, protease inhibitor cocktail (sigmafast), His6-thrombin, diethylene triamine pentaacetic acid (DTPA), isopropyl β-D-1-thiogalactopyranoside (IPTG), ferrous ammonium sulfate (Fe(NH4)2(SO4)2), imidazole, zinc sulfate (ZnSO4), β -mercaptoethanol, acrylamide:bis-acrylamide (29:1), Mal-d-PEG, phenylmethylsulfonyl fluoride (PMSF), Ethylenediaminetetraacetic acid (EDTA), pyridoxal phosphate (PLP), ferric ammonium citrate (FAC), riboflavin 5’-monophosphate sodium (riboflavin), ammonium sulfate (NH4SO4), low molecular weight size-exclusion calibration kit were from Sigma–Aldrich. HisBind Resin from Novagen, Superdex, Q-sepharose and Phenyl Sepharose columns from GE Healthcare, Amicon Ultra-15 Centrifugal Filter Units from Millipore, PD10 column from Amersham Biosciences.
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3

Comprehensive Metabolomics Standards Protocol

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All metabolite standards: arabinose, galactose, glucose, mannose, ribose, erythrose-4-phosphate, pyridoxal phosphate, xylose, acetone, fructose, pyruvate, 2-oxobutanoate, 2-oxoglutarate, oxalacetate, dihydroxyacetone phosphate, as well as glacial acetic acid (AcOH) and methanol (MeOH) (Optima grade) were purchased from Sigma Aldrich (St. Louis, MO). 18 MΩ water was obtained using the ultrapure water system (Barnstead, Dubuque, IA).
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4

Diallyl Trisulfide Cytotoxicity Assay

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Folin–Ciocialteau reagent, NADH, lactate dehydrogenase (LDH), pyridoxal phosphate (PLP), N-ethylmaleimide (NEM), bathophenanthrolinedisulfonic acid (BPDS), 2,4-dinitrofluorobenzene (DNFB), 1,4-dithio-bis-(2-nitrobenzoic acid) (DTT), acetonitrile, and crystal violet (N-hexamethylpararosaniline) were obtained from Sigma-Aldrich Corp. (St. Louis, MO, USA). Potassium cyanide (KCN) was obtained from Merck (Darmstadt, Germany), sodium 3-mercaptopyruvate, trifluoroacetic acid (TFA), and 2-mercaptoethanol from Flucka Chemie GmbH. Nε-methyl-l-lysine was purchased from Bachem (Bubendorf, Switzerland). Fetal bovine serum, trypsin, and penicillin/streptomycin were obtained from HyClone Laboratories (Utah, USA). The Cytotoxicity Detection Kit (LDH) was obtained from Roche Applied Science. All the other chemicals were of reagent grade and purchased from common commercial suppliers.
Diallyl trisulfide (DATS) was purchased from Cayman Chemical Company (Michigan, USA) and dissolved in dimethyl sulphoxide (DMSO; Sigma-Aldrich Corp., St. Louis, MO, USA), and then diluted with the medium Dulbecco’s Modified Eagle’s Medium (DMEM; HyClone Laboratories, Utah, USA) to the desired concentration prior to its use (the final concentration of DMSO in the medium was less than 0.1%).
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5

AGT1 Enzyme Kinetics Assay

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Pyridoxal phosphate (PLP), l‐alanine, sodium glyoxylate, rabbit muscle l‐lactic dehydrogenase (LDH), β‐Nicotinamide adenine dinucleotide reduced form (NADH), and isopropyl‐β‐d‐thiogalactoside (IPTG) were purchased from Sigma‐Aldrich. Protease Inhibitor Cocktails organic solvents were purchased from Nacalai tesque. All other chemicals, unless otherwise noted, were from Sigma‐Aldrich, Nacalai tesque, or Wako. The anti‐AGT1 antibody from rabbit was provided by Prof. Chris Danpure (University College London).
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6

Testicular Tissue Sulfide Assay

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Fifty mg of testicular tissues was homogenized in 500 µl of phosphate-buffered saline. After incubating the homogenates with L-cysteine (Sigma, USA), pyridoxal phosphate (Sigma, USA), and normal saline for thirty min at 37 C, trichloroacetic acid (Sigma, USA) and zinc acetate (Merck, Germany) were added. Fifteen min after adding N, N-dimethyl-p-phenylenediamine sulfate (Sigma, USA) and ferric chloride (Sigma, USA), the absorbance of aliquots was measured at 660 nm by a microplate reader (26).
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7

Purification and Analysis of Recombinant Proteins

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The substrates SHIK, phenylpyruvic acid, ATP, KCl, MgCl2, PEP, FAD, NADH, β-Mercaptoethanol, L-Glutamic acid, pyridoxal phosphate were purchased from Sigma (St. Louis, MO, USA). Prime Star Taq polymerase was purchased from Takara and the restriction enzymes and T4 DNA ligase were purchased from NEB. Ni-NTA agarose resin was supplied by GE Healthcare for His-tagged protein purification. Na2HPO4 and other organic solvents used for HPLC were purchased from Merck (German). Other chemicals used in this article otherwise demonstrated were purchased from Solarbio (Beijing, China).
All kits and markers used for the construction of clones were from Omega Bio-tek, Inc (USA).
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8

Histochemical Analysis of Brain Tissue

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The following chemicals and reagents were bought commercially from Sigma, St. Louis, MO, USA, pilocarpine, methyl scopolamine, phosphate-buffered saline (PBS), diazepam, dimethyl sulfoxide (DMSO), I-oxoglutarate, pyridoxal phosphate, methanol, trichloroacetic acid, ferric chloride (FeCl3), acetone, glutamic acid, formalin-buffered saline, hematoxylin, and eosin stains. However, Nissl’s stain was bought from VitroVivoBiotech, Gaithersburg, MD, USA, Tris-HCl buffer was supplied from Research Organics, Cleveland, OH, USA, and nuclear lysis buffer was purchased from ThermoFisher Scientific, Waltham, MA, USA.
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9

Quantifying S1P Lyase Activity in Lung Tissue

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SPL expression was determined in lung tissue lysates by western blotting: anti-S1PL (H-300); rabbit; 1:1,000; sc-67368 (Santa Cruz Biotechnology). SPL activity was determined as previously described (REF 61) with some modifications in sample preparation using a fluorogenic SPL substrate. Briefly, lung tissue samples were homogenized in 0.25% solution of Triton-X100 in potassium phosphate buffer 0.5 M (pH 7.4) and then adjusted to 10 mg protein/ml in 0.5 M potassium phosphate buffer (pH 7.4). The fluorogenic substrate (Cayman, Ann Arbor, USA) was prepared in advance by removing the solvent from 2.5 μl of a 5 mM stock solution per reaction and solubilization in 15 μl of potassium phosphate buffer (0.5 M, pH 7.4). Incubation mixtures per sample contained 75 μl of tissue lysate, 15 μl of substrate solution (125 μM final concentration), 5 μl of 0.5 mM sodium orthovanadate (25 μM final concentration, Sigma-Aldrich, Steinheim, Germany), and 5 μl of 5 mM pyridoxal phosphate (250 μM final concentration, Sigma-Aldrich, Steinheim, Germany). The reactions were incubated in black 96-well plates with clear bottoms (Greiner, Frickenhausen, Germany) for 6 h at 37 °C in the dark, stopped with 50 μl methanol, and incubated for an additional 2 h in the dark. Fluorescence intensities were measured at ex. 365 nm/em. 460 nm.
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10

Cystinotic Fibroblast Metabolism Analysis

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l-Cystine, l-homocystine, l-serine, cystathionine, iodoacetamide, pyridoxal phosphate, potassium cyanide and potassium thiocyanate were purchased from Sigma-Aldrich. All other chemicals were purchased from Fisher Scientific. Cystinotic fetal lung fibroblasts (GM00090, donor age: 24 weeks) and normal fetal lung fibroblasts (GM01379, donor age: 12 weeks) were purchased from the Coriell Institute Biorepository (Camden, New Jersey).
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