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71 protocols using lambda phosphatase

1

Alix Dephosphorylation Assay

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Alix immunoprecipitates from neurons treated with Veh or Mg2+-free glycine solution were resuspended in lambda phosphatase assay buffer (50 mM Tris-HCl pH 7.8, 5 mM dithiothreitol, 2 mM MnCl2, 100 μg/mL BSA) with or without 1600 U of lambda phosphatase (New England Biolabs, Cat# P0753S). After 60 min at 30°C, the reactions were stopped by adding 2 × SDS loading buffer and processed for WB with the indicated antibodies.
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2

Dephosphorylation of Mitotic Proteins

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Cells were cultured in medium containing 100 ng/ml nocodazole (Sigma, M1404) to arrest in mitosis for 16 h. Mitotic cells were isolated by mechanical shake-off. Then, the cell lysates were reacted with lambda phosphatase (NEB, P0753S) in lambda phosphatase buffer (20 mM Tris-HCl, pH 7.6; 250 mM NaCl, and 0.5% NP-40) supplemented with 2 mM MnCl2 at room temperature for 2 h; the reaction was stopped with Laemmli sample buffer.
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3

Phosphatase Treatment of Ana2-Plk4 Complex

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D.Mel-2 cells were co-transfected with pAct5-Ana2-FLAG and either pAct5-Plk4-NDKD (kinase-dead) or pAct5-Plk4-ND (active) in a 12-well plate. Approximately 1 × 106 cells were collected from each well 24 h post-transfection and briefly rinsed in PBS. Cells were then lysed in RIPA buffer (50 mM Tris–HCl pH 7.4; 150 mM NaCl; 1% NP-40; 0.5% Na deoxycholate; 0.1% SDS; 1× Complete EDTA-free protease inhibitor cocktail tablets from Roche) on ice for 15 min. Lysates were cleared by centrifugation and supplemented with 1× Lambda-phosphatase buffer and 1× MnCl2 solution provided along with Lambda phosphatase (New England Biolabs, catalogue number P0753S). Two samples (one of Ana2-FLAG + Plk4-NDKD and one of Ana2-FLAG + Plk4-ND) were mock-treated (no phosphatase added), while one sample (Ana2-FLAG + Plk4-ND) was treated with 200 U (0.5 µl) Lambda phosphatase for 30 min at 30°C. All samples were then boiled in Laemmli sample buffer and analysed by immunoblotting.
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4

Phosphatase Regulation of MDC1 Domains

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Bora were collected and extracted with 0.1% NP-40, then added to lambda phosphatase reaction buffer containing 14.8 U/μl of lambda phosphatase (New England BioLabs) and protease inhibitors and incubated at 30°C for 20 min. MDC1 BRCT and FHA domains were expressed as GST fusions in E. coli and purified on glutathione Sepharose (Amersham Pharmacia Biotech). The total reaction volume was transferred to a tube containing prepared glutathione Sepharose 4B beads, and the GST-BRCT pull-down analysis was performed.
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5

Viral Particle Production and Phosphatase Assay

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Cell culture supernatants containing recombinant viral particles were generated by transfection of the corresponding plasmids into 293T cells using polyethyleneimine (PEI) as described previously [37 (link), 66 (link)]. For subsequent Western blot analysis the supernatant generated by transient transfection was harvested, passed through a 0.45-μm filter and centrifuged at 4°C and 25,000 rpm for 3 h in a SW32Ti rotor (Beckman) through a 20% sucrose cushion. The particulate material was resuspended in phosphate-buffered saline (PBS). For Western Blot analysis using phosphopeptide-specific antibodies viral particles were resuspended in TBS. Subsequently, half of the sample was digested for 1 h at 30°C with Lambda Phosphatase (NEB, P0753; 7.15 U/μl Lambda PP, 1% Triton X-100, 1 mM MnCl2, 1x Lambda Phosphatase buffer) whereas the other half was mock digested prior to addition of protein sample buffer.
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6

Dephosphorylation of Protein Lysate

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Twenty micrograms protein lysate was incubated with lambda phosphatase according to the manufacturer’s protocol (New England Biolabs). Afterward, a western blot was performed with 15 µg protein, as indicated in the ‘Western Blot’ section.
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7

Phosphatase Treatment of Puf3p-FLAG

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Puf3p-FLAG was first immunoprecipitated by Anti-FLAG and eluted with 3X
FLAG peptide, following the same procedure as mapping phosphorylation sites. The
samples were treated with 400 units of Lambda phosphatase (NEB) at 30°C
for 30 min.
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8

Biochemical Assays for PFKFB3 Acetylation

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Nicotinamide and digitonin were purchased from Sigma-Aldrich. Tricostatin A was purchased from Cell Signaling Technology. Cisplatin, PFK15, etoposide and adriamycin were purchased from Selleck. Lambda phosphatase was purchased from New England Biolabs. Biotinylated PFKFB3 peptides containing either acetylated or non-acetylated K472 residue was purchased from GL Biochem Ltd.
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9

Phosphatase Treatment of Brain Fractions

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5 μl aliquots of the respective brain fractions were mixed with 1 μl lambda phosphatase (New England Biolabs, cat. no. P0753), 10x buffer and MnCl2 were added according to manufacturer’s instructions in a total volume of 10 μl. Control reactions were set up without addition of the enzyme. After incubation for 30 min at 30 °C, 2.5 μl of 4x Laemmli sample buffer were added, and samples were processed as described below for immunoblotting.
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10

Phosphatase Treatment of Affinity-Purified Samples

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Phosphatase treatment of the affinity purified samples was similar to the protocol above except that the phosphatase inhibitors were left out of all buffers and additional washing of the Talon resin 2x with 4ml of phosphatase buffer (50mM Hepes pH 7.5 / 100mM NaCl / 0.01% Brij35) plus 0.1x protease inhibitors was done. Proteins were eluted from the resin with 400ul phosphatase buffer containing 400mM imidazole by incubation and centrifugation through a filter as above.
Eluates were heated 95° for 6 min and then put on ice to denature proteins. MnCl2 buffer was added to 1mM, DTT was added to 2mM and 2ul (800 units) lambda phosphatase (New England Biolabs) was added. Samples were incubated at 30° for 4 hr., then at 10° for 12 hours.
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