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9 protocols using lambda protein phosphatase lambda pp

1

Assessing mRNA and Protein Dynamics

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Reagents were obtained from the following sources: antibodies to phospho-4E-BP1 (Thr37/46) from Cell Signalling (#2855); H3 antibodies from Abcam (#ab1791); anti-rabbit IgG secondary antibodies from KPL (#074–1506); Lambda Protein Phosphatase (Lambda PP) from New England Biolabs (#P0753S); ARTseqTM kit from Epicentre (#RPHMR12126); RNaqueous kit from Ambion (#AM1912); Torin 1 from Tocris (#4247); protease inhibitor cocktail from Sigma-Aldrich (P2714-1BTL); Halt™ Phosphatase Inhibitor Cocktail from Thermo Scientific (#78420); precast gels from BioRad (#4566033 and #4565013); To-Pro-3 iodide from Molecular Probes (#T3605); VECTASHIELD® from Vector Laboratories (#H1000); EdU from Thermo Fisher Catalog (#A10044); Click-iT™ HPG Alexa Fluor™ 488 Protein Synthesis Assay Kit from Thermo Fisher (#C10428); TMG-cap antibodies from Santa Cruz (#sc-32,724); Zymo RNA Clean & Concentrator-25 kit (#R1018); Ribo-Zero (#MRZG12324); Clarity Western ECL Substrate from BioRad (#170–5060).
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2

Invadopodia and Cytoskeletal Protein Assays

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For invadopodia assays, the FISH (Tks5) antibody was obtained from Santa Cruz, and the cortactin antibody was obtained from Millipore. For immunoblotting, the human NMHC-IIA and NMHC-IIB C- terminal antibodies were produced in-house [25 (link)], and the NMHC-IIA pS1943 antibodies were produced in collaboration with Millipore and Cell Signaling Technology. The NMHC-IIA 2B3 monoclonal antibody from Abeam was used to recognize the exogenously expressed mouse GFP-NMHC-IIA. The β-actin and vinculin antibodies were purchased from Sigma. MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenylte- trazolium bromide) was obtained from Invitrogen. Calf intestine phosphatase (CIP) and lambda protein phosphatase (lambda PP) were obtained from New England Biolabs. shRNAs against the human NMHC- IIA were obtained from Open Biosystems (sh5: clone TRC 0000029465, 5’CGCATCAACTTTGATGTCAAT3’ and sh7: clone TRC0000029467, 5’CCGCGAAGTCAGCTCCCTAAA3’). The control shRNA (shC) was obtained from Sigma (MISSION® pLKO.l-puro non-target shR NA control plasmid). Recombinant human proMMP9 was from R&D Systems (cat #911-MP-010) and recombinant human MMP2 was from Calbiochem (cat #PF023).
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3

Purification and Phosphorylation of YCF1

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Following size exclusion purification, both wild-type and E1435Q YCF1 were concentrated in a 100 kDa cutoff concentrator (Amicon) and BSA quantification was performed. For phosphorylation reactions, the concentrated protein at 3 mg/mL was incubated with c-AMP Protein Kinase A PKA (NEB) (molar ratio of 40:1) at room temperature for 1 hour. A total reaction mixture of 500 µL was suitable for downstream size exclusion purification utilizing a Superose 6 10/300 column (GE Healthcare) to remove excess PKA and phosphorylation reagents. Dephosphorylation reactions were performed with Lambda Protein Phosphatase (Lambda PP) (NEB). 1,000 units of Lambda PP were utilized per µmol of Ycf1 protein in a 500 µL reaction. Following a 1-hour treatment at 30 °C, further size exclusion chromatography was performed in a Superose 6 10/300 column (GE Healthcare) for the removal of dephosphorylation reagents.
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4

Proteomic Analysis of CDKL5 Knockout

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2.5x106 cortical neurons isolated from E16 mouse embryos were infected at DIV0 to silence CDKL5 expression. At DIV7, cells were washed and lysed in UTC buffer (7 M urea, 2 M thiourea, 4% CHAPS). Approximately 200 μg of extract were loaded on 7 cm IPG DryStrips with a linear 4–7 pH gradient and isoelectric focusing performed with an IPGphor II apparatus (GE Healthcare) according to the manufacturer’s instructions. Subsequent SDS-PAGE was performed using 8% gels and proteins were detected by western blotting. Phosphatase treatment was done by adding 100 units of Lambda Protein Phosphatase (Lambda PP; New England Biolabs) to the extract diluted in 2 ml 0.1% SDS, 0.1 mM MnCl2, and 1x phosphatase-buffer. After an overnight incubation at 30°C the samples were concentrated with Ultracel 10K centrifugal filters (Millipore) and subjected to isoelectric focusing.
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5

Phosphatase-Mediated Protein Analysis

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To analyze proteins independent of posttranslational phosphorylation, the tissue was immediately suspended in lysis buffer (PBS, containing 1% (v/v) Triton X‐100, Complete protease inhibitor) and homogenized by vigorous shearing of the tissue with five strokes of a 1 ml syringe equipped with a 21 (first stroke) and 26 (remaining strokes) gauche canula. The homogenate was incubated for 30 min on ice and subsequently centrifuged at 1000 × g for 10 min at 4°. After adjustment of protein concentrations using a BCA assay, the homogenate was treated with Lambda Protein Phosphatase (Lambda PP; New England Biolabs, Ipswich, MA, #P0753) according to the manufacture's protocol. Briefly, 50 µg protein for each sample was incubated for 45 min on 30 °C in the provided buffer supplemented with 1 M MnCl2 and 400U Lambda PP. Samples were boiled in SDS sample buffer and 10 µg of total protein per sample were subjected to SDS–PAGE and analyzed by western blotting.
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6

Protein dephosphorylation by Lambda PP

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After overnight dialysis to remove phosphatase inhibitors, protein samples (40μl) were incubated with 5μL of 10X NEBuffer for Protein MetalloPhosphatases (PMP), 5μL of 10mM MnCl2 and 1μl of Lambda Protein Phosphatase (Lambda PP, New England Biolabs) at 30°C for 3 hours. Reactions were stopped by addition of SDS sample buffer and boiling for 5 minutes at 100 °C.
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7

Antibody Detection of eIF6 and Phosphorylation

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The following antibodies were used: rabbit polyclonal antibodies against eIF6 [58 (link)], rpS6, phospho-rpS6 (Ser240/244), total 4EBP1 (Cell Signaling), P-PKCβII (Cell Signaling); anti-PKCβII (Santa Cruz); rabbit polyclonal anti-VEGFA (Abcam); mouse monoclonal antibodies against β-Actin (Sigma), PKCβ (BD-Bioscience) RACK1 IgM (BD Transduction Laboratories). Biotin was obtained from Pierce, EuroClone (EZ-LINK NHS-LC-BIOTIN). Lambda Protein Phosphatase (Lambda PP) was provided by NEB. Enzastaurin was provided by Eli Lilly and Company (Indianapolis, USA). eIF6 recombinant protein was produced in E. Coli by simultaneous co-expression with chaperones [21 (link)], followed by affinity chromatography and size exclusion chromatography (SEC; GE Healthcare).
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8

Phosphorylation Specificity of Anti-AMPK Antibody

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The specificity of the anti-phospho AMPK α for phosphorylated S. mansoni AMPK α was tested using Lambda Protein Phosphatase (Lambda PP) (New England BioLabs, P0753S). A 5 ml 1X solution of 10X NEBuffer was prepared by diluting in 1X TBST supplemented with 500 μl MnCl2. Twenty-five microliter of Lambda PP was added to each 5 ml preparation of 1X NEBuffer. PVDF membranes containing 10 μg of adult schistosome lysate per lane were incubated in 5 ml of the Lambda PP preparation either before or after incubation in anti-phospho-AMPK α diluted 1:1,000. Bound antibody was detected as described above. Phosphatase treated membranes were also incubated in anti-AMPK α 1, 2 and anti-beta tubulin as controls for protein loading.
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9

Quantifying Phosphorylation of nNOS Enzyme

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The pSer incorporation was determined using the Phosphoprotein Phosphate Estimation Assay Kit (Thermo Scientific). The manufacturer’s protocol was modified by adding 0.2% polyvinyl alcohol (PVA) to minimize the precipitation of the malachite green-phosphomolybdate complex [17 (link), 18 ]. Briefly, 52 μg wt or pSer1412 nNOS and the phosvitin standard were diluted with 0.2 mL of TBS, incubated with 0.2 mL of 2.0 N NaOH at 65 °C for 30 min, and centrifuged at 12,000 g for 3 min after adding 0.2 mL of 4.7 N HCl. The supernatant was transferred into a new tube, and PVA was added to a final concentration of 0.2 %. After 30 min incubation at room temperature in dark, the absorbances of each standard and sample at 625 nm were measured on a Cary 50 UV-vis spectrophotometer. Lambda Protein Phosphatase (Lambda PP, New England Biolabs) was further used as a negative control to dephosphorylate both the wt and pSer1412 nNOSs: the wt and pSer1412 nNOSs were each incubated with 1000 units Lambda PP in 1X Reaction Buffer with added 1 mM MnCl2 at 30 °C for 30 min. After centrifugation in a 100 K cutoff centrifuge tube, the sample was exchanged into TBS for phosphate estimation assay. The obtained number of phosphate per nNOS subunit n is listed in Table S1.
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