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7 protocols using pgex 4t

1

Cloning and Mutagenesis of Human PMVK

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Site-directed mutagenesis was used to generate the R138* mutant form of human PMVK. Wild-type and R138* PMVK cDNA were cloned into plasmids pCMV-Myc (Clontech) and pGEX-4T (GE Healthcare) for expression in mammalian cells and E. coli. The full-length coding sequence of MVK was cloned into the p3XFLAG-CMV-7.1 (MBL) mammalian expression vector. All constructs were verified by Sanger sequencing.
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2

LIMCH1 and NM-IIA Interaction Analysis

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Full-length LIMCH1 gene encompassing amino acid residues 1–1083 was PCR amplified from kiaa1102/limch1 cDNA (Kazusa DNA Research Institute, Chiba, Japan) and subcloned into pEGFP (Clontech, Mountain View, CA). Deletion mutants of LIMCH1 derived by PCR amplification or by enzyme digestion from the GFP-LIMCH1 construct were subcloned into either p3×FLAG-Myc-CMV-26 (Sigma-Aldrich) or pET-32 (Novagen). GFP-NM-IIA (Addgene plasmid #11347) obtained through Addgene (Cambridge, MA) was a kind gift from Robert Adelstein (National Heart, Lung, and Blood Institute, National Institutes of Health). Deletion mutants of NM-IIA were derived by PCR amplification of the domain from the GFP-NM-IIA construct and its subcloning into pGEX-4T (GE Healthcare, Little Chalfont, United Kingdom). Point mutations for siRNA-resistant GFP-LIMCH1 and diphospho­mimetic GFP-MRLC-S19D/T18D were introduced using site-directed mutagenesis. Cloning for the construction of truncated LIMCH1 and NM-IIA is described in detail in the Supplemental Materials.
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3

Construction and Purification of GST-Fusion Proteins

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Recombinant proteins tagged with glutathione-S-transferase (GST) were constructed by recombining the insertion sequences of pBluescript into pGEX-4T (GE Healthcare Life Sciences, Pittsburgh, PA) vector plasmids. The pBluescript plasmids were digested using a combination of EcoRI and XhoI or SmaI and XhoI. The inserted DNA fragments were isolated using GeneElute™ Minus EtBr SPIN COLUMNS (Sigma-Aldrich, St. Louis, MO). The insertion sequences were ligated in frame to SmaI- and XhoI-digested pGEX-4T-1 or EcoRI- and XhoI-digested pGEX-4T-3 using Ligation Convenience Kits (Nippon Gene, Toyama, Japan). The ligation mixtures were used to transform ECOS™ competent E. coli JM-109 (Nippon Gene) and appropriate recombinants were confirmed by DNA sequencing. The constructed pGEX recombinants with the correct insertion in the right orientation were then used to transform competent E. coli BL21-RIL-codon-plus (Stratagene). The expression of the GST-fusion proteins was induced by treating the transformed E. coli with 0.1 mM isopropyl-β-D-thiogalactoside for 3 h. The GST recombinant proteins were purified by glutathione-Sepharose column chromatography according to the manufacturer’s instructions (GE Healthcare Life Sciences) and dialyzed against 1 mM Tris–HCl (pH 7.5) and 1 mM EDTA.
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4

Purification and analysis of CDK complexes

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For Figure 5A, the nda3-KM311 strain was cultured at 30°C for 18 h and then shifted to 17°C for 13 h in YE5S to induce mitotic arrest. Cells were collected and lysed with glass beads in HB buffer. Cell extracts were incubated with agarose-conjugated p13/suc1 (Millipore, Billerica, MA) for 1.5 h at 4°C. After washing with HB buffer, the pellet was resuspended with HB buffer and used as the CDK solution.
For the assay in Figure 5C, The Cdc2-GST fusion protein was purified from S. pombe cells using a GST pull-down method. First, the cdc2+ gene was tagged with the GST gene using the standard method (Bähler et al., 1998 (link)) in the nda3-KM311 strain. The resultant strain, nda3-KM311 cdc2-GST, was cultured at 30°C for 18 h and then shifted to 17°C for 13 h. Cell extraction was done as described. Crude extracts were then incubated with glutathione Sepharose 4B (GE Healthcare) for 1.5 h at 4°C. After washing with HB buffer, the pellet was resuspended with HB buffer and used as the CDK solution. Activity of the purified Cdc2-GST was confirmed by an in vitro kinase assay using histone H1 (Calbiochem, San Diego, CA) as a substrate.
To express recombinant GST–Alp7-WT and GST–Alp7-5A in E. coli BL21 (DE3) cells, coding sequences for alp7+ and alp7-5A were amplified with PCR and cloned into the GST-containing vector pGEX-4T (GE Healthcare).
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5

Engineered Protein Expression Constructs

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Ikaros and Foxp1 cDNAs were cloned into PCDNA3.1 vectors containing either a HA or double FLAG epitope tag. For GST-tagged proteins, cDNAs were inserted into pGEX-4T (GE lifesciences). Retroviral expression constructs were derived from the pMSCV-IRES-GFP plasmid.
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6

Molecular Cloning of Apoptosis Proteins

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Full-length FADD, Caspase-8 and c-FLIPS were cloned into pcDNA3 vectors with or without a non-cleavable 1xFLAG Tag. The constructs were co-transfected into HEK293F cells with polyethylenimine (PEI; Sigma) and harvested after 16 h47 (link). GST-TRAIL-R1/R2-IcD and CD95-IcD were cloned into pGEX4T (GE Healthcare) and their respective fusion proteins produced in E coli2 (link),48 (link). Full-length FADD was cloned into the vector pTYB1 (NEB Inc.) and recombinant FADD (r-FADD) generated in E coli19 (link). Full-length procaspase-8b (MACHα2/Mch5b) was cloned in pcDNA3.1 (Invitrogen) and untagged proteins produced by in vitro transcription/translation (IVT) (Insect System; Qiagen), incorporating 35S-methionine (GE Healthcare)19 (link). Mutations were made using the Stratagene QuikChange Site-Directed Mutagenesis kit and confirmed by DNA sequencing. Proteins from c-FLIPS·Myc in pcDNA6.1 were produced by IVT (TNT T7-coupled reticulocyte lysate system; Promega).
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7

Purification of Recombinant Toxoplasma ADF Proteins

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Wild-type and mutant adf genes from T. gondii were cloned into pGEX4T (GE Healthcare, Uppsala, Sweden) and expressed as glutathione S-transferase fusion proteins in Escherichia coli strain BL21 (DE3; Life Technologies). Recombinant proteins were purified as previously described (Wong et al., 2011 (link)) and dialyzed against PBS before cleavage with thrombin protease (GE Healthcare). Untagged ADF proteins were purified by size exclusion chromatography using a Superdex 200, GL10/300 column (GE Healthcare) and eluted in 20 mM MES/10 mM NaCl, pH 7.0, for downstream biochemical analysis.
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