MassIVE MSV000084671

Description

Protein pull-down assay- Mixed erythrocytic stage 3D7 Plasmodium falciparum parasite cultures were collected and lysed using 0.15% saponin for 10 min on ice. After subsequent washes, the parasite pellet was resuspended in 2.5X volume of IP buffer (0.65% Igepal CA-360 (Sigma-Aldrich), 50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 1% Triton-X, 1 mM AEBSF, 5 uM E-64 and EDTA-free protease inhibitor cocktail (Roche)) and lysed by passing through a 26G 1/2-inch needle ten times and sonicated 7 times 10 seconds on/30 seconds off using a probe sonicator. Extracted nuclear protein lysates were incubated for 10 mins at room temperature with DNase I to remove DNA and centrifuged for 10 mins at 14,500 rcf to remove cell debris. Washed Protein A magnetic beads (Pure Proteome) were added to the protein sample and incubated for 1 hour at 4oC to preclear the lysate. Precleared lysate was transferred to a new microcentrifuge tube and split equally for the antibody and no antibody control. The anti-CRWN-like custom antibody was added at a 1:50 ratio and incubated overnight at 4oC. The negative control with no antibody was also incubated overnight. Antibody-protein complexes were recovered using Protein A magnetic beads (Pure Proteome), followed by extensive washes with wash buffer A (1% Triton-X, 1 mM EDTA in 1X PBS), wash buffer B (wash buffer A, 0.5 M NaCl) and wash buffer C (1 mM EDTA, 1X PBS). Proteins were eluted using 0.1 M glycine, pH 2.8 and the eluent was neutralized using 2 M Tris-HCl, pH 8.0. Protein eluates were TCA-precipitated overnight, then washed twice with cold acetone. Multidimensional Protein Identification Technology- The TCA-precipitated protein pellet was solubilized using Tris-HCl pH 8.5 and 8 M urea, followed by addition of TCEP (Tris(2-carboxyethyl)phosphine hydrochloride; Pierce) and CAM (chloroacetamide; Sigma) were added to a final concentration of 5 mM and 10 mM, respectively. Proteins were digested using Endoproteinase Lys-C at 1:100 w/w (Roche) at 37oC overnight. The samples were brought to a final concentration of 2 M urea and 2 mM CaCl2 and a second digestion was performed overnight at 37oC using trypsin (Promega) at 1:100 w/w. The reactions were stopped using formic acid (5% final). The samples were loaded on a split-triple-phase fused-silica micro-capillary column and placed in-line with a linear ion trap mass spectrometer (LTQ, Thermo Scientific), coupled with a Quaternary Agilent 1100 Series HPLC system. A fully automated 10-step chromatography run was carried out. Each full MS scan (400-1600 m/z) was followed by five data-dependent MS/MS scans. The number of the micro scans was set to 1 both for MS and MS/MS. The settings were as follows: repeat count 2; repeat duration 30 s; exclusion list size 500 and exclusion duration 120 s, while the minimum signal threshold was set to 100. The MS/MS data set was searched using ProLuCID (v. 1.3.3) against a database consisting of 5,530 P. falciparum non-redundant proteins (PlasmoDB-34), 36,628 Homo sapiens NR proteins (NCBI -released June 10, 2016), 193 usual contaminants, and, to estimate false discovery rates (FDRs), 42,351 randomized amino acid sequences derived from each NR protein entry. To account for alkylation by CAM, 57 Da were added statically to the cysteine residues. To account for the oxidation of methionine to methionine sulfoxide, 16 Da were added as a differential modification to the methionine residue. Peptide/spectrum matches were sorted and selected to an FDR less than 5% at the peptide and protein levels, using DTASelect in combination with swallow, an in-house software. [doi:10.25345/C5K397] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Chromatin Structure ; Genome Architecture ; Immunoprecipiatation (IP) ; CROWDED-like NUCLEI (CRWN) protein

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Publications

Batugedara G, Lu XM, Saraf A, Sardiu ME, Cort A, Abel S, Prudhomme J, Washburn MP, Florens L, Bunnik EM, Le Roch KG.
The chromatin bound proteome of the human malaria parasite.
Microb Genom. Epub 2020 Feb 4.