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For the proteomic profiling step, the purified platelet membrane fraction was pre-fractionated using 1D SDS-PAGE and processed according to the workflow shown in Figure 1A.
For further outer-membrane fractionation, the pellet (total membrane fraction) was resuspended sterilized distilled water.
The resulting pellet, deemed the crude membrane fraction, was used as the starting material for Western blotting and fractionation experiments.
Here, the E. coli membrane fraction was obtained through ultracentrifugation method.
A cell membrane fraction was prepared according to the previously described method (Frieman and Cormack 2004; Hara et al. 2012a).
The crosslinked membrane fraction was digested by trypsin and crosslinked peptides were identified by liquid chromatography-tandem mass spectrometry.
The membrane fraction was collected and incubated with 1.5% (w/v) n-dodecyl-β-D-maltopyranoside (DDM; Anatrace) for 3 h with slow stirring at 4°C.
The pellet (membrane fraction) was suspended in 20 mM sodium acetate buffer, pH 5.0/1 M NaCl and centrifuged again as described above for 1 h.
Membrane fraction was harvested and solubilized with 0.5% (w/v) n-decyl-β-d-maltopyranoside (DM; Anatrace) for 15 min at 4 °C.
The crude membrane fraction was collected from the gradient interface.
The resulting pellet, representing the total membrane fraction, was resuspended in Buffer A and Dounce homogenized.
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