Aug 29, 2024
Purification of mCh-WIPI2d-IDR (364-426aa)
- Elias Adriaenssens1
- 1Sascha Martens lab, University of Vienna, Max Perutz Labs - Vienna
External link: https://doi.org/10.1038/s41556-025-01712-y
Protocol Citation: Elias Adriaenssens 2024. Purification of mCh-WIPI2d-IDR (364-426aa). protocols.io https://dx.doi.org/10.17504/protocols.io.5qpvokk8bl4o/v1
Manuscript citation:
Adriaenssens, E., Schaar, S., Cook, A.S.I. et al. Reconstitution of BNIP3/NIX-mitophagy initiation reveals hierarchical flexibility of the autophagy machinery. Nat Cell Biol 27, 1272–1287 (2025). https://doi.org/10.1038/s41556-025-01712-y
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: May 24, 2024
Last Modified: August 29, 2024
Protocol Integer ID: 101116
Keywords: ASAPCRN, purification of mcherry wipi2d, purification of mcherry, mcherry wipi2d, protocol details the purification, purification, wipi2d, idr, mcherry, protocol detail
Funders Acknowledgements:
Aligning Science Across Parkinson’s (ASAP)
Grant ID: ASAP-000350
Marie Skłodowska-Curie MSCA Postdoctoral fellowship
Grant ID: 101062916
Abstract
This protocol details the purification of mCherry WIPI2d-IDR.
Materials
Rosetta™(DE3)pLysS Competent Cells - NovagenMerckCatalog #70956-4
Lysis buffer:
| A | B | |
| Tris-HCl, pH 7.4 | 50 mM | |
| NaCl | 300 mM | |
| MgCl2 | 2 mM | |
| Glycerol | 5% | |
| Triton X-100 | 1% | |
| Imidazole | 10 mM | |
| β-mercaptoethanol | 2 mM |
Wash buffer:
| A | B | |
| Tris-HCl, pH 7.4 | 50 mM | |
| NaCl | 300 mM | |
| Imidazole | 10 mM | |
| β-mercaptoethanol | 2 mM |
SEC buffer:
| A | B | |
| Tris-HCl, pH 7.4 | 25 mM | |
| NaCl | 150 mM | |
| DTT | 1 mM |
Troubleshooting
Purification procedure
16h 45m 30s
To purify mCherry-WIPI2d IDR (364-426aa) (available from Addgene), fuse the corresponding coding sequence of WIPI2d to a N-terminal 6xHis-TEV-mCherry-tag through cloning into a pET-DUET1 vector (available from Addgene).
After the transformation of the pET-DUET1 vector encoding 6xHis-TEV-mCherry-WIPI2d-IDR in E. coli Rosetta pLysS cells(Novagen Cat# 70956-4), grow cells in 2x Tryptone Yeast extract (TY) medium at 37 °C until an OD600 of 0.4 and then continued at 18 °C .
Once the cells reach an OD600 of 0.8, induce the protein expression with 100 micromolar (µM) isopropyl β-D-1-thiogalactopyranoside (IPTG) for 16:00:00 at 18 °C .
16h
Collect the cells by centrifugation and resuspend in lysis buffer, complete EDTA-free protease inhibitors (Roche), CIP protease inhibitor (Sigma), and DNase (Sigma)).
Lysis buffer:
| A | B | |
| Tris-HCl, pH 7.4 | 50 mM | |
| NaCl | 300 mM | |
| MgCl2 | 2 mM | |
| Glycerol | 5% | |
| Triton X-100 | 1% | |
| Imidazole | 10 mM | |
| β-mercaptoethanol | 2 mM |
Sonicate the cell lysates twice for 00:00:30 .
30s
Clear the lysates by centrifugation at 18000 rpm, 4°C, 00:45:00 in a SORVAL RC6+ centrifuge with an F21S-8x50Y rotor (Thermo Scientific).
45m
Filter the supernatant through an 0.45 µm filter and load onto a pre-equilibrated 5 ml His-Trap HP column (Cytiva).
After bind His tagged proteins to the column, was the column with three column volumes of wash buffer.
Wash buffer:
| A | B | |
| Tris-HCl, pH 7.4 | 50 mM | |
| NaCl | 300 mM | |
| Imidazole | 10 mM | |
| β-mercaptoethanol | 2 mM |
Elute the proteins with a stepwise imidazole gradient (30, 75, 100, 150, 225, 300 mM).
Pool fractions containing the 6xHis-TEV-mCherry-WIPI2d-IDR, concentrate using a 10 kDa cut-off Amicon filter (Merck Millipore) and load onto a pre-equilibrated S75 Increase 10/300 column (Cytiva).
Elute the proteins with SEC buffer.
SEC buffer:
| A | B | |
| Tris-HCl, pH 7.4 | 25 mM | |
| NaCl | 150 mM | |
| DTT | 1 mM |
Analyse the fractions by SDS-PAGE and Coomassie staining.
Pool the fractions containing purified mCherry-WIPI2d-IDR.
After concentrating the purified protein, aliquot the protein and snap-frozen in liquid nitrogen.
Store the proteins at -80 °C .