| Literature DB >> 35434660 |
Onofrio Laselva1, Evgeniy V Petrotchenko2,3, C Michael Hamilton4, Zafar Qureshi4, Christoph H Borchers2,3, Robert N Young4, Christine E Bear5,6,7.
Abstract
We describe a protocol to identify the binding site(s) for a drug called ivacaftor that potentiates the CFTR chloride channel. We use photoaffinity probes-based on the structure of ivacaftor-to covalently modify the CFTR protein at the region that constitutes the drug binding site(s). We define the methods for photo-labeling CFTR, its membrane extraction, and enzymatic digestion using trypsin. We then describe the experimental methods to identify the modified peptides by using mass spectrometry. For complete details on the use and execution of this protocol, please refer to Laselva et al. (2021). CrownEntities:
Keywords: Cell Biology; Cell Membrane; Cell-based Assays; Mass Spectrometry; Molecular/Chemical Probes; Protein Biochemistry
Mesh:
Substances:
Year: 2022 PMID: 35434660 PMCID: PMC9006651 DOI: 10.1016/j.xpro.2022.101258
Source DB: PubMed Journal: STAR Protoc ISSN: 2666-1667
Figure 1Chemical structures of VX-770, VX-770-DIAZ, and VX-770-BIOT
Figure 2Major steps for confirming specific photolabeling of CFTR with VX-770-BIOT
Figure 3Exposure of sample to UV lamp in 96 well plate (black, clear bottom) on top of ice
Figure 4Immunoblots of labeled Wt-CFTR (bound) and unlabelled Wt-CFTR (unbound)
Left panel shows that only CFTR labeled with the photo-label (bearing a biotin) is bound to the mono-avidin matrix.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Anti-CFTR | University of North Caroline at Chapel Hill - CFTR antibodies | ID: 596 |
| Anti-Calnexin | Sigma-Aldrich | Cat#C4731, RRID: |
| HEPES | Sigma-Aldrich | Cat# H3375 |
| EDTA | Sigma-Aldrich | Cat# E9884 |
| TRIS-HCl | Sigma-Aldrich | Cat# T5941 |
| MgCl2 (Magnesium chloride) | Sigma-Aldrich | Cat# M8266 |
| completeTM, Protease Inhibitor Cocktail (Roche) | Sigma-Aldrich | Cat# 4693159001 |
| Ammonium bicarbonate (ABC) | Sigma-Aldrich | Cat# 09830 |
| Acetonitrile (MeCN) | Sigma-Aldrich | Cat# 34851 |
| Trypsin, sequence grade | Promega | Cat# V5117 |
| C18 Zip-Tips | Sigma-Aldrich | Cat# ZTC18M096 |
| VX-770-Biot | Must be prepared by synthesis ( | See adjacent reference |
| VX-770-Diaz | Must be prepared by synthesis ( | See adjacent reference |
| PierceTM Monomeric Avidin Agarose | Thermo Fisher Scientific | Cat# 20228 |
| Micron-30 kDa Centrifugal filter Unit with Ultracel-30 membrane | Millipore | Cat# MRCF0R030 |
| Nitrocellulose Membrane, Roll, 0.2 μm, 30 cm × 3.5 m | Bio-Rad | Cat# 1620112 |
| 10× Tris-Glycine SDS buffer | WISENT | Cat# 880-570-LL |
| 10× Tris-Glycine buffer | WISENT | Cat# 880-560-LL |
| 10× PBS (Phosphate Buffered Saline) | WISENT | Cat# 311-410-CL |
| Pierce™ Monomeric Avidin Agarose Kit | Thermo Fisher Scientific | Cat# 20227 |
| ECL | GE Healthcare | Cat# 10308449 |
| Human Embryonic Kidney (HEK)-293 cells | Laboratory of Dr. Daniela Rotin | ID: CRL-1573 |
| ImageStudioLite | LI-COR Biosciences | |
Cell Lysis Buffer
| Reagent | Final concentration | Amount |
|---|---|---|
| HEPES | 10 mM | 1.19 g |
| EDTA | 1 mM | 0.226 g |
| ddH2O | n/a | 500 mL |
Adjust pH to 7.2 at 25°C, add ddH2O water up to 500 mL. The buffer can be stored at 4°C for 12 months.
Re-suspension Buffer
| Reagent | Final concentration | Amount |
|---|---|---|
| Tris-HCl | 40 mM | 2.42 g |
| MgCl2 | 5 mM | 0.238 g |
| EGTA | 0.1 mM | 0.019 |
| ddH2O | n/a | 500 mL |
Adjust pH to 7.5 at 25°C, add ddH2O water up to 500 mL. The buffer can be stored at 4°C for 12 months.
RIPA Buffer
| Reagent | Final concentration | Amount |
|---|---|---|
| Tris-HCl | 50 mM | 3.94 g |
| NaCl | 150 mM | 4.38 g |
| EDTA | 1 mM | 0.14 |
| SDS | 0.2% | 1 mL |
| Triton X-100 | 0.1% | 0.5 mL |
Adjust pH to 7.4 at 25°C, add ddH2O water up to 500 mL. The buffer can be stored at 4°C for 12 months.
T-PBS Buffer
| Reagent | Final concentration | Amount |
|---|---|---|
| 10× PBS | 1× | 100 mL |
| ddH2O | n/a | 900 mL |
| Tween 20 | n/a | 1 mL |
Running Buffer
| Reagent | Final concentration | Amount |
|---|---|---|
| 10× Tris-Glycine SDS buffer | 1× | 100 mL |
| ddH2O | n/a | 800 mL |
Transfer Buffer
| Reagent | Final concentration | Amount |
|---|---|---|
| 10× Tris-Glycine buffer | 1× | 100 mL |
| Methanol | n/a | 100 mL |
| ddH2O | n/a | 800 mL |