Fig. 3

Lipid–protein interactions regulate the conformational equilibrium. ΔHDX of XylE WT in PE vs. PC nanodiscs shows that PE promotes the IF conformation. a Optimized experimental procedure for HDX-MS of a transporter in nanodiscs of different lipid compositions. Following deuteration at specific time points, the exchange reaction is quenched and the nanodiscs disassembled with detergent DDM. Lipids are removed by adsorption, before enzymatic digestion and peptides identification by MS. The mass uptake of the protein in both lipid environments is then compared. b ΔHDX of WT XylE in DOPE-PG-CL nanodiscs (native-like) minus DOPC-PG-CL (control) nanodiscs mapped on the PDB structure and the topological representation. c Representative deuterium uptake plots for peptide 28–38, (d) 70–88, (e) 108–122, (f) 430–434 in DOPC-PG-CL nanodiscs (green) and DOPE-PG-CL nanodiscs (black). Standard deviations for each time point are plotted as error bars (n  =  3). All measurements were performed in triplicates