Drug binding revealed by tandem mass spectrometry of a protein-micelle complex

The protein-micelle complex formed between the protein EmrE and the lipid dodecylmaltoside has been examined by mass spectrometry. The results show that despite the unfavorable hydrophobic environment in the mass spectrometer it is possible to preserve protein submicelle complexes in the gas phase. The peaks assigned to the submicelle complexes are broad in nature and consistent with a heterogeneous distribution of lipid molecules attached to the protein complex. As such, the spectrum cannot be interpreted. To simplify this complexity we used a tandem mass spectrometry procedure in which discrete m/z values are isolated from the peak and subjected to collision-induced dissociation. These spectra reveal clusters of DDM molecules as well as sequential release of TPP⁺ and EmrE from the complex as the collision cell voltage is raised. Taken together, the results provide direct evidence for drug binding within a relevant gas-phase protein-micelle complex.