A hydrodynamic comparison of solution and gas phase proteins and their complexes.

The extent to which protein structures are preserved on transfer from solution to gas phase is a central question for native mass spectrometry. Here we compare the collision cross sections (Ω) of a wide range of different proteins and protein complexes (15-500 kDa) with their corresponding Stokes radii (RS). Using these methods, we find that Ω and RS are well correlated, implying overall preservation of protein structure in the gas phase. Accounting for protein hydration, a scaling term is required to bring Ω and RS into parity. Interestingly, the magnitude of this scaling term agrees almost entirely with the drag factor proposed by Millikan. RS were then compared with various different predicted values of Ω taken from their atomic coordinates. We find that many of the approaches used to obtained Ω from atomic coordinates miscalculate the physical sizes of the proteins in solution by as much as 20%. Rescaling of Ω estimated from atomic coordinates may therefore seem appropriate as a general method to bring theoretical values in line with those observed in solution.

Detergent release prolongs the lifetime of native-like membrane protein conformations in the gas-phase.

Recent studies have suggested that detergents can protect the structure of membrane proteins during their transition from solution to the gas-phase. Here we provide mechanistic insights into this process by interrogating the structures of membrane protein-detergent assemblies in the gas-phase using ion mobility mass spectrometry. We show a clear correlation between the population of native-like protein conformations and the degree of detergent attachment to the protein in the gas-phase. Interrogation of these protein-detergent assemblies, by tandem mass spectrometry, enables us to define the mechanism by which detergents preserve native-like protein conformations in a solvent free environment. We show that the release of detergent is more central to the survival of these conformations than the physical presence of detergent bound to the protein. We propose that detergent release competes with structural collapse for the internal energy of the ion and permits the observation of transient native-like membrane protein conformations that are otherwise lost to structural rearrangement in the gas-phase.