A new window into the molecular physiology of membrane proteins

Abstract

Integral membrane proteins comprise ∼25% of the human proteome. Yet, our understanding of their molecular physiology is still in its infancy. This can be attributed to two factors: the experimental challenges that arise from the difficult chemical nature of membrane proteins, and the unclear relationship between their activity and their native environment. New approaches are therefore required to address these challenges. Recent developments in mass spectrometry have shown that it is possible to study membrane proteins in a solvent-free environment and provide detailed insights into complex interactions, ligand binding and folding processes. Interestingly, not only detergent micelles but also lipid bilayer nanodiscs or bicelles can serve as a means for the gentle desolvation of membrane proteins in the gas phase. In this manner, as well as by direct addition of lipids, it is possible to study the effects of different membrane components on the structure and function of the protein components allowing us to add functional data to the least accessible part of the proteome.

Figure 1

Mass spectrometry provides insights from the primary to the quaternary structure of membrane proteins Top left: mass determination and MS-based sequencing shows the primary protein structure and attached components. Bottom left: hydrogen/deuterium exchange occurs predominantly in protein regions that lack a defined secondary structure. MS can be used to localize the incorporated deuterium ions and thus informs about the presence of secondary structure elements. Right: ion mobility and chemical crosslinking can be combined with MS to study tertiary and quaternary structures of proteins and their complexes. IM-MS measures the collisional cross-sections of desolvated proteins, while the identification of chemical crosslinks with MS reveals intra- and intermolecular distances. In the same manner, the effects of ligands and lipids or environmental changes such as altered pH or salt concentrations can be detected at all structural levels.

Figure 2

Possible mode for spatial regulation of membrane protein activity by specific lipids Several multimeric transporter proteins (such as AmtB, shown here) are activated by specific lipids. The lipid-free form exhibits only low transport activity (top). If the transporter is relocated to a membrane raft (bottom) with a high local content of the preferred lipid (red), the complex is stabilized, which promotes the transport of its preferred substrate (green). Such a regulatory mode would result in a strictly localized influx of the substrate, e.g. to facilitate the direct delivery of the substrate to its target proteins (grey).