Abstract
Molecular dynamics simulations have been used to characterize the effects of transfer from aqueous solution to a vacuum to inform our understanding of mass spectrometry of membrane-protein-detergent complexes. We compared two membrane protein architectures (an α-helical bundle versus a β-barrel) and two different detergent types (phosphocholines versus an alkyl sugar) with respect to protein stability and detergent packing. The β-barrel membrane protein remained stable as a protein-detergent complex in vacuum. Zwitterionic detergents formed conformationally destabilizing interactions with an α-helical membrane protein after detergent micelle inversion driven by dehydration in vacuum. In contrast, a nonionic alkyl sugar detergent resisted micelle inversion, maintaining the solution-phase conformation of the protein. This helps to explain the relative stability of membrane proteins in the presence of alkyl sugar detergents such as dodecyl maltoside.
Highlights
Membrane proteins play key roles in cell biology, accounting for ~25% of genes
The use of mass spectrometry (MS) is widespread in the characterization of watersoluble proteins, using electrospray ionization (ESI) to transport macromolecular protein complexes into the gas phase [4]
The PDCs are equilibrated in solution and adopt the normal micelle geometry, in which the hydrophobic tails are sequestered within the core, allowing the headgroups to interact with water
Summary
Membrane proteins play key roles in cell biology, accounting for ~25% of genes. Advances in structural biology are yielding an increasing number of membrane protein structures [1], with ~2800 unique structures predicted by 2020 (see, e.g., http://blanco.biomol.uci.edu/mpstruc for a summary). Relatively few membrane protein structures have been determined in the presence of a lipid bilayer environment. The majority of biophysical and structural studies are of membrane proteins in the presence of detergents. It is of interest to understand in more detail how the environment presented by detergents may influence membrane protein conformation and stability. Membrane proteins are exposed to bulk aqueous solvent, even when embedded in lipid bilayers or detergent micelles. It was thought that membrane protein complexes could not be studied using this technique, as their stability requires a membranelike environment [6]. N-dodecyl-b-D-maltoside (DDM) micelles have been shown to stabilize intact oligomeric membrane protein complexes
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