Studying membrane proteins represents a major challenge in protein biochemistry, with one of the major difficulties being the problems encountered when working outside the natural lipid environment. In vitro studies such as crystallization are reliant on the successful solubilization or reconstitution of membrane proteins, which generally involves the careful selection of solubilizing detergents and mixed lipid/detergent systems. This review will concentrate on the methods currently available for efficient reconstitution and solubilization of membrane proteins through the use of detergent micelles, mixed lipid/detergent micelles and bicelles or liposomes. We focus on the relevant molecular properties of the detergents and lipids that aid understanding of these processes. A significant barrier to membrane protein research is retaining the stability and function of the protein during solubilization, reconstitution and crystallization. We highlight some of the lessons learnt from studies of membrane protein folding in vitro and give an overview of the role that lipids can play in stabilizing the proteins.

An ability to mimic the boundaries of biological compartments would improve our understanding of self-assembly and provide routes to new materials for the delivery of drugs and biologicals and the development of protocells. We show that short designed peptides can be combined to form unilamellar spheres approximately 100 nanometers in diameter. The design comprises two, noncovalent, heterodimeric and homotrimeric coiled-coil bundles. These are joined back to back to render two complementary hubs, which when mixed form hexagonal networks that close to form cages. This design strategy offers control over chemistry, self-assembly, reversibility, and size of such particles.

Protein engineering, chemical biology, and synthetic biology would benefit from toolkits of peptide and protein components that could be exchanged reliably between systems while maintaining their structural and functional integrity. Ideally, such components should be highly defined and predictable in all respects of sequence, structure, stability, interactions, and function. To establish one such toolkit, here we present a basis set of de novo designed α-helical coiled-coil peptides that adopt defined and well-characterized parallel dimeric, trimeric, and tetrameric states. The designs are based on sequence-to-structure relationships both from the literature and analysis of a database of known coiled-coil X-ray crystal structures. These give foreground sequences to specify the targeted oligomer state. A key feature of the design process is that sequence positions outside of these sites are considered non-essential for structural specificity; as such, they are referred to as the background, are kept non-descript, and are available for mutation as required later. Synthetic peptides were characterized in solution by circular-dichroism spectroscopy and analytical ultracentrifugation, and their structures were determined by X-ray crystallography. Intriguingly, a hitherto widely used empirical rule-of-thumb for coiled-coil dimer specification does not hold in the designed system. However, the desired oligomeric state is achieved by database-informed redesign of that particular foreground and confirmed experimentally. We envisage that the basis set will be of use in directing and controlling protein assembly, with potential applications in chemical and synthetic biology. To help with such endeavors, we introduce Pcomp, an on-line registry of peptide components for protein-design and synthetic-biology applications.

The ability to maintain interactions between soluble protein subunits in the gas phase of a mass spectrometer gives critical insight into the stoichiometry and interaction networks of protein complexes. Conversely, for membrane protein complexes in micelles, the transition into the gas phase usually leads to the disruption of interactions, particularly between cytoplasmic and membrane subunits, and a mass spectrum dominated by large aggregates of detergent molecules. We show that by applying nanoelectrospray to a micellar solution of a membrane protein complex, the heteromeric adenosine 5'-triphosphate (ATP)-binding cassette transporter BtuC2D2, we can maintain the complex intact in the gas phase of a mass spectrometer. Dissociation of either transmembrane (BtuC) or cytoplasmic (BtuD) subunits uncovers modifications to the transmembrane subunits and cooperative binding of ATP. By protecting a membrane protein complex within a n-dodecyl-beta-d-maltoside micelle, we demonstrated a powerful strategy that will enable the subunit stoichiometry and ligand-binding properties of membrane complexes to be determined directly, by precise determination of the masses of intact complexes and dissociated subunits.

The design of new proteins that expand the repertoire of natural protein structures represents a formidable challenge. Success in this area would increase understanding of protein structure, and present new scaffolds that could be exploited in biotechnology and synthetic biology. Here we describe the design, characterisation and X-ray crystal structure of a new coiled-coil protein. The de novo sequence forms a stand-alone, parallel, 6-helix bundle with a channel running through it. Although lined exclusively by hydrophobic leucine and isoleucine side chains, the 6 Å channel is permeable to water. One layer of leucine residues within the channel is mutable accepting polar aspartic acid (Asp) and histidine (His) side chains, and leading to subdivision and organization of solvent within the lumen. Moreover, these mutants can be combined to form a stable and unique (Asp-His)3 heterohexamer. These new structures provide a basis for engineering de novo proteins with new functions.

Secondary transporters undergo structural rearrangements to catalyze substrate translocation across the cell membrane – yet how such conformational changes happen within a lipid environment remains poorly understood. Here, we combine hydrogen-deuterium exchange mass spectrometry (HDX-MS) with molecular dynamics (MD) simulations to understand how lipids regulate the conformational dynamics of secondary transporters at the molecular level. Using the homologous transporters XylE, LacY and GlpT from Escherichia coli as model systems, we discover that conserved networks of charged residues act as molecular switches that drive the conformational transition between different states. We reveal that these molecular switches are regulated by interactions with surrounding phospholipids and show that phosphatidylethanolamine interferes with the formation of the conserved networks and favors an inward-facing state. Overall, this work provides insights into the importance of lipids in shaping the conformational landscape of an important class of transporters.

Assembly of proteins within lipid bilayers is essential for the biogenesis and function of biological membranes. Little is known, however, about the underlying mechanism of assembly, and it is not clear whether it is possible to observe individual folding steps for integral membrane proteins either in vivo or in vitro. Fluorescence spectroscopy is used here to follow the time course of folding events for bacteriorhodopsin in mixed detergent/lipid micelles. Transient folding-intermediates are detected and binding of the retinal chromophore occurs at a late stage, when it binds to an apoprotein intermediate.

The analytical toolkit developed for investigations into watersoluble protein folding has yet to be applied in earnest to membrane proteins. A major problem is the difficulty in collecting kinetic data, which are crucial to understanding any reaction. Here, we combine kinetic and thermodynamic studies of the reversible unfolding of an ␣-helical membrane protein to provide a definitive value for the reaction free energy and a means to probe the transition state. Our analyses show that the major unfolding step in the SDS-induced denaturation of bacteriorhodopsin involves a reduction in ␣-helical structure and proceeds with a large freeenergy change; both our equilibrium and kinetic measurements predict that the free energy of unfolding in the absence of denaturant is ؉20 kcal⅐mol ؊1 , with an associated m-value of 25 kcal⅐mol ؊1 . The rate of unfolding in the absence of denaturant, ku H2O , is surprisingly very slow (Ϸ10 ؊15 s ؊1 ). The kinetics also give information on the transition state for this major unfolding step, with a value for ␤ (mf/[mf ؉ mu]) of Ϸ0.1, indicating that the transition state is close to the unfolded state. We thus present a basis for mapping the structural and energetic properties of membrane protein folding by mutagenesis and classical kinetics.bacteriorhodopsin ͉ folding ͉ free energy ͉ transition state T he folding and assembly of integral membrane proteins is a fundamental process within biological systems, yet surprisingly few quantitative studies of membrane protein folding have been performed. Many transmembrane ␣-helical proteins are unstable once they are displaced from the biological membrane, and our limited understanding of the factors affecting folding and stability presents a major barrier to studies of structure and function.Bacteriorhodopsin (bR), a light-driven proton pump from the purple membrane (PM) of Halobacterium salinarum, is the current paradigm for studies of ␣-helical membrane protein folding (1, 2). The native purple chromophore is formed by the covalent attachment of the cofactor retinal at K216 and offers a direct, quantitative measure of the folded state of the protein because it is strongly influenced by retinal isomerization and noncovalent binding pocket interactions (i.e., refs. 3 and 4).The unfolding and refolding of bR in lipid/detergent mixtures was first reported in the seminal work of London and Khorana (5). bR was found to unfold in SDS from the native purple state by way of an intermediate to give denatured apoprotein, bacterioopsin (bO), and bR was efficiently reconstituted from bO by replacing SDS with renaturing micelles. The kinetics of refolding have been investigated in considerable detail (1, 6, 7). A recent equilibrium study of this denaturation of bR (8) has also demonstrated that the free-energy change of unfolding could be measured. A full kinetic and thermodynamic study of unfolding and folding is, however, vital for a complete understanding of the reaction mechanism, but it has yet to be achieved. Here, we present such a study and prob...