Controlled 2D crystallization of membrane proteins using methyl-β-cyclodextrin

Structural insights into phosphatidylethanolamine N-methyltransferase PmtA mediating bacterial phosphatidylcholine synthesis

Phosphatidylethanolamine N-methyltransferase (PmtA) catalyzes the biosynthesis of phosphatidylcholine (PC) from phosphatidylethanolamine (PE). Although PC is one of the major phospholipids constituting bilayer membranes in eukaryotes, certain bacterial species encode PmtA, a membrane-associated methyltransferase, to produce PC, which is correlated with cellular stress responses, adaptability to environmental changes, and symbiosis or virulence with eukaryotic hosts. Depending on the organism, multiple PmtAs may be required for producing monomethyl- and dimethyl-PE derivatives along with PC, whereas in organisms such as Rubellimicrobium thermophilum, a single enzyme is sufficient to direct all three methylation steps. In this study, we present the x-ray crystal structures of PmtA from R. thermophilum in complex with dimethyl-PE and S-adenosyl-l-homocysteine, as well as in its lipid-free form. Moreover, we demonstrate that the enzyme associates with the cellular membrane via electrostatic interactions facilitated by a group of critical basic residues and can successively methylate PE and its methylated derivatives, culminating in the production of PC.

Proteomic analysis of the urothelial cancer landscape

Urothelial bladder cancer (UC) has a wide tumor biological spectrum with challenging prognostic stratification and relevant therapy-associated morbidity. Most molecular classifications relate only indirectly to the therapeutically relevant protein level. We improve the pre-analytics of clinical samples for proteome analyses and characterize a cohort of 434 samples with 242 tumors and 192 paired normal mucosae covering the full range of UC. We evaluate sample-wise tumor specificity and rank biomarkers by target relevance. We identify robust proteomic subtypes with prognostic information independent from histopathological groups. In silico drug prediction suggests efficacy of several compounds hitherto not in clinical use. Both in silico and in vitro data indicate predictive value of the proteomic clusters for these drugs. We underline that proteomics is relevant for personalized oncology and provide abundance and tumor specificity data for a large part of the UC proteome ( www.cancerproteins.org ).

A mechanistic study on the cellular uptake, intracellular trafficking, and antisense gene regulation of bottlebrush polymer-conjugated oligonucleotides

We have developed a non-cationic transfection vector in the form of bottlebrush polymer-antisense oligonucleotide (ASO) conjugates. Termed pacDNA (polymer-assisted compaction of DNA), these agents show improved biopharmaceutical characteristics and antisense potency in vivo while suppressing non-antisense side effects. Nonetheless, there still is a lack of the mechanistic understanding of the cellular uptake, subcellular trafficking, and gene knockdown with pacDNA. Here, we show that the pacDNA enters human non-small cell lung cancer cells (NCI-H358) predominantly by scavenger receptor-mediated endocytosis and macropinocytosis and trafficks via the endolysosomal pathway within the cell. The pacDNA significantly reduces a target gene expression (KRAS) in the protein level but not in the mRNA level, despite that the transfection of certain free ASOs causes ribonuclease H1 (RNase H)-dependent degradation of KRAS mRNA. In addition, the antisense activity of pacDNA is independent of ASO chemical modification, suggesting that the pacDNA always functions as a steric blocker.

Synthetic Biology: Bottom-Up Assembly of Molecular Systems

The bottom-up assembly of biological and chemical components opens exciting opportunities to engineer artificial vesicular systems for applications with previously unmet requirements. The modular combination of scaffolds and functional building blocks enables the engineering of complex systems with biomimetic or new-to-nature functionalities. Inspired by the compartmentalized organization of cells and organelles, lipid or polymer vesicles are widely used as model membrane systems to investigate the translocation of solutes and the transduction of signals by membrane proteins. The bottom-up assembly and functionalization of such artificial compartments enables full control over their composition and can thus provide specifically optimized environments for synthetic biological processes. This review aims to inspire future endeavors by providing a diverse toolbox of molecular modules, engineering methodologies, and different approaches to assemble artificial vesicular systems. Important technical and practical aspects are addressed and selected applications are presented, highlighting particular achievements and limitations of the bottom-up approach. Complementing the cutting-edge technological achievements, fundamental aspects are also discussed to cater to the inherently diverse background of the target audience, which results from the interdisciplinary nature of synthetic biology. The engineering of proteins as functional modules and the use of lipids and block copolymers as scaffold modules for the assembly of functionalized vesicular systems are explored in detail. Particular emphasis is placed on ensuring the controlled assembly of these components into increasingly complex vesicular systems. Finally, all descriptions are presented in the greater context of engineering valuable synthetic biological systems for applications in biocatalysis, biosensing, bioremediation, or targeted drug delivery.

Solubilization and Purification of α5β1 Integrin from Rat Liver for Reconstitution into Nanodiscs

Transmembrane proteins (or integral membrane proteins) are synthesized in the endoplasmic reticulum where most of them are core glycosylated prior to folding and in some cases assembly into quaternary structures. Correctly glycosylated, folded, and assembled transmembrane proteins are then shuttled to the Golgi apparatus for additional posttranslational modifications such as complex-type glycosylations, sulfation or proteolytic clipping. At the plasma membrane, the glycosylated extracellular domains are key to communicate with the cellular environment for a variety of functions, such as binding to the extracellular matrix for cell adhesion and migration, to neighboring cells for cell-cell interaction, or to extracellular components for nutrient uptake and cell signaling. Intracellular domains are essential to mediate signaling cascades, or to connect to cytosolic adaptors for internalization and intracellular compartmentalization. Despite its importance for the understanding of molecular mechanisms of transmembrane protein function, the determination of their structures has remained a challenging task. In recent years, their reconstitution in lipid nanodiscs in combination with high resolution cryo-electron microscopy has provided novel avenues to render this process more accessible. Here, we describe detailed protocols for the solubilization of heavily glycosylated α₅β₁ integrin from rat livers, its purification and reconstitution into nanodiscs. At the plasma membrane of many cells, including tumor metastases, this essential heterodimeric transmembrane protein mediates the communication between extracellular matrix and cytosolic cytoskeleton in processes of cell adhesion and migration. We expect that the protocols that are described here will provide new opportunities for the determination of the full structure of α₅β₁ integrin, as well as for the understanding of how interacting partners can regulate function and activity of this transmembrane protein.

Cyclodextrins for structural and functional studies of mechanosensitive channels

Mechanosensitive (MS) channels that are activated by the 'force-from-lipids' (FFL) principle rest in the membrane in a closed state but open a transmembrane pore in response to changes in the transmembrane pressure profile. The molecular implementations of the FFL principle vary widely between different MS channel families. The function of MS channels is often studied by patch-clamp electrophysiology, in which mechanical force or amphipathic molecules are used to activate the channels. Structural studies of MS channels in states other than the closed resting state typically relied on the use of mutant channels. Cyclodextrins (CDs) were recently introduced as a relatively easy and convenient approach to generate membrane tension. The principle is that CDs chelate hydrophobic molecules and can remove lipids from membranes, thus forcing the remaining lipids to cover more surface area and creating tension for membrane proteins residing in the membranes. CDs can be used to study the structure of MS channels in a membrane under tension by using single-particle cryo-electron microscopy to image the channels in nanodiscs after incubation with CDs as well as to characterize the function of MS channels by using patch-clamp electrophysiology to record the effect of CDs on channels inserted into membrane patches excised from proteoliposomes. Importantly, because incubation of membrane patches with CDs results in the activation of MscL, an MS channel that opens only shortly before membrane rupture, CD-mediated lipid removal appears to generate sufficient force to open most if not all types of MS channels that follow the FFL principle.

Structural dynamics of channels and transporters by high-speed atomic force microscopy

Channels and transporters are vital for transmembrane transport of ions and solutes, and also of larger compounds such as lipids and macromolecules. Therefore, they are crucial in many biological processes such as sensing, signal transduction, and the regulation of the distribution of molecules. Dysfunctions of these membrane proteins are associated to numerous diseases, and their interaction with drugs is critical in medicine. Understanding the behavior of channels and transporters requires structural and dynamic information to decipher the molecular mechanisms underlying their function. High-Speed Atomic Force Microscopy (HS-AFM) now allows the study of single transmembrane channels and transporters in action under physiological conditions, i.e., at ambient temperature and pressure, in physiological buffer and in a membrane, and in a most direct, label-free manner. In this chapter, we discuss the HS-AFM sample preparation, application, and data analysis protocols to study the structural and conformational dynamics of membrane-embedded channels and transporters.

2D Electron Crystallography of Membrane Protein Single-, Double-, and Multi-Layered Ordered Arrays

The electron cryo-microscopy (cryo-EM) approach of 2D electron crystallography allows for structure determination of two-dimensional (2D) crystals of soluble and membrane proteins, employing identical principles and methods once 2D crystals are obtained. Two-dimensional crystallization trials of membrane proteins can result in multiple outcomes of ordered arrays, which may be suited for either 2D electron crystallography, helical analysis, or MicroED.The membrane protein 2D crystals used for 2D electron crystallography are either single- or double-layered ordered proteoliposome vesicles or sheet-like membranes. We have developed a cryo-EM grid preparation approach, which allows for the analysis of stacked 2D crystals that are neither suitable for MicroED nor for directly applying 2D electron crystallography. This new grid preparation approach, the peel-blot, uses the capillary force generated by submicron filter paper and mechanical means for the separation of stacked 2D crystals into single-layered 2D crystals, for which standard 2D electron crystallography can then be employed. The preparation of 2D crystals, the peel-blot grid preparation, and the structure determination by 2D electron crystallography are described here.

Proton-Detected Solid-State NMR of the Cell-Free Synthesized α-Helical Transmembrane Protein NS4B from Hepatitis C Virus

Proton-detected 100 kHz magic-angle-spinning (MAS) solid-state NMR is an emerging analysis method for proteins with only hundreds of microgram quantities, and thus allows structural investigation of eukaryotic membrane proteins. This is the case for the cell-free synthesized hepatitis C virus (HCV) nonstructural membrane protein 4B (NS4B). We demonstrate NS4B sample optimization using fast reconstitution schemes that enable lipid-environment screening directly by NMR. 2D spectra and relaxation properties guide the choice of the best sample preparation to record 2D 1 H-detected 1 H,15 N and 3D 1 H,13 C,15 N correlation experiments with linewidths and sensitivity suitable to initiate sequential assignments. Amino-acid-selectively labeled NS4B can be readily obtained using cell-free synthesis, opening the door to combinatorial labeling approaches which should enable structural studies.

Rapid fabrication of precise high-throughput filters from membrane protein nanosheets

Biological membranes are ideal for separations as they provide high permeability while maintaining high solute selectivity due to the presence of specialized membrane protein (MP) channels. However, successful integration of MPs into manufactured membranes has remained a significant challenge. Here, we demonstrate a two-hour organic solvent method to develop 2D crystals and nanosheets of highly packed pore-forming MPs in block copolymers (BCPs). We then integrate these hybrid materials into scalable MP-BCP biomimetic membranes. These MP-BCP nanosheet membranes maintain the molecular selectivity of the three types of β-barrel MP channels used, with pore sizes of 0.8 nm, 1.3 nm, and 1.5 nm. These biomimetic membranes demonstrate water permeability that is 20-1,000 times greater than that of commercial membranes and 1.5-45 times greater than that of the latest research membranes with comparable molecular exclusion ratings. This approach could provide high performance alternatives in the challenging sub-nanometre to few-nanometre size range.

Pattern-based recognition of proteins by an array of fluorescent carbon-nanodot receptors

Protein types and concentrations in human body fluid environment have a direct correlation to health conditions, and can be used for primary screening and diagnostics of a great variety of diseases. Herein, we synthesized a series of fluorescent carbon nanodots (CDs) with various ratios of β-cyclodextrin doping, which can recognize proteins and adjust self-emission by combining both the cavity recognition effect of cyclodextrin and noncovalent bonding effect of carboxyl, amino and hydroxyl groups. The difference in β-cyclodextrin contents of various CDs will result in a differential response to various proteins, based on which a sensor array by four CDs was constructed to detect and discriminate six proteins with various subunit numbers. In order to improve the discriminative effect of the sensor array, CD-sensitive metal ions (Cu²⁺ and Fe³⁺) were introduced as sensing media to increase the action sites between the CDs and proteins, and these proteins were well discriminated by the CD@metal ion sensor array with a detection limit of 50 μM. The sensor array could work in physiological conditions (such as urine and serum) and realize multiple proteins detection. Combining with the good repeatable detection results and higher sensitivity, the sensor array based on the CDs and metal ions provides an efficient and accurate method to detect proteins, which is important for disease diagnosis through assessing protein levels.

Extracavity Effect in Cyclodextrin/Surfactant Complexation

Cyclodextrin (CD) complexation is a convenient method to sequester surfactants in a controllable way, for example, during membrane-protein reconstitution. Interestingly, the equilibrium stability of CD/surfactant inclusion complexes increases with the length of the nonpolar surfactant chain even beyond the point where all hydrophobic contacts within the canonical CD cavity are saturated. To rationalize this observation, we have dissected the inclusion complexation equilibria of a structurally well-defined CD, that is, heptakis(2,6-di- O-methyl)-β-CD (DIMEB), and a homologous series of surfactants, namely, n-alkyl- N, N-dimethyl-3-ammonio-1-propanesulfonates (SB3- x) with chain lengths ranging from x = 8 to 14. Thermodynamic parameters obtained by isothermal titration calorimetry and structural insights derived from nuclear magnetic resonance spectroscopy and molecular dynamics simulations revealed that, upon inclusion, long-chain surfactants with x = ≥10 extend beyond the canonical CD cavity. This enables the formation of hydrophobic contacts between long surfactant chains and the extracavity parts of DIMEB, which make additional favorable contributions to the stability of the inclusion complex. These results explain the finding that the stability of CD/surfactant inclusion complexes monotonously increases with the surfactant chain length even for long chains that completely fill the canonical CD cavity.

Perspective: A toolbox for protein structure determination in physiological environment through oriented, 2D ordered, site specific immobilization

Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based X-ray crystallography and cryo-electron microscopy have made major contributions in determining thousands of protein structures even from micro-sized crystals. They suffer from some limitations that have not been overcome, such as radiation damage, the natural inability to crystallize a number of proteins, and experimental conditions for structure determination that are incompatible with the physiological environment. Today, the ultra-short and ultra-bright pulses of X-ray free-electron lasers have made attainable the dream to determine protein structures before radiation damage starts to destroy the samples. However, the signal-to-noise ratio remains a great challenge to obtain usable diffraction patterns from a single protein molecule. With the perspective to overcome these challenges, we describe here a new methodology that has the potential to overcome the signal-to-noise-ratio and protein crystallization limits. Using a multidisciplinary approach, we propose to create ordered, two dimensional protein arrays with defined orientation attached on a self-assembled-monolayer. We develop a literature-based flexible toolbox capable of assembling different kinds of proteins on a functionalized surface and consider using a graphene cover layer that will allow performing experiments with proteins in physiological conditions.

Screening for the best detergent for the isolation of placental membrane proteins

Although membrane proteins (MPs) play crucial roles in physiological processes, information on them are insufficient, mostly due to their peculiar nature and surrounding which demand specific procedures for their extraction (using detergents) and analysis. A pallet of ten detergents and β-cyclodextrin was employed to investigate their efficiency in extracting total placental MPs, glycoproteins and insulin-like growth factor receptors (IR/IGF1R/IGF2R). Regardless of detergent used, the identity of major extracted proteins was the same. Glycoproteins extracted with Triton X-100 contained the greatest variety and quantity of glycans recognised by fifteen lectins, pointing to this detergent as universal medium for the extraction of membrane glycoproteins. Glycoproteins extracted using Brij 35 exhibited weak interaction with only seven lectins and were differently recognised by lectins of the similar glycan specificity. Brij 35, Tween 20, saponin and digitonin selectively extracted IGF2R compared to other two receptors. Pilot experiments should be conducted in order to choose adequate detergent for the extraction of specific MP. To obtain preparations enriched in specific receptor of the insulin/IGF system sequential solubilisation of placental MPs can be proposed: to use Brij 35 to extract IGF2R and subject the insoluble remaining suspension to Triton X-114 in order to extract most of IGF1R with small amounts of IR.

The CRACAM Robot: Two-Dimensional Crystallization of Membrane Protein

Membrane proteins are key cellular components that perform essential functions. They are major therapeutic targets. Electron crystallography can provide structural experimental information at atomic scale for membrane proteins forming two-dimensional (2D) crystals. There are two different methods to produce 2D crystals of membrane proteins. (1) either directly in the bulk of the solution (2) or under a lipid monolayer at the air-water interface. This extra lipid monolayer helps to pre-orient the proteins in order to facilitate the growth of 2D crystals. We present here these two methods for 2D crystallization of membrane proteins implemented in a fully automated robot called CRACAM. These methods require small volume of low concentration of proteins, making it possible to explore more conditions with the same amount of protein. These automated methods outperform traditional 2D crystallization approaches in terms of accuracy, flexibility, and throughput.

3D reconstruction of two-dimensional crystals

Electron crystallography of two-dimensional (2D) crystals determines the structure of membrane proteins in the lipid bilayer by imaging with cryo-electron microscopy and image processing. Membrane proteins can be packed in regular 2D arrays by their reconstitution in the presence of lipids at low lipid to protein weight-to-weight ratio. The crystal quality depends on the protein purity and homogeneity, its stability, and on the crystallization conditions. A 2D crystal presents the membrane protein in a functional and fully lipidated state. Electron crystallography determines the 3D structure even of small membrane proteins up to atomic resolution, but 3D density maps have a better resolution in the membrane plane than in the vertical direction. This problem can be partly eliminated by applying an iterative algorithm that exploits additional known constraints about the 2D crystal. 2D electron crystallography is particularly attractive for the structural analysis of membrane proteins that are too small for single particle analyses and too unstable to form 3D crystals. With the recent introduction of direct electron detector cameras, the routine determination of the atomic 3D structure of membrane-embedded membrane proteins is in reach.

New ganglio-tripod amphiphiles (TPAs) for membrane protein solubilization and stabilization: implications for detergent structure-property relationships

Detergents are widely used for membrane protein research; however, membrane proteins encapsulated in micelles formed by conventional detergents tend to undergo structural degradation, necessitating the development of new agents with enhanced efficacy. Here we prepared several hydrophobic variants of ganglio-tripod amphiphiles (TPAs) derived from previously reported TPAs and evaluated for a multi-subunit, pigment protein superassembly. In this study, TPA-16 was found to be most efficient in protein solubilization while TPA-15 proved most favourable in long-term protein stability. The current study combined with previous TPA studies enabled us to elaborate on a few detergent structure-property relationships that could provide useful guidelines for novel amphiphile design.

Inducing two-dimensional crystallization of membrane proteins by dialysis for electron crystallography

Electron crystallography is an electron cryo-microscopy (cryo-EM) method that is particularly suitable for structure-function studies of small membrane proteins, which are crystallized in two-dimensional (2D) arrays for subsequent cryo-EM data collection and image processing. This approach allows for structural analysis of membrane proteins in a close-to-native, phospholipid bilayer environment. The process of growing 2D crystals from purified membrane proteins by dialysis detergent removal is described in this chapter. A short section covers screening for and identifying 2D crystals by transmission electron microscopy, and in the last section, optimization of the purification to obtain crystals of higher quality is discussed.

Membrane protein structure from rotational diffusion

The motional averaging of powder pattern line shapes is one of the most fundamental aspects of sold-state NMR. Since membrane proteins in liquid crystalline phospholipid bilayers undergo fast rotational diffusion, all of the signals reflect the angles of the principal axes of their dipole-dipole and chemical shift tensors with respect to the axis defined by the bilayer normal. The frequency span and sign of the axially symmetric powder patterns that result from motional averaging about a common axis provide sufficient structural restraints for the calculation of the three-dimensional structure of a membrane protein in a phospholipid bilayer environment. The method is referred to as rotationally aligned (RA) solid-state NMR and demonstrated with results on full-length, unmodified membrane proteins with one, two, and seven trans-membrane helices. RA solid-state NMR is complementary to other solid-state NMR methods, in particular oriented sample (OS) solid-state NMR of stationary, aligned samples. Structural distortions of membrane proteins from the truncations of terminal residues and other sequence modifications, and the use of detergent micelles instead of phospholipid bilayers have also been demonstrated. Thus, it is highly advantageous to determine the structures of unmodified membrane proteins in liquid crystalline phospholipid bilayers under physiological conditions. RA solid-state NMR provides a general method for obtaining accurate and precise structures of membrane proteins under near-native conditions.

Advanced molecular self-assemblies facilitated by simple molecules

Advanced materials are often based on smart molecular self-assemblies that either respond to external stimuli or have hierarchical structures. Approaches to this goal usually stem from complicated molecular design and difficult organic synthesis. In this invited feature article, we demonstrate that desired molecular self-assemblies can be made conveniently by introducing simple functional molecules into amphiphilic systems. We show that upon introducing specific small molecules which serve as responders, modulators, or even building blocks, smart supramolecular architectures can be achieved which avoid complicated organic synthesis. We expect that this could be a general and economical way to produce advanced materials in the near future.

Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization

Electron crystallography is well suited for studying the structure of membrane proteins in their native lipid bilayer environment. This technique relies on electron cryomicroscopy of two-dimensional (2D) crystals, grown generally by reconstitution of purified membrane proteins into proteoliposomes under conditions favoring the formation of well-ordered lattices. Growing these crystals presents one of the major hurdles in the application of this technique. To identify conditions favoring crystallization a wide range of factors that can lead to a vast matrix of possible reagent combinations must be screened. However, in 2D crystallization these factors have traditionally been surveyed in a relatively limited fashion. To address this problem we carried out a detailed analysis of published 2D crystallization conditions for 12 β-barrel and 138 α-helical membrane proteins. From this analysis we identified the most successful conditions and applied them in the design of new sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Using these matrices we have run 19 crystallization screens for 16 different membrane proteins totaling over 1300 individual crystallization conditions. Six membrane proteins have yielded diffracting 2D crystals suitable for structure determination, indicating that these new matrices show promise to accelerate the success rate of membrane protein 2D crystallization.

Supramolecular assemblies obtained by mixing different cyclodextrins and AOT or BHDC reverse micelles

In this contribution we show the effect of the surfactant polar head and the external solvent on the incorporation of different cyclodextrins (CDs) {α-CD, β-CD, γ-CD, decenylsuccinyl-β-CD (Mod-β-CD), and hydroxypropyl-β-CD (hp-β-CD)} in different reverse micelles (RMs) {benzene/sodium 1,4-bis(2-ethylhexyl) sulfosuccinate(AOT)/water, and benzene/benzyl-n-hexadecyldimethylammonium chloride (BHDC)/water} and compare them with previous results obtained in n-heptane/AOT/water RMs. To investigate the different systems, we have used UV-vis spectrophotometry, induced circular dichroism spectroscopy (ICD), and the achiral molecular probe methyl orange (MO). The results show dramatic differences changing the external solvent and the surfactant, which are explained by considering the differences in the RMs interface composition, the water-surfactant interaction, and the CDs' location in the different media investigated. None of the CDs were incorporated into the benzene/AOT/water RMs at any [H2O]/[surfactant] ratio studied (W0) whereas it was previously shown that Mod-β-CD and hp-β-CD could be included in n-heptane/AOT/water RMs. However, all of the CDs are incorporated in benzene/BHDC/water RMs at W0 > 10 and hp-β-CD is dissolved even at W0 = 0. Different from what was found in n-heptane/AOT RMs, in BHDC RMs MO showed ICD signals with two different CDs: Mod-β-CD and hp-β-CD. The results are explained by considering the known difference in the interfacial water structure for AOT and BHDC RMs and the electron-rich region on the secondary hydroxyl (wider side of the CDs), which helps to solubilize all CDs in BHDC. This study shows that chiral cyclodextrin could be available for a guest in an organic medium such as the RMs. Therefore we have created a potentially powerful nanoreactor with two different confined regions in the same aggregate: the polar core of the RMs and the chiral hydrophobic cavity of cyclodextrin.

3D cryo-electron reconstruction of BmrA, a bacterial multidrug ABC transporter in an inward-facing conformation and in a lipidic environment

ABC (ATP-binding cassette) membrane exporters are efflux transporters of a wide diversity of molecule across the membrane at the expense of ATP. A key issue regarding their catalytic cycle is whether or not their nucleotide-binding domains (NBDs) are physically disengaged in the resting state. To settle this controversy, we obtained structural data on BmrA, a bacterial multidrug homodimeric ABC transporter, in a membrane-embedded state. BmrA in the apostate was reconstituted in lipid bilayers forming a mixture of ring-shaped structures of 24 or 39 homodimers. Three-dimensional models of the ring-shaped structures of 24 or 39 homodimers were calculated at 2.3 nm and 2.5 nm resolution from cryo-electron microscopy, respectively. In these structures, BmrA adopts an inward-facing open conformation similar to that found in mouse P-glycoprotein structure with the NBDs separated by 3 nm. Both lipidic leaflets delimiting the transmembrane domains of BmrA were clearly resolved. In planar membrane sheets, the NBDs were even more separated. BmrA in an ATP-bound conformation was determined from two-dimensional crystals grown in the presence of ATP and vanadate. A projection map calculated at 1.6 nm resolution shows an open outward-facing conformation. Overall, the data are consistent with a mechanism of drug transport involving large conformational changes of BmrA and show that a bacterial ABC exporter can adopt at least two open inward conformations in lipid membrane.

Cryo-electron microscopy of membrane proteins

Electron crystallography is used to study membrane proteins in the form of planar, two-dimensional (2D) crystals, or other crystalline arrays such as tubular crystals. This method has been used to determine the atomic resolution structures of bacteriorhodopsin, tubulin, aquaporins, and several other membrane proteins. In addition, a large number of membrane protein structures were studied at a slightly lower resolution, whereby at least secondary structure motifs could be identified.In order to conserve the structural details of delicate crystalline arrays, cryo-electron microscopy (cryo-EM) allows imaging and/or electron diffraction of membrane proteins in their close-to-native state within a lipid bilayer membrane.To achieve ultimate high-resolution structural information of 2D crystals, meticulous sample preparation for electron crystallography is of outmost importance. Beam-induced specimen drift and lack of specimen flatness can severely affect the attainable resolution of images for tilted samples. Sample preparations that sandwich the 2D crystals between symmetrical carbon films reduce the beam-induced specimen drift, and the flatness of the preparations can be optimized by the choice of the grid material and the preparation protocol.Data collection in the cryo-electron microscope using either the imaging or the electron diffraction mode has to be performed applying low-dose procedures. Spot-scanning further reduces the effects of beam-induced drift. Data collection using automated acquisition schemes, along with improved and user-friendlier data processing software, is increasingly being used and is likely to bring the technique to a wider user base.

Real-time monitoring of membrane-protein reconstitution by isothermal titration calorimetry

Phase diagrams offer a wealth of thermodynamic information on aqueous mixtures of bilayer-forming lipids and micelle-forming detergents, providing a straightforward means of monitoring and adjusting the supramolecular state of such systems. However, equilibrium phase diagrams are of very limited use for the reconstitution of membrane proteins because of the occurrence of irreversible, unproductive processes such as aggregation and precipitation that compete with productive reconstitution. Here, we exemplify this by dissecting the effects of the K⁺ channel KcsA on the process of bilayer self-assembly in a mixture of Escherichia coli polar lipid extract and the nonionic detergent octyl-β-d-glucopyranoside. Even at starting concentrations in the low micromolar range, KcsA has a tremendous impact on the supramolecular organization of the system, shifting the critical lipid/detergent ratios at the onset and completion of vesicle formation by more than 2-fold. Thus, equilibrium phase diagrams obtained for protein-free lipid/detergent mixtures would be misleading when used to guide the reconstitution process. To address this issue, we demonstrate that, even under such nonequilibrium conditions, high-sensitivity isothermal titration calorimetry can be exploited to monitor the progress of membrane-protein reconstitution in real time, in a noninvasive manner, and at high resolution to yield functional proteoliposomes with a narrow size distribution for further downstream applications.

Structural and functional analysis of the native peripherin-ROM1 complex isolated from photoreceptor cells

Peripherin and its homologue ROM1 are retina-specific members of the tetraspanin family of integral membrane proteins required for morphogenesis and maintenance of photoreceptor outer segments, regions that collect light stimuli. Over 100 pathogenic mutations in peripherin cause inherited rod- and cone-related dystrophies in humans. Peripherin and ROM1 interact in vivo and are predicted to form a core heterotetrameric complex capable of creating higher order oligomers. However, structural analysis of tetraspanin proteins has been hampered by their resistance to crystallization. Here we present a simplified methodology for high yield purification of peripherin-ROM1 from bovine retinas that permitted its biochemical and biophysical characterization. Using size exclusion chromatography and blue native gel electrophoresis, we confirmed that the core native peripherin-ROM1 complex exists as a tetramer. Peripherin, but not ROM1, is glycosylated and we examined the glycosylation site and glycan composition of ROM1 by liquid chromatographic tandem mass spectrometry. Mass spectrometry was used to analyze the native complex in detergent micelles, demonstrating its tetrameric state. Our electron microscopy-generated structure solved to 18 Å displayed the tetramer as an elongated structure with an apparent 2-fold symmetry. Finally, we demonstrated that peripherin-ROM1 tetramers induce membrane curvature when reconstituted in lipid vesicles. These results provide critical insights into this key retinal component with a poorly defined function.

Lipid bilayer preparations of membrane proteins for oriented and magic-angle spinning solid-state NMR samples

Solid-state NMR spectroscopy has been used successfully for characterizing the structure and dynamics of membrane proteins as well as their interactions with other proteins in lipid bilayers. Such an environment is often necessary for achieving native-like structures. Sample preparation is the key to this success. Here we present a detailed description of a robust protocol that results in high-quality membrane protein samples for both magic-angle spinning and oriented-sample solid-state NMR. The procedure is demonstrated using two proteins: CrgA (two transmembrane helices) and Rv1861 (three transmembrane helices), both from Mycobacterium tuberculosis. The success of this procedure relies on two points. First, for samples for both types of NMR experiment, the reconstitution of the protein from a detergent environment to an environment in which it is incorporated into liposomes results in 'complete' removal of detergent. Second, for the oriented samples, proper dehydration followed by rehydration of the proteoliposomes is essential. By using this protocol, proteoliposome samples for magic-angle spinning NMR and uniformly aligned samples (orientational mosaicity of <1°) for oriented-sample NMR can be obtained within 10 d.

Reconstitution of a Kv channel into lipid membranes for structural and functional studies

To study the lipid-protein interaction in a reductionistic fashion, it is necessary to incorporate the membrane proteins into membranes of well-defined lipid composition. We are studying the lipid-dependent gating effects in a prototype voltage-gated potassium (Kv) channel, and have worked out detailed procedures to reconstitute the channels into different membrane systems. Our reconstitution procedures take consideration of both detergent-induced fusion of vesicles and the fusion of protein/detergent micelles with the lipid/detergent mixed micelles as well as the importance of reaching an equilibrium distribution of lipids among the protein/detergent/lipid and the detergent/lipid mixed micelles. Our data suggested that the insertion of the channels in the lipid vesicles is relatively random in orientations, and the reconstitution efficiency is so high that no detectable protein aggregates were seen in fractionation experiments. We have utilized the reconstituted channels to determine the conformational states of the channels in different lipids, record electrical activities of a small number of channels incorporated in planar lipid bilayers, screen for conformation-specific ligands from a phage-displayed peptide library, and support the growth of 2D crystals of the channels in membranes. The reconstitution procedures described here may be adapted for studying other membrane proteins in lipid bilayers, especially for the investigation of the lipid effects on the eukaryotic voltage-gated ion channels.

Overview of electron crystallography of membrane proteins: crystallization and screening strategies using negative stain electron microscopy

Electron cryomicroscopy, or cryoEM, is an emerging technique for studying the three-dimensional structures of proteins and large macromolecular machines. Electron crystallography is a branch of cryoEM in which structures of proteins can be studied at resolutions that rival those achieved by X-ray crystallography. Electron crystallography employs two-dimensional crystals of a membrane protein embedded within a lipid bilayer. The key to a successful electron crystallographic experiment is the crystallization, or reconstitution, of the protein of interest. This unit describes ways in which protein can be expressed, purified, and reconstituted into well-ordered two-dimensional crystals. A protocol is also provided for negative stain electron microscopy as a tool for screening crystallization trials. When large and well-ordered crystals are obtained, the structures of both protein and its surrounding membrane can be determined to atomic resolution.

Two-dimensional crystallization by dialysis for structural studies of membrane proteins by the cryo-EM method electron crystallography

Two-dimensional (2D) crystals of integral membrane proteins, comprising ordered protein reconstituted into a synthetic lipid bilayer, can be induced to form from detergent solubilized and purified membrane protein sources via the addition of exogenous lipid and the subsequent removal of the solubilizing detergent. This is most commonly accomplished by dialysis of a small volume of ternary protein-detergent-lipid mixture against a large volume of buffer, and can be carried out using common, easily available materials. Following successful crystallization, electron crystallographic data obtained by electron cryo-microscopy (cryo-EM) of vitrified 2D crystals can be used to determine the structure of the lipid bilayer-embedded integral membrane protein.

Detergent-mediated incorporation of transmembrane proteins in giant unilamellar vesicles with controlled physiological contents

Giant unilamellar vesicles (GUVs) are convenient biomimetic systems of the same size as cells that are increasingly used to quantitatively address biophysical and biochemical processes related to cell functions. However, current approaches to incorporate transmembrane proteins in the membrane of GUVs are limited by the amphiphilic nature or proteins. Here, we report a method to incorporate transmembrane proteins in GUVs, based on concepts developed for detergent-mediated reconstitution in large unilamellar vesicles. Reconstitution is performed either by direct incorporation from proteins purified in detergent micelles or by fusion of purified native vesicles or proteoliposomes in preformed GUVs. Lipid compositions of the membrane and the ionic, protein, or DNA compositions in the internal and external volumes of GUVs can be controlled. Using confocal microscopy and functional assays, we show that proteins are unidirectionally incorporated in the GUVs and keep their functionality. We have successfully tested our method with three types of transmembrane proteins. GUVs containing bacteriorhodopsin, a photoactivable proton pump, can generate large transmembrane pH and potential gradients that are light-switchable and stable for hours. GUVs with FhuA, a bacterial porin, were used to follow the DNA injection by T5 phage upon binding to its transmembrane receptor. GUVs incorporating BmrC/BmrD, a bacterial heterodimeric ATP-binding cassette efflux transporter, were used to demonstrate the protein-dependent translocation of drugs and their interactions with encapsulated DNA. Our method should thus apply to a wide variety of membrane or peripheral proteins for producing more complex biomimetic GUVs.

Diffusion and interaction dynamics of individual membrane protein complexes confined in micropatterned polymer-supported membranes

Micropatterned polymer-supported membranes (PSM) are established as a tool for confining the diffusion of transmembrane proteins for single molecule studies. To this end, a photochemical surface modification with hydrophobic tethers on a PEG polymer brush is implemented for capturing of lipid vesicles and subsequent fusion. Formation of contiguous membranes within micropatterns is confirmed by scanning force microscopy, fluorescence recovery after photobleaching (FRAP), and super-resolved single-molecule tracking and localization microscopy. Free diffusion of transmembrane proteins reconstituted into micropatterned PSM is demonstrated by FRAP and by single-molecule tracking. By exploiting the confinement of diffusion within micropatterned PSM, the diffusion and interaction dynamics of individual transmembrane receptors are quantitatively resolved.

High-throughput methods for electron crystallography

Membrane proteins play a tremendously important role in cell physiology and serve as a target for an increasing number of drugs. Structural information is key to understanding their function and for developing new strategies for combating disease. However, the complex physical chemistry associated with membrane proteins has made them more difficult to study than their soluble cousins. Electron crystallography has historically been a successful method for solving membrane protein structures and has the advantage of providing a native lipid environment for these proteins. Specifically, when membrane proteins form two-dimensional arrays within a lipid bilayer, electron microscopy can be used to collect images and diffraction and the corresponding data can be combined to produce a three-dimensional reconstruction, which under favorable conditions can extend to atomic resolution. Like X-ray crystallography, the quality of the structures are very much dependent on the order and size of the crystals. However, unlike X-ray crystallography, high-throughput methods for screening crystallization trials for electron crystallography are not in general use. In this chapter, we describe two alternative methods for high-throughput screening of membrane protein crystallization within the lipid bilayer. The first method relies on the conventional use of dialysis for removing detergent and thus reconstituting the bilayer; an array of dialysis wells in the standard 96-well format allows the use of a liquid-handling robot and greatly increases throughput. The second method relies on titration of cyclodextrin as a chelating agent for detergent; a specialized pipetting robot has been designed not only to add cyclodextrin in a systematic way, but to use light scattering to monitor the reconstitution process. In addition, the use of liquid-handling robots for making negatively stained grids and methods for automatically imaging samples in the electron microscope are described.

Membrane protein structure determination by electron crystallography

During the past year, electron crystallography of membrane proteins has provided structural insights into the mechanism of several different transporters and into their interactions with lipid molecules within the bilayer. From a technical perspective there have been important advances in high-throughput screening of crystallization trials and in automated imaging of membrane crystals with the electron microscope. There have also been key developments in software, and in molecular replacement and phase extension methods designed to facilitate the process of structure determination.

Electron crystallography--the waking beauty of structural biology

Since its debut in the mid 1970s, electron crystallography has been a valuable alternative in the structure determination of biological macromolecules. Its reliance on single-layered or double-layered two-dimensionally ordered arrays and the ability to obtain structural information from small and disordered crystals make this approach particularly useful for the study of membrane proteins in a lipid bilayer environment. Despite its unique advantages, technological hurdles have kept electron crystallography from reaching its full potential. Addressing the issues, recent initiatives developed high-throughput pipelines for crystallization and screening. Adding progress in automating data collection, image analysis and phase extension methods, electron crystallography is poised to raise its profile and may lead the way in exploring the structural biology of macromolecular complexes.

Advances in structural and functional analysis of membrane proteins by electron crystallography

Electron crystallography is a powerful technique for the study of membrane protein structure and function in the lipid environment. When well-ordered two-dimensional crystals are obtained the structure of both protein and lipid can be determined and lipid-protein interactions analyzed. Protons and ionic charges can be visualized by electron crystallography and the protein of interest can be captured for structural analysis in a variety of physiologically distinct states. This review highlights the strengths of electron crystallography and the momentum that is building up in automation and the development of high throughput tools and methods for structural and functional analysis of membrane proteins by electron crystallography.

Looking back at a quarter-century of research at the Maurice E. Müller Institute for Structural Biology

The Maurice E. Müller Institute, embedded in the infrastructure of the Biozentrum, University of Basel, was founded in 1985 and financed by the Maurice E. Müller Foundation of Switzerland. For 26 years its two founders, Ueli Aebi and Andreas Engel, pursued the vision of integrated structural biology. This paper reviews selected publications issuing from the Maurice E. Müller Institute for Structural Biology and marks the end of this era.

Versatility of cyclodextrins in self-assembly systems of amphiphiles

Recently, cyclodextrins (CDs) were found to play important yet complicated (or even apparently opposite sometimes) roles in self-assembly systems of amphiphiles or surfactants. Herein, we try to review and clarify the versatility of CDs in surfactant assembly systems by 1) classifying the roles played by CDs into two groups (modulator and building unit) and four subgroups (destructive and constructive modulators, amphiphilic and unamphiphilic building units), 2) comparing these subgroups, and 3) analyzing mechanisms. As a modulator, although CDs by themselves do not participate into the final surfactant aggregates, they can greatly affect the aggregates in two ways. In most cases CDs will destroy the aggregates by depleting surfactant molecules from the aggregates (destructive), or in certain cases CDs can promote the aggregates to grow by selectively removing the less-aggregatable surfactant molecules from the aggregates (constructive). As an amphiphilic building unit, CDs can be chemically (by chemical bonds) or physically (by host-guest interaction) attached to a hydrophobic moiety, and the resultant compounds act as classic amphiphiles. As an unamphiphilic building unit, CD/surfactant complexes or even CDs on their own can assemble into aggregates in an unconventional, unamphiphilic manner driven by CD-CD H-bonds. Moreover, special emphasis is put on two recently appeared aspects: the constructive modulator and unamphiphilic building unit.

Local and global dynamics of the G protein-coupled receptor CXCR1

The local and global dynamics of the chemokine receptor CXCR1 are characterized using a combination of solution NMR and solid-state NMR experiments. In isotropic bicelles (q = 0.1), only 13% of the expected number of backbone amide resonances is observed in (1)H/(15)N HSQC solution NMR spectra of uniformly (15)N-labeled samples; extensive deuteration and the use of TROSY made little difference in the 800 MHz spectra. The limited number of observed amide signals is ascribed to mobile backbone sites and assigned to specific residues in the protein; 19 of the signals are from residues at the N-terminus and 25 from residues at the C-terminus. The solution NMR spectra display no evidence of local backbone motions from residues in the transmembrane helices or interhelical loops of CXCR1. This finding is reinforced by comparisons of solid-state NMR spectra of both magnetically aligned and unoriented bilayers containing either full-length or doubly N- and C-terminal truncated CXCR1 constructs. CXCR1 undergoes rapid rotational diffusion about the normal of liquid crystalline phospholipid bilayers; reductions in the frequency span and a change to axial symmetry are observed for both carbonyl carbon and amide nitrogen chemical shift powder patterns of unoriented samples containing (13)C- and (15)N-labeled CXCR1. In contrast, when the phospholipids are in the gel phase, CXCR1 does not undergo rapid global reorientation on the 10(4) Hz time scale defined by the carbonyl carbon and amide nitrogen chemical shift powder patterns.

Automatic TEM image analysis of membranes for 2D crystal detection

TEM image processing tools are devised for the assessment of 2D-crystallization experiments. The algorithms search for the presence and assess the quality of crystalline membranes. The retained scenario emulates the decisions of a microscopist in selecting targets and assessing the sample. Crystallinity is automatically assessed through the diffraction patterns of high magnification images acquired on pertinent regions selected at lower magnifications. Further algorithms have been developed for membrane characterization. Tests on images of different samples, acquired on different microscopes led to good results.