Electron crystallography as a technique to study the structure on membrane proteins in a lipidic environment

Structural Flexibility of Proteins Dramatically Alters Membrane Stability─A Novel Aspect of Lipid-Protein Interaction

Protein isoforms are structural variants with changes in the overall flexibility predominantly at the tertiary level. For membrane associated proteins, such structural flexibility or rigidity affects membrane stability by playing modulatory roles in lipid-protein interaction. Herein, we investigate the protein chain flexibility mediated changes in the mechanistic behavior of phospholipid model membranes in the presence of two well-known isoforms, erythroid (ER) and nonerythroid (NER) spectrin. We show dramatic alterations of membrane elasticity and stability induced by spectrin in the Langmuir monolayers of phosphatidylocholine (PC) and phosphatidylethanolamine (PE) by a combination of isobaric relaxation, surface pressure-area isotherm, X-ray scattering, and microscopy measurements. The NER spectrin drives all monolayers to possess an approximately equal stability, and that required 25-fold increase and 5-fold decrease of stability in PC and PE monolayers, respectively. The untilting transition of the PC membrane in the presence of NER spectrin observed in X-ray measurements can explain better membrane packing and stability.

Structures of Multisubunit Membrane Complexes With the CRYO ARM 200

Progress in structural membrane biology has been significantly accelerated by the ongoing ‘Resolution Revolution’ in cryo-electron microscopy (cryo-EM). In particular, structure determination by single-particle analysis has evolved into the most powerful method for atomic model building of multisubunit membrane protein complexes. This has created an ever-increasing demand in cryo-EM machine time, which to satisfy is in need of new and affordable cryo-electron microscopes. Here, we review our experience in using the JEOL CRYO ARM 200 prototype for the structure determination by single-particle analysis of three different multisubunit membrane complexes: the Thermus thermophilus V-type ATPase V_O complex, the Thermosynechococcus elongatus photosystem I monomer and the flagellar motor lipopolysaccharide peptidoglycan ring (LP ring) from Salmonella enterica.

Native-like environments afford novel mechanistic insights into membrane proteins

Advances in cryogenic electron microscopy (cryo-EM) enabled routine near-atomic structure determination of membrane proteins, while nanodisc technology has provided a way to provide membrane proteins with a native or native-like lipid environment. After giving a brief history of membrane mimetics, we present example structures of membrane proteins in nanodiscs that revealed information not provided by structures obtained in detergent. We describe how the lipid environment surrounding the membrane protein can be custom designed during nanodisc assembly and how it can be modified after assembly to test functional hypotheses. Because nanodiscs most closely replicate the physiologic environment of membrane proteins and often afford novel mechanistic insights, we propose that nanodiscs ought to become the standard for structural studies on membrane proteins.

Insights into lipid-protein interactions from computer simulations

Lipid-protein interactions play an important direct role in the function of many membrane proteins. We argue they are key players in membrane structure, modulate membrane proteins in more subtle ways than direct binding, and are important for understanding the mechanism of classes of hydrophobic drugs. By directly comparing membrane proteins from different families in the same, complex lipid mixture, we found a unique lipid environment for every protein. Extending this work, we identified both differences and similarities in the lipid environment of GPCRs, dependent on which family they belong to and in some cases their conformational state, with particular emphasis on the distribution of cholesterol. More recently, we have been studying modes of coupling between protein conformation and local membrane properties using model proteins. In more applied approaches, we have used similar methods to investigate specific hypotheses on interactions of lipid and lipid-like molecules with ion channels. We conclude this perspective with some considerations for future work, including a new more sophisticated coarse-grained force field (Martini 3), an interactive visual exploration framework, and opportunities to improve sampling.

Lipid–Protein Interactions in Plasma Membrane Organization and Function

Lipid–protein interactions in cells are involved in various biological processes, including metabolism, trafficking, signaling, host–pathogen interactions, and transmembrane transport. At the plasma membrane, lipid–protein interactions play major roles in membrane organization and function. Several membrane proteins have motifs for specific lipid binding, which modulate protein conformation and consequent function. In addition to such specific lipid–protein interactions, protein function can be regulated by the dynamic, collective behavior of lipids in membranes. Emerging analytical, biochemical, and computational technologies allow us to study the influence of specific lipid–protein interactions, as well as the collective behavior of membranes on protein function. In this article, we review the recent literature on lipid–protein interactions with a specific focus on the current state-of-the-art technologies that enable novel insights into these interactions.

Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Building protein networks in synthetic systems from the bottom-up

The recent development of synthetic biology has expanded the capability to design and construct protein networks outside of living cells from the bottom-up. The new capability has enabled us to assemble protein networks for the basic study of cellular pathways, expression of proteins outside cells, and building tissue materials. Furthermore, the integration of natural and synthetic protein networks has enabled new functions of synthetic or artificial cells. Here, we review the underlying technologies for assembling protein networks in liposomes, water-in-oil droplets, and biomaterials from the bottom-up. We cover the recent applications of protein networks in biological transduction pathways, energy self-supplying systems, cellular environmental sensors, and cell-free protein scaffolds. We also review new technologies for assembling protein networks, including multiprotein purification methods, high-throughput assay screen platforms, and controllable fusion of liposomes. Finally, we present existing challenges towards building protein networks that rival the complexity and dynamic response akin to natural systems. This review addresses the gap in our understanding of synthetic and natural protein networks. It presents a vision towards developing smart and resilient protein networks for various biomedical applications.

Emerging Diversity in Lipid-Protein Interactions

Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable membrane environment for proteins to being embedded in to detailed roles in complicated and well-regulated protein functions. Experimental and computational advances are converging in a rapidly expanding research area of lipid–protein interactions. Experimentally, the database of high-resolution membrane protein structures is growing, as are capabilities to identify the complex lipid composition of different membranes, to probe the challenging time and length scales of lipid–protein interactions, and to link lipid–protein interactions to protein function in a variety of proteins. Computationally, more accurate membrane models and more powerful computers now enable a detailed look at lipid–protein interactions and increasing overlap with experimental observations for validation and joint interpretation of simulation and experiment. Here we review papers that use computational approaches to study detailed lipid–protein interactions, together with brief experimental and physiological contexts, aiming at comprehensive coverage of simulation papers in the last five years. Overall, a complex picture of lipid–protein interactions emerges, through a range of mechanisms including modulation of the physical properties of the lipid environment, detailed chemical interactions between lipids and proteins, and key functional roles of very specific lipids binding to well-defined binding sites on proteins. Computationally, despite important limitations, molecular dynamics simulations with current computer power and theoretical models are now in an excellent position to answer detailed questions about lipid–protein interactions.

Single-Vesicle Assays Using Liposomes and Cell-Derived Vesicles: From Modeling Complex Membrane Processes to Synthetic Biology and Biomedical Applications

The plasma membrane is of central importance for defining the closed volume of cells in contradistinction to the extracellular environment. The plasma membrane not only serves as a boundary, but it also mediates the exchange of physical and chemical information between the cell and its environment in order to maintain intra- and intercellular functions. Artificial lipid- and cell-derived membrane vesicles have been used as closed-volume containers, representing the simplest cell model systems to study transmembrane processes and intracellular biochemistry. Classical examples are studies of membrane translocation processes in plasma membrane vesicles and proteoliposomes mediated by transport proteins and ion channels. Liposomes and native membrane vesicles are widely used as model membranes for investigating the binding and bilayer insertion of proteins, the structure and function of membrane proteins, the intramembrane composition and distribution of lipids and proteins, and the intermembrane interactions during exo- and endocytosis. In addition, natural cell-released microvesicles have gained importance for early detection of diseases and for their use as nanoreactors and minimal protocells. Yet, in most studies, ensembles of vesicles have been employed. More recently, new micro- and nanotechnological tools as well as novel developments in both optical and electron microscopy have allowed the isolation and investigation of individual (sub)micrometer-sized vesicles. Such single-vesicle experiments have revealed large heterogeneities in the structure and function of membrane components of single vesicles, which were hidden in ensemble studies. These results have opened enormous possibilities for bioanalysis and biotechnological applications involving unprecedented miniaturization at the nanometer and attoliter range. This review will cover important developments toward single-vesicle analysis and the central discoveries made in this exciting field of research.

Lipid-Protein Interactions Are Unique Fingerprints for Membrane Proteins

Cell membranes contain hundreds of different proteins and lipids in an asymmetric arrangement. Our current understanding of the detailed organization of cell membranes remains rather elusive, because of the challenge to study fluctuating nanoscale assemblies of lipids and proteins with the required spatiotemporal resolution. Here, we use molecular dynamics simulations to characterize the lipid environment of 10 different membrane proteins. To provide a realistic lipid environment, the proteins are embedded in a model plasma membrane, where more than 60 lipid species are represented, asymmetrically distributed between the leaflets. The simulations detail how each protein modulates its local lipid environment in a unique way, through enrichment or depletion of specific lipid components, resulting in thickness and curvature gradients. Our results provide a molecular glimpse of the complexity of lipid-protein interactions, with potentially far-reaching implications for our understanding of the overall organization of real cell membranes.

Electron cryomicroscopy as a powerful tool in biomedical research

A human cell is a precisely regulated system that relies on the complex interaction of molecules. Structural insights into the cellular machinery at the atomic level allow us to understand the underlying regulatory mechanism and provide us with a roadmap for the development of novel drugs to fight diseases. Facilitated by recent technological breakthroughs, the Nobel prize-winning technique electron cryomicroscopy (cryo-EM) has become a versatile and extremely powerful tool to solve routinely near-atomic resolution three-dimensional protein structures. Consequently, it has become the focus of attention for structure-based drug design. In this review, we describe the basics of cryo-EM and highlight its growing role in biomedical research. Furthermore, we discuss latest developments as well as future perspectives.

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal

Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm3, i.e. no more than 6 × 105 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures.

Applications of NMR to membrane proteins

Membrane proteins present a challenge for structural biology. In this article, we review some of the recent developments that advance the application of NMR to membrane proteins, with emphasis on structural studies in detergent-free, lipid bilayer samples that resemble the native environment. NMR spectroscopy is not only ideally suited for structure determination of membrane proteins in hydrated lipid bilayer membranes, but also highly complementary to the other principal techniques based on X-ray and electron diffraction. Recent advances in NMR instrumentation, spectroscopic methods, computational methods, and sample preparations are driving exciting new efforts in membrane protein structural biology.

Removal of Vesicle Structures From Transmission Electron Microscope Images

In this paper, we address the problem of imaging membrane proteins for single-particle cryo-electron microscopy reconstruction of the isolated protein structure. More precisely, we propose a method for learning and removing the interfering vesicle signals from the micrograph, prior to reconstruction. In our approach, we estimate the subspace of the vesicle structures and project the micrographs onto the orthogonal complement of this subspace. We construct a 2D statistical model of the vesicle structure, based on higher order singular value decomposition (HOSVD), by considering the structural symmetries of the vesicles in the polar coordinate plane. We then propose to lift the HOSVD model to a novel hierarchical model by summarizing the multidimensional HOSVD coefficients by their principal components. Along with the model, a solid vesicle normalization scheme and model selection criterion are proposed to make a compact and general model. The results show that the vesicle structures are accurately separated from the background by the HOSVD model that is also able to adapt to the asymmetries of the vesicles. This is a promising result and suggests even wider applicability of the proposed approach in learning and removal of statistical structures.

Two-dimensional crystallization of monomeric bovine cytochrome c oxidase with bound cytochrome c in reconstituted lipid membranes

Mitochondrial cytochrome c oxidase utilizes electrons provided by cytochrome c for the active vectorial transport of protons across the inner mitochondrial membrane through the reduction of molecular oxygen to water. Direct structural evidence on the transient cytochrome c oxidase–cytochrome c complex thus far, however, remains elusive and its physiological relevant oligomeric form is unclear. Here, we report on the 2D crystallization of monomeric bovine cytochrome c oxidase with tightly bound cytochrome c at a molar ratio of 1:1 in reconstituted lipid membranes at the basic pH of 8.5 and low ionic strength.

Single-particle electron microscopy in the study of membrane protein structure

Single-particle electron microscopy (EM) provides the great advantage that protein structure can be studied without the need to grow crystals. However, due to technical limitations, this approach played only a minor role in the study of membrane protein structure. This situation has recently changed dramatically with the introduction of direct electron detection device cameras, which allow images of unprecedented quality to be recorded, also making software algorithms, such as three-dimensional classification and structure refinement, much more powerful. The enhanced potential of single-particle EM was impressively demonstrated by delivering the first long-sought atomic model of a member of the biomedically important transient receptor potential channel family. Structures of several more membrane proteins followed in short order. This review recounts the history of single-particle EM in the study of membrane proteins, describes the technical advances that now allow this approach to generate atomic models of membrane proteins and provides a brief overview of some of the membrane protein structures that have been studied by single-particle EM to date.

Membrane protein structures without crystals, by single particle electron cryomicroscopy

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Electron microscopy of membrane proteins as single particles.

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Membrane protein structures without crystals.

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Direct electron detectors have high signal to noise.

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Medium to high-resolution structures of molecules between 0.13 and 2 MDa.

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Sub-tomogram averaging to study membrane proteins in situ.

It is an exciting period in membrane protein structural biology with a number of medically important protein structures determined at a rapid pace. However, two major hurdles still remain in the structural biology of membrane proteins. One is the inability to obtain large amounts of protein for crystallization and the other is the failure to get well-diffracting crystals. With single particle electron cryomicroscopy, both these problems can be overcome and high-resolution structures of membrane proteins and other labile protein complexes can be obtained with very little protein and without the need for crystals. In this review, I highlight recent advances in electron microscopy, detectors and software, which have allowed determination of medium to high-resolution structures of membrane proteins and complexes that have been difficult to study by other structural biological techniques.

Two-dimensional protein crystals for solar energy conversion

Two-dimensional photosynthetic protein crystals provide a high density of aligned reaction centers. We reconstitute the robust light harvesting protein Photosystem I into a 2D crystal with lipids and integrate the crystals into a photo-electrochemical device. A 4-fold photocurrent enhancement is measured by incorporating conjugated oligoelectrolytes to form a supporting conductive bilayer in the device which produces a high photocurrent of ∼600 μA per mg PSI deposited.

Modulation of glycan recognition by clustered saccharide patches

All cells in nature are covered with a dense and complex array of glycan chains. Specific recognition and binding of glycans is a critical aspect of cellular interactions, both within and between species. Glycan-protein interactions tend to be of low affinity but high specificity, typically utilizing multivalency to generate the affinity required for biologically relevant binding. This review focuses on a higher level of glycan organization, the formation of clustered saccharide patches (CSPs), which can constitute unique ligands for highly specific interactions. Due to technical challenges, this aspect of glycan recognition remains poorly understood. We present a wealth of evidence for CSPs-mediated interactions, and discuss recent advances in experimental tools that are beginning to provide new insights into the composition and organization of CSPs. The examples presented here are likely the tip of the iceberg, and much further work is needed to elucidate fully this higher level of glycan organization.

Self-assembled lipid and membrane protein polyhedral nanoparticles

We demonstrate that membrane proteins and phospholipids can self-assemble into polyhedral arrangements suitable for structural analysis. Using the Escherichia coli mechanosensitive channel of small conductance (MscS) as a model protein, we prepared membrane protein polyhedral nanoparticles (MPPNs) with uniform radii of ∼ 20 nm. Electron cryotomographic analysis established that these MPPNs contain 24 MscS heptamers related by octahedral symmetry. Subsequent single-particle electron cryomicroscopy yielded a reconstruction at ∼ 1-nm resolution, revealing a conformation closely resembling the nonconducting state. The generality of this approach has been addressed by the successful preparation of MPPNs for two unrelated proteins, the mechanosensitive channel of large conductance and the connexon Cx26, using a recently devised microfluidics-based free interface diffusion system. MPPNs provide not only a starting point for the structural analysis of membrane proteins in a phospholipid environment, but their closed surfaces should facilitate studies in the presence of physiological transmembrane gradients, in addition to potential applications as drug delivery carriers or as templates for inorganic nanoparticle formation.

Two-dimensional crystallization of intact F-ATP synthase isolated from bovine heart mitochondria

Mitochondrial F-ATP synthase produces the majority of ATP for cellular functions requiring free energy. The structural basis for proton motive force-driven rotational catalysis of ATP formation in the holoenzyme remains to be determined. Here, the purification and two-dimensional crystallization of bovine heart mitochondrial F-ATP synthase are reported. Two-dimensional crystals of up to 1 µm in size were grown by dialysis-mediated detergent removal from a mixture of decylmaltoside-solubilized 1,2-dimyristoyl-sn-glycero-3-phosphocholine and F-ATP synthase against a detergent-free buffer. A projection map calculated from an electron micrograph of a negatively stained two-dimensional crystal revealed unit-cell parameters of a = 185.0, b = 170.3 Å, γ = 92.5°.

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.

A pipeline for comprehensive and automated processing of electron diffraction data in IPLT

Electron crystallography of two-dimensional crystals allows the structural study of membrane proteins in their native environment, the lipid bilayer. Determining the structure of a membrane protein at near-atomic resolution by electron crystallography remains, however, a very labor-intense and time-consuming task. To simplify and accelerate the data processing aspect of electron crystallography, we implemented a pipeline for the processing of electron diffraction data using the Image Processing Library and Toolbox (IPLT), which provides a modular, flexible, integrated, and extendable cross-platform, open-source framework for image processing. The diffraction data processing pipeline is organized as several independent modules implemented in Python. The modules can be accessed either from a graphical user interface or through a command line interface, thus meeting the needs of both novice and expert users. The low-level image processing algorithms are implemented in C++ to achieve optimal processing performance, and their interface is exported to Python using a wrapper. For enhanced performance, the Python processing modules are complemented with a central data managing facility that provides a caching infrastructure. The validity of our data processing algorithms was verified by processing a set of aquaporin-0 diffraction patterns with the IPLT pipeline and comparing the resulting merged data set with that obtained by processing the same diffraction patterns with the classical set of MRC programs.

High-density reconstitution of functional water channels into vesicular and planar block copolymer membranes

The exquisite selectivity and unique transport properties of membrane proteins can be harnessed for a variety of engineering and biomedical applications if suitable membranes can be produced. Amphiphilic block copolymers (BCPs), developed as stable lipid analogs, form membranes that functionally incorporate membrane proteins and are ideal for such applications. While high protein density and planar membrane morphology are most desirable, BCP–membrane protein aggregates have so far been limited to low protein densities in either vesicular or bilayer morphologies. Here, we used dialysis to reproducibly form planar and vesicular BCP membranes with a high density of reconstituted aquaporin-0 (AQP0) water channels. We show that AQP0 retains its biological activity when incorporated at high density in BCP membranes, and that the morphology of the BCP–protein aggregates can be controlled by adjusting the amount of incorporated AQP0. We also show that BCPs can be used to form two-dimensional crystals of AQP0.

Structure of RPE65 isomerase in a lipidic matrix reveals roles for phospholipids and iron in catalysis

RPE65 is a key metalloenzyme responsible for maintaining visual function in vertebrates. Despite extensive research on this membrane-bound retinoid isomerase, fundamental questions regarding its enzymology remain unanswered. Here, we report the crystal structure of RPE65 in a membrane-like environment. These crystals, obtained from enzymatically active, nondelipidated protein, displayed an unusual packing arrangement wherein RPE65 is embedded in a lipid-detergent sheet. Structural differences between delipidated and nondelipidated RPE65 uncovered key residues involved in substrate uptake and processing. Complementary iron K-edge X-ray absorption spectroscopy data established that RPE65 as isolated contained a divalent iron center and demonstrated the presence of a tightly bound ligand consistent with a coordinated carboxylate group. These results support the hypothesis that the Lewis acidity of iron could be used to promote ester dissociation and generation of a carbocation intermediate required for retinoid isomerization.

Molecular driving forces defining lipid positions around aquaporin-0

Lipid-protein interactions play pivotal roles in biological membranes. Electron crystallographic studies of the lens-specific water channel aquaporin-0 (AQP0) revealed atomistic views of such interactions, by providing high-resolution structures of annular lipids surrounding AQP0. It remained unclear, however, whether these lipid structures are representative of the positions of unconstrained lipids surrounding an individual protein, and what molecular determinants define the lipid positions around AQP0. We addressed these questions by using molecular dynamics simulations and crystallographic refinement, and calculated time-averaged densities of dimyristoyl-phosphatidylcholine lipids around AQP0. Our simulations demonstrate that, although the experimentally determined crystallographic lipid positions are constrained by the crystal packing, they appropriately describe the behavior of unconstrained lipids around an individual AQP0 tetramer, and thus likely represent physiologically relevant lipid positions.While the acyl chains were well localized, the lipid head groups were not. Furthermore, in silico mutations showed that electrostatic interactions do not play a major role attracting these phospholipids towards AQP0. Instead, the mobility of the protein crucially modulates the lipid localization and explains the difference in lipid density between extracellular and cytoplasmic leaflets. Moreover, our simulations support a general mechanism in which membrane proteins laterally diffuse accompanied by several layers of localized lipids, with the positions of the annular lipids being influenced the most by the protein surface. We conclude that the acyl chains rather than the head groups define the positions of dimyristoyl-phosphatidylcholine lipids around AQP0. Lipid localization is largely determined by the mobility of the protein surface, whereas hydrogen bonds play an important but secondary role.

Cell membranes: the lipid perspective

Although cell membranes are packed with proteins mingling with lipids, remarkably little is known about how proteins interact with lipids to carry out their function. Novel analytical tools are revealing the astounding diversity of lipids in membranes. The issue is now to understand the cellular functions of this complexity. In this Perspective, we focus on the interface of integral transmembrane proteins and membrane lipids in eukaryotic cells. Clarifying how proteins and lipids interact with each other will be important for unraveling membrane protein structure and function. Progress toward this goal will be promoted by increasing overlap between different fields that have so far operated without much crosstalk.

Small-Angle X-ray Scattering Investigations of Biomolecular Confinement, Loading, and Release from Liquid-Crystalline Nanochannel Assemblies

This Perspective explores the recent progress made by means of small-angle scattering methods in structural studies of phase transitions in amphiphilic liquid-crystalline systems with nanochannel architectures and outlines some future directions in the area of hierarchically organized and stimuli-responsive nanochanneled assemblies involving biomolecules. Time-resolved small-angle X-ray scattering investigations using synchrotron radiation enable monitoring of the structural dynamics, the modulation of the nanochannel hydration, as well as the key changes in the soft matter liquid-crystalline organization upon stimuli-induced phase transitions. They permit establishing of the inner nanostructure transformation kinetics and determination of the precise sizes of the hydrophobic membraneous compartments and the aqueous channel diameters in self-assembled network architectures. Time-resolved structural studies accelerate novel biomedical, pharmaceutical, and nanotechnology applications of nanochannel soft materials by providing better control of DNA, peptide and protein nanoconfinement, and release from diverse stimuli-responsive nanocarrier systems.

Biophysics of α-synuclein membrane interactions

Membrane proteins participate in nearly all cellular processes; however, because of experimental limitations, their characterization lags far behind that of soluble proteins. Peripheral membrane proteins are particularly challenging to study because of their inherent propensity to adopt multiple and/or transient conformations in solution and upon membrane association. In this review, we summarize useful biophysical techniques for the study of peripheral membrane proteins and their application in the characterization of the membrane interactions of the natively unfolded and Parkinson's disease (PD) related protein, α-synuclein (α-syn). We give particular focus to studies that have led to the current understanding of membrane-bound α-syn structure and the elucidation of specific membrane properties that affect α-syn-membrane binding. Finally, we discuss biophysical evidence supporting a key role for membranes and α-syn in PD pathogenesis. This article is part of a Special Issue entitled: Membrane protein structure and function.

Self-aligned wet-cell for hydrated microbiology observation in TEM

This paper describes a Self-Aligned Wet (SAW) cell suitable for direct-cell or bacteria incubation and observation in a wet environment inside a transmission electron microscope. This SAW cell is fabricated by a bulk-micromachining process and composed of two structurally complementary counterparts (an out-frame and an in-frame), where each contain a silicon nitride film based observation window. The in- and out-frames can be self-aligned via a mechanism of surface tension from a bio-sample droplet without the aid of positioning stages. The liquid chamber is enclosed between two silicon nitride membranes that are thin enough to allow high energy electrons to penetrate while also sustaining the pressure difference between the TEM vacuum and the vapor pressure within the liquid chamber. A large field of view (150 μm × 150 μm) in a SAW cell is favored and formed from a larger sized observation window in the out-frame, which is fabricated using a unique circular membrane formation process. In this paper, we introduce a novel design to circumvent the challenges of charging/heating problems in silicon nitride that arise from interactions with an electron beam. This paper also demonstrates TEM observations of D. Radiodurans growth in a liquid environment within a thicker chamber (20 μm) within a SAW cell.

A helical processing pipeline for EM structure determination of membrane proteins

Electron crystallography plays a key role in the structural biology of integral membrane proteins (IMPs) by offering one of the most direct means of providing insight into the functional state of these molecular machines in their lipid-associated forms, and also has the potential to facilitate examination of physiologically relevant transitional states and complexes. Helical or tubular crystals, which are the natural product of proteins crystallizing on the surface of a cylindrical vesicle, offer some unique advantages, such as three-dimensional (3D) information from a single view, compared to other crystalline forms. While a number of software packages are available for processing images of helical crystals to produce 3D electron density maps, widespread exploitation of helical image reconstruction is limited by a lack of standardized approaches and the initial effort and specialized expertise required. Our goal is to develop an integrated pipeline to enable structure determination by transmission electron microscopy (TEM) of IMPs in the form of tubular crystals. We describe here the integration of standard Fourier-Bessel helical analysis techniques into Appion, an integrated, database-driven pipeline.

The use of trehalose in the preparation of specimens for molecular electron microscopy

Biological specimens have to be prepared for imaging in the electron microscope in a way that preserves their native structure. Two-dimensional (2D) protein crystals to be analyzed by electron crystallography are best preserved by sugar embedding. One of the sugars often used to embed 2D crystals is trehalose, a disaccharide used by many organisms for protection against stress conditions. Sugars such as trehalose can also be added to negative staining solutions used to prepare proteins and macromolecular complexes for structural studies by single-particle electron microscopy (EM). In this review, we describe trehalose and its characteristics that make it so well suited for preparation of EM specimens and we review specimen preparation methods with a focus on the use of trehalose.

Specificity of intramembrane protein-lipid interactions

Our concept of biological membranes has markedly changed, from the fluid mosaic model to the current model that lipids and proteins have the ability to separate into microdomains, differing in their protein and lipid compositions. Since the breakthrough in crystallizing membrane proteins, the most powerful method to define lipid-binding sites on proteins has been X-ray and electron crystallography. More recently, chemical biology approaches have been developed to analyze protein-lipid interactions. Such methods have the advantage of providing highly specific cellular probes. With the advent of novel tools to study functions of individual lipid species in membranes together with structural analysis and simulations at the atomistic resolution, a growing number of specific protein-lipid complexes are defined and their functions explored. In the present article, we discuss the various modes of intramembrane protein-lipid interactions in cellular membranes, including examples for both annular and nonannular bound lipids. Furthermore, we will discuss possible functional roles of such specific protein-lipid interactions as well as roles of lipids as chaperones in protein folding and transport.

Regulation of human EGF receptor by lipids

The human epidermal growth factor receptor (EGFR) is a key representative of tyrosine kinase receptors, ubiquitous actors in cell signaling, proliferation, differentiation, and migration. Although the receptor is well-studied, a central issue remains: How does the compositional diversity and functional diversity of the surrounding membrane modulate receptor function? Reconstituting human EGFR into proteoliposomes of well-defined and controlled lipid compositions represents a minimal synthetic approach to systematically address this question. We show that lipid composition has little effect on ligand-binding properties of the EGFR but rather exerts a profound regulatory effect on kinase domain activation. Here, the ganglioside GM3 but not other related lipids strongly inhibited the autophosphorylation of the EGFR kinase domain. This inhibitory action of GM3 was only seen in liposomes compositionally poised to phase separate into coexisting liquid domains. The inhibition by GM3 was released by either removing the neuraminic acid of the GM3 headgroup or by mutating a membrane proximal lysine of EGFR (K642G). Our results demonstrate that GM3 exhibits the potential to regulate the allosteric structural transition from inactive to a signaling EGFR dimer, by preventing the autophosphorylation of the intracellular kinase domain in response to ligand binding.

Cryo-EM structure of the ribosome-SecYE complex in the membrane environment

The ubiquitous SecY/Sec61–complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent solubilized Sec–complexes have been reported. Here, we present a single–particle cryo–electron microscopy structure of the SecYEG complex in a membrane environment at sub–nanometer resolution, bound to a translating ribosome. Using the SecYEG complex reconstituted in a so–called Nanodisc, we could trace the nascent polypeptide chain from the peptidyl transferase center into the membrane. The reconstruction allowed for the identification of ribosome–lipid interactions. The rRNA helix 59 (H59) directly contacts the lipid surface and appears to modulate the membrane in immediate vicinity to the proposed lateral gate of the PCC. Based on our map and molecular dynamics simulations we present a model of a signal anchor–gated PCC in the membrane.

Mechanically, magnetically, and "rotationally aligned" membrane proteins in phospholipid bilayers give equivalent angular constraints for NMR structure determination

The native environment for membrane proteins is the highly asymmetric phospholipid bilayer, and this has a large effect on both their structure and dynamics. Reproducing this environment in samples suitable for spectroscopic and diffraction experiments is a key issue, and flexibility in sample preparation is essential to accommodate the diverse size, shape, and other physical properties of membrane proteins. In most cases, to ensure that the biological activities are maintained, this means reconstituting the proteins in fully hydrated planar phospholipid bilayers. The asymmetric character of protein-containing bilayers means that it is possible to prepare either oriented or unoriented (powder) samples. Here we demonstrate the equivalence of mechanical, magnetic, and what we refer to as "rotational alignment" of membrane proteins in phospholipid bilayer samples for solid-state NMR spectroscopy. The trans-membrane domain of virus protein "u" (Vpu) from human immunodeficiency virus (HIV-1) and the full-length membrane-bound form of fd bacteriophage coat protein in phospholipid bilayers are used as examples. The equivalence of structural constraints from oriented and unoriented (powder) samples of membrane proteins is based on two concepts: (1) their alignment is defined by the direction of the bilayer normal relative to the magnetic field and (2) they undergo rapid rotational diffusion about the same bilayer normal in liquid crystalline membranes. The measurement of angular constraints relative to a common external axis system defined by the bilayer normal for all sites in the protein is an essential element of oriented sample (OS) solid-state NMR.

The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins

The New York Consortium on Membrane Protein Structure (NYCOMPS) was formed to accelerate the acquisition of structural information on membrane proteins by applying a structural genomics approach. NYCOMPS comprises a bioinformatics group, a centralized facility operating a high-throughput cloning and screening pipeline, a set of associated wet labs that perform high-level protein production and structure determination by x-ray crystallography and NMR, and a set of investigators focused on methods development. In the first three years of operation, the NYCOMPS pipeline has so far produced and screened 7,250 expression constructs for 8,045 target proteins. Approximately 600 of these verified targets were scaled up to levels required for structural studies, so far yielding 24 membrane protein crystals. Here we describe the overall structure of NYCOMPS and provide details on the high-throughput pipeline.

Current limitations in native mass spectrometry based structural biology

Nowadays, mass spectrometry plays an important role in structural biology. At one end it can be used to investigate intact protein complexes, providing details about the complex composition, topology, stability, and dynamics, whereas at the other end the protein's identity and possible modifications can be visualized using proteomics approaches. Combining all this information allows the generation of detailed models for functional biological assemblies. Here, a perspective on the application of native mass spectrometry in structural biology is presented. The potential of this technique and some important current limitations are discussed. This includes issues regarding the quality/homogeneity of the sample, the dissociation efficiency of protein complexes during tandem mass spectrometric analysis, and some boundaries of ion mobility mass spectrometry.

Specimen preparation for electron diffraction of thin crystals

Electron crystallography has become a powerful approach for structural characterization of two-dimensional (2-D) protein crystals. The crystallographic approach provides the simplest route to the type of averaging that is essential for obtaining high resolution structural information from radiation-sensitive samples such as organic molecules. Several atomic or near atomic resolution protein structures have been solved by using cryo-electron crystallography and most of them involved using both image and electron diffraction data. An essential step in either type of work is preparation of specimens suitable for electron microscopy which retain their native state and high degree of order. Methods for preserving samples in a near-native, hydrated state have been developed, with minor variations for different specimens. The major challenge of collecting electron diffraction data particularly at high tilt angle is the blurring of diffraction spots due to imperfect flatness of the crystals. This paper discusses specimen preparation methods for electron crystallographic data collection of 2-D protein crystals with particular emphasis on the factors which affect the flatness of crystals. We also discuss some of the aspects of the data collection protocols which are particular to work with crystals.