Dynamics properties of membrane proteins in native cell membranes revealed by solid-state NMR spectroscopy.

Cell membranes provide an environment that is essential to the functions of membrane proteins. Cell membranes are mainly composed of proteins and highly diverse phospholipids. The influence of diverse lipid compositions of native cell membranes on the dynamics of the embedded membrane proteins has not been examined. Here we employ solid-state NMR to investigate the dynamics of E. coli Aquaporin Z (AqpZ) in its native inner cell membranes, and reveal the influence of diverse lipid compositions on the dynamics of AqpZ by comparing it in native cell membranes to that in POPC/POPG bilayers. We demonstrate that the dynamic rigidity of AqpZ generally conserves in both native cell membranes and POPC/POPG bilayers, due to its tightly packed tetrameric structure. In the gel and the liquid crystal phases of lipids, our experimental results show that AqpZ is more dynamic in native cell membranes than that in POPC/POPG bilayers. In addition, we observe that phase transitions of lipids in native membranes are less sensitive to temperature variations compared with that in POPC/POPG bilayers, which results in that the dynamics of AqpZ is less affected by the phase transitions of lipids in native cell membranes than that in POPC/POPG bilayers. This study provides new insights into the dynamics of membrane proteins in native cell membranes.

Localization atomic force microscopy.

Understanding structural dynamics of biomolecules at the single-molecule level is vital to advancing our knowledge of molecular mechanisms. Currently, there are few techniques that can capture dynamics at the sub-nanometre scale and in physiologically relevant conditions. Atomic force microscopy (AFM)1 has the advantage of analysing unlabelled single molecules in physiological buffer and at ambient temperature and pressure, but its resolution limits the assessment of conformational details of biomolecules2. Here we present localization AFM (LAFM), a technique developed to overcome current resolution limitations. By applying localization image reconstruction algorithms3 to peak positions in high-speed AFM and conventional AFM data, we increase the resolution beyond the limits set by the tip radius, and resolve single amino acid residues on soft protein surfaces in native and dynamic conditions. LAFM enables the calculation of high-resolution maps from either images of many molecules or many images of a single molecule acquired over time, facilitating single-molecule structural analysis. LAFM is a post-acquisition image reconstruction method that can be applied to any biomolecular AFM dataset.

3D imaging and quantitative analysis of small solubilized membrane proteins and their complexes by transmission electron microscopy.

Inherently unstable, detergent-solubilized membrane protein complexes can often not be crystallized. For complexes that have a mass of >300 kDa, cryo-electron microscopy (EM) allows their three-dimensional (3D) structure to be assessed to a resolution that makes secondary structure elements visible in the best case. However, many interesting complexes exist whose mass is below 300 kDa and thus need alternative approaches. Two methods are reviewed: (i) Mass measurement in a scanning transmission electron microscope, which has provided important information on the stoichiometry of membrane protein complexes. This technique is applicable to particulate, filamentous and sheet-like structures. (ii) 3D-EM of negatively stained samples, which determines the molecular envelope of small membrane protein complexes. Staining and dehydration artifacts may corrupt the quality of the 3D map. Staining conditions thus need to be optimized. 3D maps of plant aquaporin SoPIP2;1 tetramers solubilized in different detergents illustrate that the flattening artifact can be partially prevented and that the detergent itself contributes significantly. Another example discussed is the complex of G protein-coupled receptor rhodopsin with its cognate G protein transducin.

Electron crystallography for structural and functional studies of membrane proteins.

Membrane proteins are important research targets for basic biological sciences and drug design, but studies of their structure and function are considered difficult to perform. Studies of membrane structures have been greatly facilitated by technological and instrumental advancements in electron microscopy together with methodological advancements in biology. Electron crystallography is especially useful in studying the structure and function of membrane proteins. Electron crystallography is now an established method of analyzing the structures of membrane proteins in lipid bilayers, which resembles their natural biological environment. To better understand the neural system function from a structural point of view, we developed the cryo-electron microscope with a helium-cooled specimen stage, which allows for analysis of the structures of membrane proteins at a resolution higher than 3 Å. This review introduces recent instrumental advances in cryo-electron microscopy and presents some examples of structure analyses of membrane proteins, such as bacteriorhodopsin, water channels and gap junction channels. This review has two objectives: first, to provide a personal historical background to describe how we came to develop the cryo-electron microscope and second, to discuss some of the technology required for the structural analysis of membrane proteins based on cryo-electron microscopy.

Observation of membrane proteins in situ: AQPcic, the insect aquaporin example.

Aquaporins are water-selective channels widely distributed in prokaryotes, plants, and animals. Looking for the presence of a water channel in the filter chamber (FC) of a homopteran insect (Cicadella viridis), we conducted an electron microscopic study. On thin sections, FC displays thin epithelia with developed basal membrane folds (BMFs). Freeze fracture performed on FC shows an amazing network of intramembrane particles. Epithelial cell membranes were purified and observed by negative staining for control purity. Membrane solubilisation followed by PAGE showed that a 25-kDa polypeptide (P25) is the major protein constituent. Using a specific antibody, we located P25 on thin sections on the microvilli and on BMFs of the epithelial cells. Immunogold localisation of P25 on negatively stained membranes and examination of Pt/C shadowed membranes demonstrated that P25 has an asymmetric insertion within the membrane. cDNA cloning and heterologous expression confirmed that P25 is an aquaporin; thus, we called it AQPcic. The native state of crystallisation of this aquaporin in the membrane appeared to be unique and favourable for a structural investigation by negative staining, cryo-electron microscopy, and image processing. We demonstrated that, in the native membrane, AQPcic is a homotetramer forming a regular two-dimensional array.

Evaluation of imaging plates as recording medium for images of negatively stained single particles and electron diffraction patterns of two-dimensional crystals.

We evaluated imaging plates (IPs) and the DITABIS Micron scanner for their use in recording images of negatively stained single-particle specimens and electron diffraction patterns of two-dimensional crystals. We first established the optimal imaging and read-out conditions for images of negatively stained single-particle specimens using the signal-to-noise ratio of the images as the evaluation criterion. We found that images were best recorded on IPs at a magnification of 67,000x, read out with a gain setting of 20,000 and a laser power setting of 30% with subsequent binning over 2 x 2 pixels. Our results show that for images of negatively stained specimens, for which the resolution is limited to approximately 20 A, IPs are a good alternative to EM film. We also compared IPs with a 2K x 2K Gatan charge-coupled device (CCD) camera for their use in recording electron diffraction patterns of sugar-embedded two-dimensional crystals. Diffraction patterns of aquaporin-0 recorded on IPs and with the CCD camera showed reflections beyond 3 A and had similar R(Friedel) as well as R(merge) values. IPs can thus be used to collect diffraction patterns, but CCD cameras are more convenient and remain the best option for recording electron diffraction patterns.

The 2DX robot: a membrane protein 2D crystallization Swiss Army knife.

Among the state-of-the-art techniques that provide experimental information at atomic scale for membrane proteins, electron crystallography, atomic force microscopy and solid state NMR make use of two-dimensional crystals. We present a cyclodextrin-driven method for detergent removal implemented in a fully automated robot. The kinetics of the reconstitution processes is precisely controlled, because the detergent complexation by cyclodextrin is of stoichiometric nature. The method requires smaller volumes and lower protein concentrations than established 2D crystallization methods, making it possible to explore more conditions with the same amount of protein. The method yielded highly ordered 2D crystals diffracting to high resolution from the pore-forming toxin Aeromonas hydrophila aerolysin (2.9A), the plant aquaporin SoPIP2;1 (3.1A) and the human aquaporin-8 (hAQP8; 3.3A). This new method outperforms traditional 2D crystallization approaches in terms of accuracy, flexibility, throughput, and allows the usage of detergents having low critical micelle concentration (CMC), which stabilize the structure of membrane proteins in solution.

Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF.

The glycerol uptake facilitator, GlpF, a major intrinsic protein found in Escherichia coli, selectively conducts water and glycerol across the inner membrane. The free energy landscape characterizing the assisted transport of glycerol by this homotetrameric aquaglyceroporin has been explored by means of equilibrium molecular dynamics over a timescale spanning 0.12 micros. To overcome the free energy barriers of the conduction pathway, an adaptive biasing force is applied to the glycerol molecule confined in each of the four channels. The results illuminate the critical role played by intramolecular relaxation on the diffusion properties of the permeant. These free energy calculations reveal that glycerol tumbles and isomerizes on a timescale comparable to that spanned by its adaptive-biasing-force-assisted conduction in GlpF. As a result, reorientation and conformational equilibrium of glycerol in GlpF constitute a bottleneck in the molecular simulations of the permeation event. A profile characterizing the position-dependent diffusion of the permeant has been determined, allowing reaction rate theory to be applied for investigating conduction kinetics based on the measured free energy landscape.

Human cataract lens membrane at subnanometer resolution.

Human pathologies often originate from molecular disorders. Therefore, imaging technology as one of the bases for the identification and understanding of pathologies must provide views of single molecules at subnanometer resolution. Membrane proteins mediate many of life's most important processes, and their malfunction is often lethal or leads to severe disease. The membrane proteins aquaporin-0 (AQP0) and connexons form junctional microdomains between healthy lens core cells in which AQP0 form square arrays surrounded by connexons. Malfunction of both proteins results in the formation of cataract. We have used high-resolution atomic force microscopy (AFM) to image junctional microdomains in membranes from an individual human eye lens with senile cataract. Images at subnanometer resolution report individual helix-connecting loops of four amino acid residues on the AQP0 surface. We describe the supramolecular assembly and the conformational state of AQP0 in junctional microdomains, where a mixture of truncated junctional and full-length water channel AQP0 form square arrays. Imaging of microdomain borders revealed individual AQP0 tetramers and no associated connexon, indicating a lack of metabolite transport, waste accumulation, and enlarged regions of non-adhering membranes, causing cataract in this individual. This first high-resolution view of the membrane of this pathological human tissue provides insights into cataract pathology at the single membrane protein level, and indicates the power of the AFM as a future tool in medical imaging at subnanometer resolution.

Structural models of the supramolecular organization of AQP0 and connexons in junctional microdomains.

Membrane proteins perform many essential cellular functions. Over the last years, substantial advances have been made in our understanding of the structure and function of isolated membrane proteins. However, like soluble proteins, many membrane proteins assemble into supramolecular complexes that perform specific functions in specialized membrane domains. Since supramolecular complexes of membrane proteins are difficult to study by conventional approaches, little is known about their composition, organization and assembly. The high signal-to-noise ratio of the images that can be obtained with an atomic force microscope (AFM) makes this instrument a powerful tool to image membrane protein complexes within native membranes. Recently, we have reported high-resolution topographs of junctional microdomains in native eye lens membranes containing two-dimensional (2D) arrays of aquaporin-0 (AQP0) surrounded by connexons. While both proteins are involved in cell adhesion, AQP0 is a specific water channel whereas connexons form cell-cell communication channels with broad substrate specificity. Here, we have performed a detailed analysis of the supramolecular organization of AQP0 tetramers and connexon hexamers in junctional microdomains in the native lens membrane. We present first structural models of these junctional microdomains, which we generated by docking atomic models of AQP0 and connexons into the AFM topographs. The AQP0 2D arrays in the native membrane show the same molecular packing of tetramers seen in highly ordered double-layered 2D crystals obtained through reconstitution of purified AQP0. In contrast, the connexons that surround the AQP0 arrays are only loosely packed. Based on our AFM observations, we propose a mechanism that may explain the supramolecular organization of AQP0 and connexons in junctional domains in native lens membranes.

Immunolocalization of aquaporins in vocal fold epithelia.

OBJECTIVE: To investigate the presence of aquaporin (AQP) water channels 1, 2, and 3 in stratified squamous vocal fold epithelium. DESIGN: Immunolocalization analysis of excised ovine vocal fold epithelia. SUBJECTS: Sheep. INTERVENTIONS: Ovine vocal fold epithelia were prepared for immunoelectron microscopy using primary antibodies directed against AQP-1, AQP-2, and AQP-3. Photographic profiles of epithelium exposed to each antibody were used to calculate the immunogold labeling density of the plasma membrane and cytoplasm. MAIN OUTCOME MEASURES: Density of immunolabeling was compared across 3 regions that represent cell layers closest to the glottal lumen for the plasma membrane and cytoplasm, respectively. RESULTS: Labeling densities of AQP-1 and AQP-2 were significantly greater for the plasma membrane region of the luminal cells than for deeper cell layers. Cytoplasmic labeling and labeling of circular structures was greatest for cell layers 2 through 5 beneath the vocal fold surface compared with the surface cell layer. Immunogold labeling of AQP-3, an aquaglyceroporin, in vocal fold epithelium was inconclusive. CONCLUSION: Aquaporins 1 and 2, associated with the plasma membrane region of ovine vocal fold epithelial cells, demonstrate the presence of an intrinsic mechanism to permit transcellular water flux in response to osmotic gradients.

Aquaporin-11 containing a divergent NPA motif has normal water channel activity.

Recently, two novel mammalian aquaporins (AQPs), AQPs 11 and 12, have been identified and classified as members of a new AQP subfamily, the "subcellular AQPs". In members of this subfamily one of the two asparagine-proline-alanine (NPA) motifs, which play a crucial role in selective water conduction, are not completely conserved. Mouse AQP11 (mAQP11) was expressed in Sf9 cells and purified using the detergent Fos-choline 10. The protein was reconstituted into liposomes, which were used for water conduction studies with a stopped-flow device. Single water permeability (pf) of AQP11 was measured to be 1.72+/-0.03x10(-13) cm(3)/s, suggesting that other members of the subfamily with incompletely conserved NPA motifs may also function as water channels.

The supramolecular architecture of junctional microdomains in native lens membranes.

Gap junctions formed by connexons and thin junctions formed by lens-specific aquaporin 0 (AQP0) mediate the tight packing of fibre cells necessary for lens transparency. Gap junctions conduct water, ions and metabolites between cells, whereas junctional AQP0 seems to be involved in cell adhesion. High-resolution atomic force microscopy (AFM) showed the supramolecular organization of these proteins in native lens core membranes, in which AQP0 forms two-dimensional arrays that are surrounded by densely packed gap junction channels. These junctional microdomains simultaneously provide adhesion and communication between fibre cells. The AFM topographs also showed that the extracellular loops of AQP0 in junctional microdomains adopt a conformation that closely resembles the structure of junctional AQP0, in which the water pore is thought to be closed. Finally, time-lapse AFM imaging provided insights into AQP0 array formation. This first high-resolution view of a multicomponent eukaryotic membrane shows how membrane proteins self-assemble into functional microdomains.

The structure of aquaporins.

The ubiquitous members of the aquaporin (AQP) family form transmembrane pores that are either exclusive for water (aquaporins) or are also permeable for other small neutral solutes such as glycerol (aquaglyceroporins). The purpose of this review is to provide an overview of our current knowledge of AQP structures and to describe the structural features that define the function of these membrane pores. The review will discuss the mechanisms governing water conduction, proton exclusion and substrate specificity, and how the pore permeability is regulated in different members of the AQP family.

Aquaporin-1 in the peritoneal membrane: implications for peritoneal dialysis and endothelial cell function.

PD (peritoneal dialysis) is an established mode of renal replacement therapy, based on the exchange of fluid and solutes between blood in peritoneal capillaries and a dialysate that has been introduced into the peritoneal cavity. The dialysis process involves diffusive and convective transports and osmosis through the PM (peritoneal membrane). Computer simulations predicted that the PM contains ultrasmall pores (radius <3 A, 1 A=10(-10) m), responsible for up to 50% of UF (ultrafiltration), i.e. the osmotically driven water movement during PD. Several lines of evidence suggest that AQP1 (aquaporin-1) is the ultrasmall pore responsible for transcellular water permeability during PD. Treatment with corticosteroids induces the expression of AQP1 in the PM and improves water permeability and UF in rats without affecting the osmotic gradient and permeability for small solutes. Studies in knockout mice provided further evidence that osmotically driven water transport across the PM is mediated by AQP1. AQP1 and eNOS (endothelial nitric oxide synthase) show a distinct regulation within the endothelium lining the peritoneal capillaries. In acute peritonitis, the up-regulation of eNOS and increased release of nitric oxide dissipate the osmotic gradient and prevent UF, whereas AQP1 expression is unchanged. These results illustrate the usefulness of the PM to investigate the role and regulation of AQP1 in the endothelium. The results also emphasize the critical role of AQP1 during PD and suggest that manipulation of AQP1 expression may be used to increase water permeability across the PM.

The 4.5 A structure of human AQP2.

Located in the principal cells of the collecting duct, aquaporin-2 (AQP2) is responsible for the regulated water reabsorption in the kidney and is indispensable for the maintenance of body water balance. Disregulation or malfunctioning of AQP2 can lead to severe diseases such as nephrogenic diabetes insipidus, congestive heart failure, liver cirrhosis and pre-eclampsia. Here we present the crystallization of recombinantly expressed human AQP2 into two-dimensional protein-lipid arrays and their structural characterization by atomic force microscopy and electron crystallography. These crystals are double-layered sheets that have a diameter of up to 30 microm, diffract to 3 A(-1) and are stacked by contacts between their cytosolic surfaces. The structure determined to 4.5 A resolution in the plane of the membrane reveals the typical aquaporin fold but also a particular structure between the stacked layers that is likely to be related to the cytosolic N and C termini.

Fluid and cellular pathways of rat lymph nodes in relation to lymphatic labyrinths and Aquaporin-1 expression.

The aim of the present study was to examine the organization of lymph fluid and cellular pathways and distribution of the membrane water channel Aquaporin-1 (AQP-1) in rat lymph nodes. Lymph fluid and cellular pathways within lymph nodes were examined by fluorescent protein tracer/confocal microscopy and by scanning electron microscopy (SEM), While the distribution of AQP-1 was studied immunohistochemically. Tracer studies showed the subcapsular sinuses continued directly at the hilum or via the intermediate sinuses to the medullary sinuses, and lymphatic labyrinths originating with blind-ends in the deep cortex drained into medullary sinuses. Afferent lymph tracers were also observed in node cortex interstitium. By SEM, lymphatic labyrinths appeared densely filled with lymphocytes and had few intraluminal sinus reticular cells, while medullary sinuses possessed well-developed networks of sinus reticular cells. The presence of many lymphocytes wedged in the walls of the lymphatic labyrinth suggested that lymphocytes migrate between the node parenchyma and lymphatic labyrinths. AQP-1 was distributed on the membrane of lymphatic endothelium and reticular cells as well as on both luminal and abluminal cell membranes of high endothelial venules (HEVs). Our SEM findings support the concept that lymphocytes migrate from the node parenchyma into lymphatic labyrinths in the deep cortex. The nodal distribution of AQP-1 plus the presence of a polarized distribution of ion pumps and/or ion channels in the HEV endothelium hypothesized in our discussion could explain the mechanism of the reported lymph-to-plasma fluid flux in lymph nodes and also facilitate the entry of afferent lymph antigens into the node cortex interstitium.

Robert Feulgen Lecture. Microscopic assessment of membrane protein structure and function.

Membrane proteins represent an important class of proteins that are encoded by about 40% of all genes, but compared to soluble proteins structural information is sparse. Most of the atomic coordinates currently available are from bacterial membrane proteins and have been obtained by X-ray crystallography. Recent results demonstrate the imaging power of the atomic force microscope and the accuracy of electron crystallography. These methods allow membrane proteins to be studied while embedded in the bilayer, and thus in a functional state. The low signal-to-noise ratio of cryoelectron microscopy is overcome by crystallizing membrane proteins in a two-dimensional protein-lipid membrane, allowing its atomic structure to be determined. In contrast, the high signal-to-noise ratio of atomic force microscopy allows individual protein surfaces to be imaged at subnanometer resolution, and their conformational states to be sampled. This review discusses examples of microscopic membrane protein structure determination and illuminates recent progress.