Reconstitution of functional water channels in liposomes containing purified red cell CHIP28 protein

Molecular Dynamics Simulations of the Eye Lens Water Channel Aquaporin 0 from Fish

Aquaporin 0 (AQP0) plays a key role in water circulation in the eye lens through a variety of functions. In contrast to mammalian genomes, zebrafish contains two aqp0 genes leading to a separation of AQP0 multiple functions between the two gene products, Aqp0a and Aqp0b. A notable feature of the zebrafish AQP0 paralogs is the increased water permeability of Aqp0b relative to Aqp0a as well as a severa lfold increase relative to mammalian AQP0. Here, we report equilibrium molecular dynamics (MD) simulations on the microsecond timescale to identify the structural basis underlying the differences in water permeability between zebrafish AQP0 paralogs and between AQP0 mammalian and fish orthologs. Our simulations are able to reproduce the experimental trends in water permeability. Our results suggest that a substitution of a key Y23 residue in mammalian AQP0 for F23 in fish AQP0 orthologs introduces significant changes in the conformational dynamics of the CS-I structural motif, which, in conjunction with different levels of hydration of the channel vestibule, can account for the differences in permeabilities between fish and mammalian AQP0 orthologs and between zebrafish AQP0 paralogs.

Bio-Inspired Functional Materials for Environmental Applications

With the global population expected to reach 9.7 billion by 2050, there is an urgent need for advanced materials that can address existing and developing environmental issues. Many current synthesis processes are environmentally unfriendly and often lack control over size, shape, and phase of resulting materials. Based on knowledge from biological synthesis and assembly processes, as well as their resulting functions (e.g., photosynthesis, self-healing, anti-fouling, etc.), researchers are now beginning to leverage these biological blueprints to advance bio-inspired pathways for functional materials for water treatment, air purification and sensing. The result has been the development of novel materials that demonstrate enhanced performance and address sustainability. Here, an overview of the progress and potential of bio-inspired methods toward functional materials for environmental applications is provided. The challenges and opportunities for this rapidly expanding field and aim to provide a valuable resource for researchers and engineers interested in developing sustainable and efficient processes and technologies is discussed.

Generating Concentration Gradients across Membranes for Molecular Dynamics Simulations of Periodic Systems

The plasma membrane forms the boundary between a living entity and its environment and acts as a barrier to permeation and flow of substances. Several computational means of calculating permeability have been implemented for molecular dynamics (MD) simulations-based approaches. Except for double bilayer systems, most permeability studies have been performed under equilibrium conditions, in large part due to the challenges associated with creating concentration gradients in simulations utilizing periodic boundary conditions. To enhance the scientific understanding of permeation and complement the existing computational means of characterizing membrane permeability, we developed a non-equilibrium method that enables the generation and maintenance of steady-state gradients in MD simulations. We utilize PBCs advantageously by imposing a directional bias to the motion of permeants so that their crossing of the boundary replenishes the gradient, like a previous study on ions. Under these conditions, a net flow of permeants across membranes may be observed to determine bulk permeability by a direct application of J=PΔc. In the present study, we explore the results of its application to an exemplary O2 and POPC bilayer system, demonstrating accurate and precise permeability measurements. In addition, we illustrate the impact of permeant concentration and the choice of thermostat on the permeability. Moreover, we demonstrate that energetics of permeation can be closely examined by the dissipation of the gradient across the membrane to gain nuanced insights into the thermodynamics of permeability.

Mechanosensitive aquaporins

Cellular systems must deal with mechanical forces to satisfy their physiological functions. In this context, proteins with mechanosensitive properties play a crucial role in sensing and responding to environmental changes. The discovery of aquaporins (AQPs) marked a significant breakthrough in the study of water transport. Their transport capacity and regulation features make them key players in cellular processes. To date, few AQPs have been reported to be mechanosensitive. Like mechanosensitive ion channels, AQPs respond to tension changes in the same range. However, unlike ion channels, the aquaporin's transport rate decreases as tension increases, and the molecular features of the mechanism are unknown. Nevertheless, some clues from mechanosensitive ion channels shed light on the AQP-membrane interaction. The GxxxG motif may play a critical role in the water permeation process associated with structural features in AQPs. Consequently, a possible gating mechanism triggered by membrane tension changes would involve a conformational change in the cytoplasmic extreme of the single file region of the water pathway, where glycine and histidine residues from loop B play a key role. In view of their transport capacity and their involvement in relevant processes related to mechanical forces, mechanosensitive AQPs are a fundamental piece of the puzzle for understanding cellular responses.

Entropic barrier of water permeation through single-file channels

Facilitated water permeation through narrow biological channels is fundamental for all forms of life. Despite its significance in health and disease as well as for biotechnological applications, the energetics of water permeation are still elusive. Gibbs free energy of activation is composed of an enthalpic and an entropic component. Whereas the enthalpic contribution is readily accessible via temperature dependent water permeability measurements, estimation of the entropic contribution requires information on the temperature dependence of the rate of water permeation. Here, we estimate, by means of accurate activation energy measurements of water permeation through Aquaporin-1 and by determining the accurate single channel permeability, the entropic barrier of water permeation through a narrow biological channel. Thereby the calculated value for [Formula: see text] = 2.01 ± 0.82 J/(mol·K) links the activation energy of 3.75 ± 0.16 kcal/mol with its efficient water conduction rate of ~10¹⁰ water molecules/second. This is a first step in understanding the energetic contributions in various biological and artificial channels exhibiting vastly different pore geometries.

Wetting hysteresis induces effective unidirectional water transport through a fluctuating nanochannel

We propose a water pump that actively transports water molecules through nanochannels. Spatially asymmetric noise fluctuations imposed on the channel radius cause unidirectional water flow without osmotic pressure, which can be attributed to hysteresis in the cyclic transition between the wetting/drying states. We show that the water transport depends on fluctuations, such as white, Brownian, and pink noises. Because of the high-frequency components in white noise, fast switching of open and closed states inhibits channel wetting. Conversely, pink and Brownian noises generate high-pass filtered net flow. Brownian fluctuation leads to a faster water transport rate, whereas pink noise has a higher capability to overcome pressure differences in the opposite direction. A trade-off relationship exists between the resonant frequency of the fluctuation and the flow amplification. The proposed pump can be considered as an analogy for the reversed Carnot cycle, which is the upper limit of the energy conversion efficiency.

Transport Characteristics of Aquaporins

Aquaporins (AQP) are a class of the integral membrane proteins. The main physiological function of AQPs is to facilitate the water transport across plasma membrane of cells. However, the transport of various kinds of small molecules by AQPs is an interesting topic. Studies using in vitro cell models have found that AQPs mediated transport of small molecules, including glycerol, urea, carbamides, polyols, purines, pyrimidines and monocarboxylates, and gases such as CO2, NO, NH3, H2O2 and O2, although the high intrinsic membrane permeabilities for these gases make aquaporin-facilitated transport not dominant in physiological mechanism. AQPs are also considered to transport silicon, antimonite, arsenite and some ions; however, most data about transport characteristics of AQPs are derived from in vitro experiments. The physiological significance of AQPs that are permeable to various small molecules is necessary to be determined by in vivo experiments. This chapter will provide information about the transport characteristics of AQPs.

Aquaporin Gating: A New Twist to Unravel Permeation through Water Channels

Aquaporins (AQPs) are small transmembrane tetrameric proteins that facilitate water, solute and gas exchange. Their presence has been extensively reported in the biological membranes of almost all living organisms. Although their discovery is much more recent than ion transport systems, different biophysical approaches have contributed to confirm that permeation through each monomer is consistent with closed and open states, introducing the term gating mechanism into the field. The study of AQPs in their native membrane or overexpressed in heterologous systems have experimentally demonstrated that water membrane permeability can be reversibly modified in response to specific modulators. For some regulation mechanisms, such as pH changes, evidence for gating is also supported by high-resolution structures of the water channel in different configurations as well as molecular dynamics simulation. Both experimental and simulation approaches sustain that the rearrangement of conserved residues contributes to occlude the cavity of the channel restricting water permeation. Interestingly, specific charged and conserved residues are present in the environment of the pore and, thus, the tetrameric structure can be subjected to alter the positions of these charges to sustain gating. Thus, is it possible to explore whether the displacement of these charges (gating current) leads to conformational changes? To our knowledge, this question has not yet been addressed at all. In this review, we intend to analyze the suitability of this proposal for the first time.

Quantitative characterization of the path of glucose diffusion facilitated by human glucose transporter 1

Glucose transporter GLUT1 is ubiquitously expressed in the human body from the red cells to the blood-brain barrier to the skeletal muscles. It is physiologically relevant to understand how GLUT1 facilitates diffusion of glucose across the cell membrane. It is also pathologically relevant because GLUT1 deficiency causes neurological disorders and anemia and because GLUT1 overexpression fuels the abnormal growth of cancer cells. This article presents a quantitative investigation of GLUT1 based on all-atom molecular-dynamics (MD) simulations of the transporter embedded in lipid bilayers of asymmetric inner-and-outer-leaflet lipid compositions, subject to asymmetric intra-and-extra-cellular environments. This is in contrast with the current literature of MD studies that have not considered both of the aforementioned asymmetries of the cell membrane. The equilibrium (unbiased) dynamics of GLUT1 shows that it can facilitate glucose diffusion across the cell membrane without undergoing large-scale conformational motions. The Gibbs free-energy profile, which is still lacking in the current literature of GLUT1, quantitatively characterizes the diffusion path of glucose from the periplasm, through an extracellular gate of GLUT1, on to the binding site, and off to the cytoplasm. This transport mechanism is validated by the experimental data that GLUT1 has low water-permeability, uptake-efflux symmetry, and 10 kcal/mol Arrhenius activation barrier around 37 °C.

Determining small-molecule permeation through lipid membranes

The passive permeability of cell membranes is of key importance in biology, biomedical research and biotechnology as it determines the extent to which various molecules such as drugs, products of metabolism, and toxins can enter or leave the cell unaided by dedicated transport proteins. The quantification of passive solute permeation is possible with radio-isotope distribution experiments, spectroscopic measurements and molecular dynamics simulations. This protocol describes stopped-flow fluorimetry measurements performed on lipid vesicles and living yeast cells to estimate the osmotic permeability of water and solutes across (bio)membranes. Encapsulation of the fluorescent dye calcein into lipid vesicles allows monitoring of volume changes upon osmotic shifts of the medium via (de)quenching of the fluorophore, which we interpret using a well-defined physical model that takes the dynamics of the vesicles into account to calculate the permeability coefficients of solutes. We also present analogous procedures to probe weak acid and base permeability in vesicles and cells by using the read-out of encapsulated or expressed pH-sensitive probes. We describe the preparation of synthetic vesicles of varying lipid composition and determination of vesicle size distribution by dynamic light scattering. Data on membrane permeation are obtained using either conventional or stopped-flow kinetic fluorescence measurements on instruments available in most research institutes and are analyzed with a suite of user-friendly MATLAB scripts ( https://doi.org/10.5281/zenodo.6511116 ). Collectively, these procedures provide a comprehensive toolbox for determining membrane permeability coefficients in a variety of experimental systems, and typically take 2-3 d.

The Hidden Intricacies of Aquaporins: Remarkable Details in a Common Structural Scaffold

Evolution turned aquaporins (AQPs) into the most efficient facilitators of passive water flow through cell membranes at no expense of solute discrimination. In spite of a plethora of solved AQP structures, many structural details remain hidden. Here, by combining extensive sequence- and structural-based analysis of a unique set of 20 non-redundant high-resolution structures and molecular dynamics simulations of four representatives, key aspects of AQP stability, gating, selectivity, pore geometry, and oligomerization, with a potential impact on channel functionality, are identified. The general view of AQPs possessing a continuous open water pore is challenged and it is depicted that AQPs' selectivity is not exclusively shaped by pore-lining residues but also by the relative arrangement of transmembrane helices. Moreover, this analysis reveals that hydrophobic interactions constitute the main determinant of protein thermal stability. Finally, a numbering scheme of the conserved AQP scaffold is established, facilitating direct comparison of, for example, disease-causing mutations and prediction of potential structural consequences. Additionally, the results pave the way for the design of optimized AQP water channels to be utilized in biotechnological applications.

Light and Scanning Electron Microscopy of Red Blood Cells From Humans and Animal Species Providing Insights into Molecular Cell Biology

We reviewed the many discoveries in cell biology, made since the 17^th century, which have been based on red blood cells (RBCs). The advances in molecular and structural biology in the past 40 years have enabled the discovery with these cells, most notably, of the first water channel protein (WCP) called today aquaporin1 (AQP1). The main aim of our work reviewed was to examine by light and electron microscopy a very wide range of RBCs from reptiles, birds, monotremes, marsupials and placentals, in order to estimate from these images the RBC cell volume and surface area. The diffusional water permeability of the RBC membrane from these species has further been measured with a nuclear magnetic resonance (NMR) spectroscopy technique. The significance of the observed permeability of RBCs to water and possible influences on the whole body are discussed.

Osmoregulation and the Hypothalamic Supraoptic Nucleus: From Genes to Functions

Due to the relatively high permeability to water of the plasma membrane, water tends to equilibrate its chemical potential gradient between the intra and extracellular compartments. Because of this, changes in osmolality of the extracellular fluid are accompanied by changes in the cell volume. Therefore, osmoregulatory mechanisms have evolved to keep the tonicity of the extracellular compartment within strict limits. This review focuses on the following aspects of osmoregulation: 1) the general problems in adjusting the "milieu interieur" to challenges imposed by water imbalance, with emphasis on conceptual aspects of osmosis and cell volume regulation; 2) osmosensation and the hypothalamic supraoptic nucleus (SON), starting with analysis of the electrophysiological responses of the magnocellular neurosecretory cells (MNCs) involved in the osmoreception phenomenon; 3) transcriptomic plasticity of SON during sustained hyperosmolality, to pinpoint the genes coding membrane channels and transporters already shown to participate in the osmosensation and new candidates that may have their role further investigated in this process, with emphasis on those expressed in the MNCs, discussing the relationships of hydration state, gene expression, and MNCs electrical activity; and 4) somatodendritic release of neuropeptides in relation to osmoregulation. Finally, we expect that by stressing the relationship between gene expression and the electrical activity of MNCs, studies about the newly discovered plastic-regulated genes that code channels and transporters in the SON may emerge.

Ultrafast water permeation through nanochannels with a densely fluorous interior surface

Ultrafast water permeation in aquaporins is promoted by their hydrophobic interior surface. Polytetrafluoroethylene has a dense fluorine surface, leading to its strong water repellence. We report a series of fluorous oligoamide nanorings with interior diameters ranging from 0.9 to 1.9 nanometers. These nanorings undergo supramolecular polymerization in phospholipid bilayer membranes to form fluorous nanochannels, the interior walls of which are densely covered with fluorine atoms. The nanochannel with the smallest diameter exhibits a water permeation flux that is two orders of magnitude greater than those of aquaporins and carbon nanotubes. The proposed nanochannel exhibits negligible chloride ion (Cl^-) permeability caused by a powerful electrostatic barrier provided by the electrostatically negative fluorous interior surface. Thus, this nanochannel is expected to show nearly perfect salt reflectance for desalination.

Quantitative measurement of diffusion-weighted imaging signal using expression-controlled aquaporin-4 cells: Comparative study of 2-compartment and diffusion kurtosis imaging models

The purpose of this study was to compare parameter estimates for the 2-compartment and diffusion kurtosis imaging models obtained from diffusion-weighted imaging (DWI) of aquaporin-4 (AQP4) expression-controlled cells, and to look for biomarkers that indicate differences in the cell membrane water permeability. DWI was performed on AQP4-expressing and non-expressing cells and the signal was analyzed with the 2-compartment and diffusion kurtosis imaging models. For the 2-compartment model, the diffusion coefficients (Df, Ds) and volume fractions (Ff, Fs, Ff = 1-Fs) of the fast and slow compartments were estimated. For the diffusion kurtosis imaging model, estimates of the diffusion kurtosis (K) and corrected diffusion coefficient (D) were obtained. For the 2-compartment model, Ds and Fs showed clear differences between AQP4-expressing and non-expressing cells. Fs was also sensitive to cell density. There was no clear relationship with the cell type for the diffusion kurtosis imaging model parameters. Changes to cell membrane water permeability due to AQP4 expression affected DWI of cell suspensions. For the 2-compartment and diffusion kurtosis imaging models, Ds was the parameter most sensitive to differences in AQP4 expression.

The energetic barrier to single-file water flow through narrow channels

Various nanoscopic channels of roughly equal diameter and length facilitate single-file diffusion at vastly different rates. The underlying variance of the energetic barriers to transport is poorly understood. First, water partitioning into channels so narrow that individual molecules cannot overtake each other incurs an energetic penalty. Corresponding estimates vary widely depending on how the sacrifice of two out of four hydrogen bonds is accounted for. Second, entropy differences between luminal and bulk water may arise: additional degrees of freedom caused by dangling OH-bonds increase entropy. At the same time, long-range dipolar water interactions decrease entropy. Here, we dissect different contributions to Gibbs free energy of activation, ΔG ^‡, for single-file water transport through narrow channels by analyzing experimental results from water permeability measurements on both bare lipid bilayers and biological water channels that (i) consider unstirred layer effects and (ii) adequately count the channels in reconstitution experiments. First, the functional relationship between water permeabilities and Arrhenius activation energies indicates negligible differences between the entropies of intraluminal water and bulk water. Second, we calculate ΔG ^‡ from unitary water channel permeabilities using transition state theory. Plotting ΔG ^‡ as a function of the number of H-bond donating or accepting pore-lining residues results in a 0.1 kcal/mol contribution per residue. The resulting upper limit for partial water dehydration amounts to 2 kcal/mol. In the framework of biomimicry, our analysis provides valuable insights for the design of synthetic water channels. It thus may aid in the urgent endeavor towards combating global water scarcity.

Controlling Water Flow through a Synthetic Nanopore with Permeable Cations

There is presently intense interest in the development of synthetic nanopores that recapitulate the functional properties of biological water channels for a wide range of applications. To date, all known synthetic water channels have a hydrophobic lumen, and while many exhibit a comparable rate of water transport as biological water channels, there is presently no rationally designed system with the ability to regulate water transport, a critical property of many natural water channels. Here, we describe a self-assembling nanopore consisting of stacked macrocyclic molecules with a hybrid hydrophilic/hydrophobic lumen exhibiting water transport that can be regulated by alkali metal ions. Stopped-flow kinetic assays reveal a non-monotonic-dependence of transport on cation size as well as a strikingly broad range of water flow, from essentially none in the presence of the sodium ion to as high a flow as that of the biological water channel, aquaporin 1, in the absence of the cations. All-atom molecular dynamics simulations show that the mechanism underlying the observed sensitivity is the binding of cations to defined sites within this hybrid pore, which perturbs water flow through the channel. Thus, beyond revealing insights into factors that can modulate a high-flux water transport through sub-nm pores, the obtained results provide a proof-of-concept for the rational design of next-generation, controllable synthetic water channels.

Unimolecular Helix-Based Transmembrane Nanochannel with a Smallest Luminal Cavity of 1 Å Expressing High Proton Selectivity and Transport Activity

Natural protein channels have evolved with exquisite structures to transport ions selectively and rapidly. Learning from nature to construct biomimetic artificial channels is always challenging. Herein we present a unimolecular transmembrane proton channel by quinoline-derived helix, which exhibited highly selective and ultrafast proton transport behaviors. This helix-based channel possesses a small luminal cavity of 1 Å in diameter, which could efficiently reject the permeation of cations, anions or water molecules but only permits the translocation of protons owing to the size effect. The proton flow rate exceeded 10⁷ H⁺ s^-1 channel^-1 and reached the same magnitude with gramicidin A. Mechanism investigation revealed that the directionally arrayed NH-chain inside the synthetic channel played a pivotal role during the proton flux. This work not only presented a helix-based channel with the smallest observable nanopore, but also unveiled an unexplored pathway for realizing efficient transport of protons via the consecutive NH-chain.

2D Material Nanofiltration Membranes: From Fundamental Understandings to Rational Design

Since the discovery of 2D materials, 2D material nanofiltration (NF) membranes have attracted great attention and are being developed with a tremendously fast pace, due to their energy efficiency and cost effectiveness for water purification. The most attractive aspect for 2D material NF membranes is that, anomalous water and ion permeation phenomena have been constantly observed because of the presence of the severely confined nanocapillaries (<2 nm) in the membrane, leading to its great potential in achieving superior overall performance, e.g., high water flux, high rejection rates of ions, and high resistance to swelling. Hence, fundamental understandings of such water and ion transport behaviors are of great significance for the continuous development of 2D material NF membranes. In this work, the microscopic understandings developed up to date on 2D material NF membranes regarding the abnormal transport phenomena are reviewed, including ultrafast water and ion permeation rates with the magnitude several orders higher than that predicted by conventional diffusion behavior, ion dehydration, ionic Coulomb blockade, ion-ion correlations, etc. The state-of-the-art structural designs for 2D material NF membranes are also reviewed. Discussion and future perspectives are provided highlighting the rational design of 2D material membrane structures in the future.

High-Performance Biomimetic Water Channel: The Constructive Interplay of Interaction Parameters and Hydrophilic Doping Levels

In this study, we introduce a superfast biomimetic water channel mimicking the hydrophobicity scales of the Aquaporin (AQP) pore lining. Molecular dynamics simulation is used to scrutinize the impact of hydrophilic doping level in the nanotube and the water-wall interaction strength on water permeability. In the designed biomimetic channel, the constructive interplay of Lennard-Jones (LJ) ε parameters and hydrophilic doping levels increased the possibility of ultrafast water transport. Moreover, a unique set of LJ parameters is discovered for each biomimetic channel with different hydrophilic doping levels, enhancing water permeation. Inside high-performance biomimetic channels, water distribution surprisingly implies a varying pore geometry that narrows down in the middle, mimicking the pattern obtained from GplF pore analysis, evoking the narrow pore induced by the aromatic/arginine selectivity filter. This exciting accordance occurred as a result of tailoring specific hydrophilic arrays within the hydrophobic channel backbone by mimicking the AQP pore interior. The main takeaway of hydrophilic doping arrays implanted within the hydrophobic nanotube is to break the large barrier in the water-wall vdW energy profile into multiple reduced ones to increase water conduction. Consequently, the "water jumping" phenomenon in the middle of the biomimetic channel occurs under specific circumstances. The biomimetic channel with the highest value of water permeability of about 13.67 ± 0.66 × 10^-13 cm³·s^-1 exhibits the best mechanism for artificial water channels (AWCs), serving superfast water transport considering the low entrance barrier and weak water-wall interaction.

Aquaporins - Expression, purification and characterization

Aquaporin water channels facilitate the bi-directional flow of water and small, neutral solutes down an osmotic gradient in all kingdoms of life. Over the last two decades, the availability of high-quality protein has underpinned progress in the structural and functional characterization of these water channels. In particular, recombinant protein technology has guaranteed the supply of aquaporin samples that were of sufficient quality and quantity for further study. Here we review the features of successful expression, purification and characterization strategies that have underpinned these successes and that will drive further breakthroughs in the field. Overall, Escherichia coli is a suitable host for prokaryotic isoforms, while Pichia pastoris is the most commonly-used recombinant host for eukaryotic variants. Generally, a two-step purification procedure is suitable after solubilization in glucopyranosides and most structures are determined by X-ray following crystallization.

Highlighting membrane protein structure and function: A celebration of the Protein Data Bank

Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.

Fake It 'Till You Make It-The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics

Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.

Biomimetic Approach for Highly Selective Artificial Water Channels Based on Tubular Pillar[5]arene Dimers

Artificial water channels mimicking natural aquaporins (AQPs) can be used for selective and fast transport of water. Here, we quantify the transport performances of peralkyl-carboxylate-pillar[5]arenes dimers in bilayer membranes. They can transport ≈10⁷ water molecules/channel/second, within one order of magnitude of the transport rates of AQPs, rejecting Na⁺ and K⁺ cations. The dimers have a tubular structure, superposing pillar[5]arene pores of 5 Å diameter with twisted carboxy-phenyl pores of 2.8 Å diameter. This biomimetic platform, with variable pore dimensions within the same structure, offers size restriction reminiscent of natural proteins. It allows water molecules to selectively transit and prevents bigger hydrated cations from passing through the 2.8 Å pore. Molecular simulations prove that dimeric or multimeric honeycomb aggregates are stable in the membrane and form water pathways through the bilayer. Over time, a significant shift of the upper vs. lower layer occurs initiating new unexpected water permeation events through toroidal pores.

Cell-Like Behaviors of Dynamic Graphene Bubbles with Fast Water Transport

Ultrafast water transport in graphitic nanoenvironment is fundamentally important in the research of biomimetic membranes for potential applications in separation and energy. Yet, the form of graphitic nanostructures has not been fully explored with only carbon nanotubes and graphene nanochannels reported. Here, we fabricated dynamic graphene bubbles via strain engineering of chemical vapor deposition (CVD)-grown graphene on metal substrates. These graphene bubbles could switch between an inflated state and a deflated state continuously with the control of environmental moisture flow. It is demonstrated that water vapors transport through graphene wrinkles and condense inside graphene bubbles. The water transport rates across these graphene bubbles were calculated via dynamic Newton rings, which is comparable to that of carbon nanotubes and aquaporin. The discovery of dynamic graphene bubbles hosting the ability of fast water transport is helpful for an advanced understanding of the nanofluidic phenomenon and its future applications.

Functional Analysis of Aquaporin Water Permeability Using an Escherichia coli-Based Cell-Free Protein Synthesis System

Aquaporins are essential water channel proteins found in all kingdoms of life. Although the water permeability of aquaporins has been well characterized, sample preparation for aquaporin water permeability assays remains challenging and time-consuming. Besides the difficulty in overexpressing membrane proteins in a cell-based expression system, the unique requirement for homogeneity in aquaporin proteoliposome sample preparations for water transport assays further increases the complexity. In this study, a complementary Cell-free Protein Synthesis (CFPS) method is described in detail, providing three different strategies for the preparation of aquaporin proteoliposome samples. Aquaporin can be produced either as a pellet fraction and then resolubilized, or co-translationally as a detergent-soluble fraction. Furthermore, aquaporin can be directly incorporated into liposomes, which was included in the CFPS reactions. Although proteoliposomes tend to fuse during the incubation of the CFPS reactions, an additional treatment of the fused samples with detergent, followed by a detergent removal step, can re-form homogenously sized proteoliposomes suitable for functional analysis. Using this method, we successfully characterized aquaporins from both prokaryotic and eukaryotic organisms. In particular, in the presence of liposomes, the developed CFPS expression system is a fast and convenient method for sample preparation for the functional analysis of aquaporins.

N-Glycanase 1 Transcriptionally Regulates Aquaporins Independent of Its Enzymatic Activity

Patients with pathogenic mutations in NGLY1 cannot make tears and have global developmental delay and liver dysfunction. Traditionally, NGLY1 cleaves intact N-glycans from misfolded, retrotranslocated glycoproteins before proteasomal degradation. We demonstrate that Ngly1-null mouse embryonic fibroblasts, NGLY1 knockout human cells, and patient fibroblasts are resistant to hypotonic lysis. Ngly1-deficient mouse embryonic fibroblasts swell slower and have reduced aquaporin1 mRNA and protein expression. Ngly1 knockdown and overexpression confirms that Ngly1 regulates aquaporin1 and hypotonic cell lysis. Patient fibroblasts and NGLY1 knockout cells show reduced aquaporin11 mRNA, supporting NGLY1 as regulating expression of multiple aquaporins across species. Complementing Ngly1-deficient cells with catalytically inactive NGLY1 (p.Cys309Ala) restores normal hypotonic lysis and aquaporin1 protein. We show that transcription factors Atf1/Creb1 regulate aquaporin1 and that the Atf1/Creb1 signaling pathway is disrupted in Ngly1-deficient mouse embryonic fibroblasts. These results identify a non-enzymatic, regulatory function of NGLY1 in aquaporin transcription, possibly related to alacrima and neurological symptoms.

Pathways and Challenges for Biomimetic Desalination Membranes with Sub-Nanometer Channels

Transmembrane protein channels, including ion channels and aquaporins that are responsible for fast and selective transport of water, have inspired membrane scientists to exploit and mimic their performance in membrane technologies. These biomimetic membranes comprise discrete nanochannels aligned within amphiphilic matrices on a robust support. While biological components have been used directly, extensive work has also been conducted to produce stable synthetic mimics of protein channels and lipid bilayers. However, the experimental performance of biomimetic membranes remains far below that of biological membranes. In this review, we critically assess the status and potential of biomimetic desalination membranes. We first review channel chemistries and their transport behavior, identifying key characteristics to optimize water permeability and salt rejection. We compare various channel types within an industrial context, considering transport performance, processability, and stability. Through a re-examination of previous vesicular stopped-flow studies, we demonstrate that incorrect permeability equations result in an overestimation of the water permeability of nanochannels. We find in particular that the most optimized aquaporin-bearing bilayer had a pure water permeability of 2.1 L m^-2 h^-1 bar^-1, which is comparable to that of current state-of-the-art polymeric desalination membranes. Through a quantitative assessment of biomimetic membrane formats, we analytically show that formats incorporating intact vesicles offer minimal benefit, whereas planar biomimetic selective layers could allow for dramatically improved salt rejections. We then show that the persistence of nanoscale defects explains observed subpar performance. We conclude with a discussion on optimal strategies for minimizing these defects, which could enable breakthrough performance.

Water-ion permselectivity of narrow-diameter carbon nanotubes

Carbon nanotube (CNT) pores, which mimic the structure of the aquaporin channels, support extremely high water transport rates that make them strong candidates for building artificial water channels and high-performance membranes. Here, we measure water and ion permeation through 0.8-nm-diameter CNT porins (CNTPs)-short CNT segments embedded in lipid membranes-under optimized experimental conditions. Measured activation energy of water transport through the CNTPs agrees with the barrier values typical for single-file water transport. Well-tempered metadynamics simulations of water transport in CNTPs also report similar activation energy values and provide molecular-scale details of the mechanism for water entry into these channels. CNTPs strongly reject chloride ions and show water-salt permselectivity values comparable to those of commercial desalination membranes.

Stopped-flow Light Scattering Analysis of Red Blood Cell Glycerol Permeability

Stopped-Flow Light Scattering (SFLS) is a method devised to analyze the kinetics of fast chemical reactions that result in a significant change of the average molecular weight and/or in the shape of the reaction substrates. Several modifications of the original stopped-flow system have been made leading to a significant extension of its technical applications. One of these modifications allows the biophysical characterization of the water and solute permeability of biological and artificial membranes. Here, we describe a protocol of SFLS to measure the glycerol permeability of isolated human red blood cells (RBCs) and evaluate the pharmacokinetics properties (selectivity and potency) of isoform-specific inhibitors of AQP3, AQP7 and AQP9, three mammalian aquaglyceroporins allowing transport of glycerol across membranes. Suspensions of RBCs (1% hematocrit) are exposed to an inwardly directed gradient of 100 mM glycerol in a SFLS apparatus at 20 °C and the resulting changes in scattered light intensity are recorded at a monochromatic wavelength of 530 nm for 120 s. The SFLS apparatus is set up to have a dead time of 1.6-ms and 99% mixing efficiency in less than 1 ms. Data are fitted to a single exponential function and the related time constant (τ, seconds) of the cell-swelling phase of light scattering corresponding to the osmotic movement of water that accompanies the entry of glycerol into erythrocytes is measured. The coefficient of glycerol permeability ( P_gly , cm/s) of RBCs is calculated with the following equation: P_gly = 1/[(S/V)τ] where τ (s) is the fitted exponential time constant and S/V is the surface-to-volume ratio (cm^-1) of the analyzed RBC specimen. Pharmacokinetics of the isoform-specific inhibitors of AQP3, AQP7 and AQP9 are assessed by evaluating the extent of RBC P_gly values resulting after the exposure to serial concentrations of the blockers.

The study of isotopic enrichment of water in human plasma and erythrocyte

Life does not sustain without water. For water, there is a natural abundance of stable isotope hydrogen and oxygen. Water molecules get across cell membranes through a plasma membrane protein, named aquaporin. Moreover, the kidney is the main organ to maintain water homeostasis. Here, we study the stable isotopic ratios of hydrogen and oxygen in human blood plasma and erythrocyte corresponding to kidney functions. We extract waters from human plasma and erythrocyte, collected from 110 participants, including 51 clinically stable outpatients with end-stage renal disease (ESRD) and 59 subjects with normal renal function (NRF). We observed that (i) both extracellular (blood plasma) and intracellular (erythrocyte) biology waters are isotopic differences between the ESRD and NRF participants, (ii) the natural abundance of isotopic waters of ESRD is hypo-isotopic, and (iii) the isotopic enrichment of water between erythrocyte and blood plasma are distinct. In addition, we introduce an empirical formula using entropy transformation to describe isotopic water enrichment for biology. Accordingly, the natural abundance of stable isotope water of blood plasma and erythrocyte may be possibly put in practice a new sign for assessments of kidney dysfunctions.

In silico simulations of erythrocyte aquaporins with quantitative in vitro validation

Modelling water and membrane lipids is an essential element in the computational research of biophysical/biochemical processes such as water transport across the cell membrane. In this study, we examined the accuracies of two popular water models, TIP3P and TIP4P, in the molecular dynamics simulations of erythrocyte aquaporins (AQP1 and AQP3). We modelled the erythrocyte membrane as an asymmetric lipid bilayer with appropriate lipid compositions of its inner and outer leaflet, in comparison with a symmetric lipid bilayer of a single lipid type. We computed the AQP1/3 permeabilities with the transition state theory with full correction for recrossing events. We also conducted cell swelling assays for water transport across the erythrocyte membrane. The experimental results agree with the TIP3P water–erythrocyte membrane model, in confirmation of the expected accuracy of the erythrocyte membrane model, the TIP3P water model, and the CHARMM parameters for water–protein interactions.

Quantitatively predictive study of aquaporins in model erythrocyte membrane validated with cellular experiments.

Micropipette Aspiration-Based Assessment of Single Channel Water Permeability

Measurements of the unitary hydraulic conductivity of membrane channels, p_f , may be hampered by difficulties in producing sufficient quantities of purified and reconstituted proteins. Low yield expression, the purely empiric choice of detergents, as well as protein aggregation and misfolding during reconstitution may result in an average of less than one reconstituted channel per large unilamellar vesicle. This limits their applicability for p_f measurements, independent of whether light scattering or fluorescence quenching of encapsulated dyes is monitored. Here the micropipette aspiration technique is adopted because its superb sensitivity allows resolving p_f values for one order of magnitude smaller protein densities in sphingomyelin and cholesterol rich giant unilamellar vesicles (GUVs). Protein density is derived from intensity fluctuations that fluorescently labeled channels in the aspirated GUV induce by diffusing through the diffraction limited spot. A perfusion system minimizes unstirred layers in the immediate membrane vicinity as demonstrated by the distribution of both encapsulated and extravesicular aqueous dyes. p_f amounted to 2.4 ± 0.1 × 10^-13 cm³ s^-1 for aquaporin-1 that served as a test case. The new assay paves the way for directly monitoring the effect that interaction of aquaporins with other proteins or inhibitors may have on p_f on a single sample.

The Uropathogenic Specific Protein Gene usp from Escherichia coli and Salmonella bongori is a Novel Member of the TyrR and H-NS Regulons

The Escherichia coli PAIusp is a small pathogenicity island encoding usp, for the uropathogenic specific protein (Usp), a genotoxin and three associated downstream imu1-3 genes that protect the producer against its own toxin. Bioinformatic analysis revealed the presence of the PAIusp also in publically available Salmonella bongori and Salmonella enterica subps. salamae genome sequences. PAIusp is in all examined sequences integrated within the aroP-pdhR chromosomal intergenic region. The focus of this work was identification of the usp promoter and regulatory elements controlling its activity. We show that, in both E. coli and S. bongori, the divergent TyrR regulated P3 promoter of the aroP gene, encoding an aromatic amino acid membrane transporter, drives usp transcription while H-NS acts antagonistically repressing expression. Our results show that the horizontally acquired PAIusp has integrated into the TyrR regulatory network and that environmental factors such as aromatic amino acids, temperature and urea induce usp expression.

Peritoneal Function: The Role of Aquaporins

The aquaporins (AQPs) constitute a large family of water channels that play a part in transcellular water movement in many tissues. They are particularly abundant and important in the kidney and the lung. Derangement of AQP structure or function leads to a variety of water-balance disorders. Aquaporin-1 (AQP1) is constitutively expressed in the endothelial cells of the capillaries and venules that provide the ultrasmall pores predicted by the three-pore model of water movement during peritoneal dialysis. The ultrasmall pores are critical for ultrafiltration. In addition, AQP1 and AQP3 are constitutively expressed in peritoneal mesothelial cells. The expression of those AQPs is upregulated by hyperosmolality. Reduced expression or function of AQP1 may be responsible for some cases of ultrafiltration failure, but further evidence is required to establish that link.

Epigenetic Modifications May Regulate the Activation of the Hypopharyngeal Gland of Honeybees (Apis Mellifera) During Winter

DNA methylation is an epigenetic modification primarily responsible for individual phenotypic variation. This modification has been reported to play an important role in caste, brain plasticity, and body development in honeybees (Apis mellifera). Here, we report the DNA methylation profile of honeybee hypopharyngeal glands, from atrophy in winter to arousal in the following spring, through the use of whole-genome bisulfite sequencing. Consistent with previous studies in other Apis species, we found low methylation levels of the hypopharyngeal gland genome that were mostly of the CG type. Notably, we observed a strong preference for CpG methylation, which was localized in promoters and exon regions. This result further indicated that, in honeybees, DNA methylation may regulate gene expression by mediating alternative splicing, in addition to silencing gene in the promoter regions. After assessment by correlation analysis, we identified seven candidate proteins encoded by differentially methylated genes, including aristaless-related homeobox, forkhead box protein O, headcase, alpha-amylase, neural-cadherin, epidermal growth factor receptor, and aquaporin, which are reported to be involved in cell growth, proliferation, and differentiation. Hypomethylation followed by upregulated expression of these candidates suggested that DNA methylation may play significant roles in the activation of hypopharyngeal glands in overwintering honeybees. Overall, this study elucidates epigenetic modification differences in honeybee hypopharyngeal glands by comparing an inactive winter state to an aroused state in the following spring, which could provide further insight into the evolution of insect sociality and regulatory plasticity.

Single-chain heteropolymers transport protons selectively and rapidly

Precise protein sequencing and folding are believed to generate the structure and chemical diversity of natural channels^1,2, both of which are essential to synthetically achieve proton transport performance comparable to that seen in natural systems. Geometrically defined channels have been fabricated using peptides, DNAs, carbon nanotubes, sequence-defined polymers and organic frameworks^3-13. However, none of these channels rivals the performance observed in their natural counterparts. Here we show that without forming an atomically structured channel, four-monomer-based random heteropolymers (RHPs)¹⁴ can mimic membrane proteins and exhibit selective proton transport across lipid bilayers at a rate similar to those of natural proton channels. Statistical control over the monomer distribution in an RHP leads to segmental heterogeneity in hydrophobicity, which facilitates the insertion of single RHPs into the lipid bilayers. It also results in bilayer-spanning segments containing polar monomers that promote the formation of hydrogen-bonded chains^15,16 for proton transport. Our study demonstrates the importance of the adaptability that is enabled by statistical similarity among RHP chains and of the modularity provided by the chemical diversity of monomers, to achieve uniform behaviour in heterogeneous systems. Our results also validate statistical randomness as an unexplored approach to realize protein-like behaviour at the single-polymer-chain level in a predictable manner.

Prokaryotic Aquaporins

Aquaporins are integral membrane proteins that facilitate the diffusion of water and other small, uncharged solutes across the cellular membrane and are widely distributed in organisms from humans to bacteria. However, the characteristics of prokaryotic aquaporins remain largely unknown. We investigated the distribution and sequence characterization of aquaporins in prokaryotic organisms and summarized the transport characteristics, physiological functions, and regulatory mechanisms of prokaryotic aquaporins. Aquaporin homologues were identified in 3315 prokaryotic genomes retrieved from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, but the protein clustering pattern is not completely congruent with the phylogeny of the species that carry them. Moreover, prokaryotic aquaporins display diversified aromatic/arginine constriction region (ar/R) amino acid compositions, implying multiple functions. The typical water and glycerol transport characterization, physiological functions, and regulations have been extensively studied in Escherichia coli AqpZ and GlpF. A Streptococcus aquaporin has recently been verified to facilitate the efflux of endogenous H₂O₂, which not only contributes to detoxification but also to species competitiveness, improving our understanding of prokaryotic aquaporins. Furthermore, recent studies revealed novel regulatory mechanisms of prokaryotic aquaporins at post-translational level. Thus, we propose that intensive investigation on prokaryotic aquaporins would extend the functional categories and working mechanisms of these ubiquitous, intrinsic membrane proteins.

Higher Expression Levels of Aquaporin Family of Proteins in the Kidneys of Arid-Desert Living Lepus yarkandensis

Lepus yarkandensis specifically lives in arid climate with rare precipitation of Tarim Basin in western China. Aquaporins (AQPs) are a family of channel proteins that facilitate water transportation across cell membranes. Kidney AQPs play vital roles in renal tubule water permeability and maintenance of body water homeostasis. This study aimed to investigate whether kidney AQPs exhibit higher expression in arid-desert living animals. Immunohistochemistry results revealed localization of AQP1 to the capillary endothelial cells in glomerulus and epithelial cells in proximal tubule and descending thin limbs, AQP2 to the apical plasma membrane of principal cells in the cortical collecting duct (CCD), outer medullary collecting duct (OMCD), and IMCD cells in the initial inner medullary collecting duct (IMCD1) and middle IMCD (IMCD2), and AQP3 and AQP4 to the basolateral plasma membrane of principal cells and IMCD cells in CCD, OMCD, IMCD1, and IMCD2 in L. yarkandensis kidneys. Quantitative real-time PCR analysis showed higher mRNA levels of AQP1, AQP2, AQP3, and AQP4 in L. yarkandensis kidneys compared with Oryctolagus cuniculus. Similar results were obtained by western blotting. Our results suggested that higher expression levels of AQP1, AQP2, AQP3, and AQP4 in L. yarkandensis kidneys favored for drawing more water from the tubular fluid.

Modeling water purification by an aquaporin-inspired graphene-based nano-channel

Understanding the mechanism of water and particle transport through thin-film membranes is essential to improve the water permeability and the salt rejection rate of the purification progress. In this research, mimicking from the structure and operation of the aquaporin channel, graphene-based nano-channels were designed to be used as a water filter. The effects of variation of the channel's main elements, such as the width of the bottleneck and charges attached to the channel on its efficiency, were investigated via molecular dynamics simulations. We observe that the water flow through the channel decreases by increasing the charge, while the ion rejection rate of the channel is enhanced. Moreover, we find that the geometry and shape of the bottleneck part of the channel can affect the channel water flow and its selectivity. Finally, the pressure and the flow velocity in the channel were considered by using finite element models, and the results indicate that they are high at the entrance of the channel. The outcomes of this study can be used to improve the molecular knowledge of water desalination, which might be helpful in designing more efficient membranes. Graphical abstract As the piston pushed the solution to pass through the nano-channel, positive and negative ions are remained in the first box, by sensing electric field generated from the attached charges to the bottleneck part of the channel. Atomistic structure of channel is shown in the right part of the figure and the generated electric field is shown in the left part of the figure.