Single-file transport of water through membrane channels

Water will Find Its Way: Transport through Narrow Tunnels in Hydrolases

An aqueous environment is vital for life as we know it, and water is essential for nearly all biochemical processes at the molecular level. Proteins utilize water molecules in various ways. Consequently, proteins must transport water molecules across their internal network of tunnels to reach the desired action sites, either within them or by functioning as molecular pipes to control cellular osmotic pressure. Despite water playing a crucial role in enzymatic activity and stability, its transport has been largely overlooked, with studies primarily focusing on water transport across membrane proteins. The transport of molecules through a protein's tunnel network is challenging to study experimentally, making molecular dynamics simulations the most popular approach for investigating such events. In this study, we focused on the transport of water molecules across three different α/β-hydrolases: haloalkane dehalogenase, epoxide hydrolase, and lipase. Using a 5 μs adaptive simulation per system, we observed that only a few tunnels were responsible for the majority of water transport in dehalogenase, in contrast to a higher diversity of tunnels in other enzymes. Interestingly, water molecules could traverse narrow tunnels with subangstrom bottlenecks, which is surprising given the commonly accepted water molecule radius of 1.4 Å. Our analysis of the transport events in such narrow tunnels revealed a markedly increased number of hydrogen bonds formed between the water molecules and protein, likely compensating for the steric penalty of the process. Overall, these commonly disregarded narrow tunnels accounted for ∼20% of the total water transport observed, emphasizing the need to surpass the standard geometrical limits on the functional tunnels to properly account for the relevant transport processes. Finally, we demonstrated how the obtained insights could be applied to explain the differences in a mutant of the human soluble epoxide hydrolase associated with a higher incidence of ischemic stroke.

A hard sphere model for single-file water transport across biological membranes

We use Gürsey's statistical mechanics of a one-dimensional fluid to find a formula for theP f / P d ratio in the transport of hard spheres across a membrane through a narrow channel that can accommodate molecular movement only in single file. P f is the membrane permeability for osmotic flow and P d the permeability for exchange across the membrane in the absence of osmotic flow. The deviation of the ratio from unity indicates the degree of cooperative transport relative to ordinary diffusion of independent molecules. In contrast to an early idea thatP f / P d must be equal to the number of molecules in the channel, regardless of the physical nature of the interactions among the molecules, we find a functional dependence on the fractional occupancy of the length of the channel by the hard spheres. We also attempt a random walk calculation for P d individually, which gives a result for P f as well when combined with the ratio.

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.

Equation of state of hard-disk fluids under single-file confinement

The exact transfer-matrix solution for the longitudinal equilibrium properties of the single-file hard-disk fluid is used to study the limiting low- and high-pressure behaviors analytically as functions of the pore width. In the low-pressure regime, the exact third and fourth virial coefficients are obtained, which involve single and double integrals, respectively. Moreover, we show that the standard irreducible diagrams do not provide a complete account of the virial coefficients in confined geometries. The asymptotic equation of state in the high-pressure limit is seen to present a simple pole at the close-packing linear density, as in the hard-rod fluid, but, in contrast to the latter case, the residue is 2. Since, for an arbitrary pressure, the exact transfer-matrix treatment requires the numerical solution of an eigenvalue integral equation, we propose here two simple approximations to the equation of state, with different complexity levels, and carry out an extensive assessment of their validity and practical convenience vs the exact solution and available computer simulations.

Trapped Pore Waters in the Open Proton Channel HV 1

The voltage-gated proton channel, H_V 1, is crucial for innate immune responses. According to alternative hypotheses, protons either hop on top of an uninterrupted water wire or bypass titratable amino acids, interrupting the water wire halfway across the membrane. To distinguish between both hypotheses, the water mobility for the putative case of an uninterrupted wire is estimated. The predicted single-channel water permeability 2.3 × 10^-12 cm³ s^-1 reflects the permeability-governing number of hydrogen bonds between water molecules in single-file configuration and pore residues. However, the measured unitary water permeability does not confirm the predicted value. Osmotic deflation of reconstituted lipid vesicles reveals negligible water permeability of the H_V 1 wild-type channel and the D174A mutant open at 0 mV. The conductance of 1400 H⁺ s^-1 per wild-type channel agrees with the calculated diffusion limit for a ≈2 Å capture radius for protons. Removal of a charged amino acid (D174) at the pore mouth decreases H⁺ conductance by reducing the capture radius. At least one intervening amino acid contributes to H⁺ conductance while interrupting the water wire across the membrane.

Tutorial for Stopped-Flow Water Flux Measurements: Why a Report about “Ultrafast Water Permeation through Nanochannels with a Densely Fluorous Interior Surface” Is Flawed

Millions of years of evolution have produced proteinaceous water channels (aquaporins) that combine perfect selectivity with a transport rate at the edge of the diffusion limit. However, Itoh et al. recently claimed in Science that artificial channels are 100 times faster and almost as selective. The published deflation kinetics of vesicles containing channels or channel elements indicate otherwise, since they do not demonstrate the facilitation of water transport. In an illustrated tutorial on the experimental basis of stopped-flow measurements, we point out flaws in data processing. In contrast to the assumption voiced in Science, individual vesicles cannot simultaneously shrink with two different kinetics. Moreover, vesicle deflation within the dead time of the instrument cannot be detected. Since flawed reports of ultrafast water channels in Science are not a one-hit-wonder as evidenced by a 2018 commentary by Horner and Pohl in Science, we further discuss the achievable limits of single-channel water permeability. After analyzing (i) diffusion limits for permeation through narrow channels and (ii) hydrodynamics in the surrounding reservoirs, we conclude that it is unlikely to fundamentally exceed the evolutionarily optimized water-channeling performance of the fastest aquaporins while maintaining near-perfect selectivity.

Arginine transportation mechanism through cationic amino acid transporter 1: insights from molecular dynamics studies

Metabolic and signaling mechanisms in mammalian cells are facilitated by the transportation of L-arginine (Arg) across the plasma membrane through cationic amino acid transporter (CAT) proteins. Due to a lack of argininosuccinate synthase (ASS) activity in various tumor cells such as acute myeloid leukemia, acute lymphocytic leukemia, and chronic lymphocytic leukemia, these tumor entities are arginine-auxotrophic and therefore depend on the uptake of the amino acid arginine. Cationic amino acid transporter-1 (CAT-1) is the leading arginine importer expressed in the aforementioned tumor entities. Hence, in the present study, to investigate the transportation mechanism of arginine in CAT-1, we performed molecular dynamics (MD) simulation methods on the modeled human CAT-1. The MM-PBSA approach was conducted to determine the critical residues interacting with arginine within the corresponding binding site of CAT-1. In addition, we found out that the water molecules have the leading role in forming the transportation channel within CAT-1. The conductive structure of CAT-1 was formed only when the water molecules were continuously distributed across the channel. Steered molecular dynamics (SMD) simulation approach showed various energy barriers against arginine transportation through CAT-1, especially while crossing the bottlenecks of the related channel. These findings at the molecular level might shed light on identifying the crucial amino acids in the binding of arginine to eukaryotic CATs and also provide fundamental insights into the arginine transportation mechanisms through CAT-1. Understanding the transportation mechanism of arginine is essential to developing CAT-1 blockers, which can be potential medications for some types of cancers.Communicated by Ramaswamy H. Sarma.

Honey, I shrunk the extracellular space: Measurements and mechanisms of astrocyte swelling

Astrocyte volume fluctuation is a physiological phenomenon tied closely to the activation of neural circuits. Identification of underlying mechanisms has been challenging due in part to use of a wide range of experimental approaches that vary between research groups. Here, we first review the many methods that have been used to measure astrocyte volume changes directly or indirectly. While the field has recently shifted towards volume analysis using fluorescence microscopy to record cell volume changes directly, established metrics corresponding to extracellular space dynamics have also yielded valuable insights. We then turn to analysis of mechanisms of astrocyte swelling derived from many studies, with a focus on volume changes tied to increases in extracellular potassium concentration ([K+ ]o ). The diverse methods that have been utilized to generate the external [K+ ]o environment highlight multiple scenarios of astrocyte swelling mediated by different mechanisms. Classical potassium buffering theories are tempered by many recent studies that point to different swelling pathways optimized at particular [K+ ]o and that depend on local/transient versus more sustained increases in [K+ ]o .

Solitons in Overdamped Brownian Dynamics

Solitons are commonly known as waves that propagate without dispersion. Here, we show that they can occur for driven overdamped Brownian dynamics of hard spheres in periodic potentials at high densities. The solitons manifest themselves as periodic sequences of different assemblies of particles moving in the limit of zero noise, where transport of single particles is not possible. They give rise to particle currents at even low temperature that appear in bandlike structures around certain hard-sphere diameters. At high temperatures, the bandlike structures are washed out by the noise, but the particle transport is still dominated by the solitons. All these predicted features should occur in a broad class of periodic systems and are amenable to experimental tests.

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.

Molecular-Level Control over Ionic Conduction and Ionic Current Direction by Designing Macrocycle-Based Ionomers

Poor ionic conductivity of the catalyst-binding, sub-micrometer-thick ionomer layers in energy conversion and storage devices is a huge challenge. However, ionomers are rarely designed keeping in mind the specific issues associated with nanoconfinement. Here, we designed nature-inspired ionomers (calix-2) having hollow, macrocyclic, calix[4]arene-based repeat units with precise, sub-nanometer diameter. In ≤100 nm-thick films, the in-plane proton conductivity of calix-2 was up to 8 times higher than the current benchmark ionomer Nafion at 85% relative humidity (RH), while it was 1-2 orders of magnitude higher than Nafion at 20-25% RH. Confocal laser scanning microscopy and other synthetic techniques allowed us to demonstrate the role of macrocyclic cavities in boosting the proton conductivity. The systematic self-assembly of calix-2 chains into ellipsoids in thin films was evidenced from atomic force microscopy and grazing incidence small-angle X-ray scattering measurements. Moreover, the likelihood of alignment and stacking of macrocyclic units, the presence of one-dimensional water wires across this macrocycle stacks, and thus the formation of long-range proton conduction pathways were suggested by atomistic simulations. We not only did see an unprecedented improvement in thin-film proton conductivity but also saw an improvement in proton conductivity of bulk membranes when calix-2 was added to the Nafion matrices. Nafion-calix-2 composite membranes also took advantage of the asymmetric charge distribution across calix[4]arene repeat units collectively and exhibited voltage-gating behavior. The inclusion of molecular macrocyclic cavities into the ionomer chemical structure can thus emerge as a promising design concept for highly efficient ion-conducting and ion-permselective materials for sustainable energy applications.

The role of water coordination in the pH-dependent gating of hAQP10

Human aquaporin 10 (hAQP10) is an aquaglyceroporin that assists in maintaining glycerol flux in adipocytes during lipolysis at low pH. Hence, a molecular understanding of the pH-sensitive glycerol conductance may open up for drug development in obesity and metabolically related disorders. Control of hAQP10-mediated glycerol flux has been linked to the cytoplasmic end of the channel, where a unique loop is regulated by the protonation status of histidine 80 (H80). Here, we performed unbiased molecular dynamics simulations of three protonation states of H80 to unravel channel gating. Strikingly, at neutral pH, we identified a water coordination pattern with an inverted orientation of the water molecules in vicinity of the loop. Protonation of H80 results in a more hydrophobic loop conformation, causing loss of water coordination and leaving the pore often dehydrated. Our results indicate that the loss of such water interaction network may be integral for the destabilization of the loop in the closed configuration at low pH. Additionally, a residue unique to hAQP10 (F85) reveals structural importance by flipping into the channel in correlation with loop movements, indicating a loop-stabilizing role in the closed configuration. Taken together, our simulations suggest a unique gating mechanism combining complex interaction networks between water molecules and protein residues at the loop interface. Considering the role of hAQP10 in adipocytes, the detailed molecular insights of pH-regulation presented here will help to understand glycerol pathways in these cells and may assist in drug discovery for better management of human adiposity and obesity.

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.

Experimental and conceptual approaches to root water transport

BACKGROUND

Root water transport, which critically contributes to the plant water status and thereby plant productivity, has been the object of extensive experimental and theoretical studies. However, root systems represent an intricate assembly of cells in complex architectures, including many tissues at distinct developmental stages. Our comprehension of where and how molecular actors integrate their function in order to provide the root with its hydraulic properties is therefore still limited.

SCOPE

Based on current literature and prospective discussions, this review addresses how root water transport can be experimentally measured, what is known about the underlying molecular actors, and how elementary water transport processes are scaled up in numerical/mathematical models.

CONCLUSIONS

The theoretical framework and experimental procedures on root water transport that are in use today have been established a few decades ago. However, recent years have seen the appearance of new techniques and models with enhanced resolution, down to a portion of root or to the tissue level. These advances pave the way for a better comprehension of the dynamics of water uptake by roots in the soil.

Prolonged Association between Water Molecules under Hydrophobic Nanoconfinement

We present an investigation of the dynamics of water confined among rigid carbon rods and between parallel graphene sheets with molecular dynamics simulations. Diffusion coefficients, activation energy of diffusion, and residence-time correlation functions as a function of confinement geometry reveal a retardation of water dynamics under hydrophobic confinement compared to bulk water. In fact, water under various confinements possesses longer associations with its neighbors and exhibits diffusion dynamics characteristic of a lower temperature. Analysis of the residence-time correlation functions reveals long and short residence times, which we relate to the diffusion coefficient and activation energy of diffusion, respectively. Additional investigations reveal how the level of confining surface hydrophobicity affects water dynamics, further broadening our understanding of water diffusion inside diverse media. Overall, this study sheds light on the physical origin of retarded water dynamics under hydrophobic confinement and the close relationship between residence times and diffusion behavior.

Scattering versus fluorescence self-quenching: more than a question of faith for the quantification of water flux in large unilamellar vesicles?

The endeavors to understand the determinants of water permeation through membrane channels, the effect of the lipid or polymer membrane on channel function, the development of specific water flow inhibitors, the design of artificial water channels and aquaporins for the use in industrial water filtration applications all rely on accurate ways to quantify water permeabilities (P f). A commonly used method is to reconstitute membrane channels into large unilamellar vesicles (LUVs) and to subject these vesicles to an osmotic gradient in a stopped-flow device. Fast recordings of either scattered light intensity or fluorescence self-quenching signals are taken as a readout for vesicle volume change, which in turn can be recalculated to accurate P f values. By means of computational and experimental data, we discuss the pros and cons of using scattering versus self-quenching experiments or subjecting vesicles to hypo- or hyperosmotic conditions. In addition, we explicate for the first time the influence of the LUVs size distribution, channel distribution between vesicles and remaining detergent after protein reconstitution on P f values. We point out that results such as the single channel water permeability (p f) depend on the membrane matrix or on the direction of the applied osmotic gradient may be direct results of the measurement and analysis procedure.

Lipid II Binding and Transmembrane Properties of Various Antimicrobial Lanthipeptides

There has been an alarming rise in antibacterial resistant infections in recent years due to the widespread use of antibiotics, and there is a dire need for the development of new antibiotics utilizing novel modes of action. Lantibiotics are promising candidates to engage in the fight against resistant strains of bacteria due to their unique modes of action, including interference with cell wall synthesis by binding to lipid II and creating pores in bacterial membranes. In this study, we use atomic-scale molecular dynamics computational studies to compare both the lipid II binding ability and the membrane interactions of five lanthipeptides that are commonly used in antimicrobial research: nisin, Mutacin 1140 (MU1140), gallidermin, NVB302, and NAI107. Among the five peptides investigated, nisin is found to be the most efficient at forming water channels through a membrane, whereas gallidermin and MU1140 are found to be better at binding the lipid II molecules. Nisin's effectiveness in facilitating water transport across the membrane is due to the creation of several different water trajectories along with no significant water delay points along the paths. The shorter peptide deoxyactagardine B (NVB302) was found to not form a water channel. These detailed observations provide insights into the dual mechanisms of the action of lantibiotic peptides and can facilitate the design and development of novel lanthipeptides by strategic placement of different residues.

An update on passive transport in and out of plant cells

Transport across membranes is critical for plant survival. Membranes are the interfaces at which plants interact with their environment. The transmission of energy and molecules into cells provides plants with the source material and power to grow, develop, defend, and move. An appreciation of the physical forces that drive transport processes is thus important for understanding the plant growth and development. We focus on the passive transport of molecules, describing the fundamental concepts and demonstrating how different levels of abstraction can lead to different interpretations of the driving forces. We summarize recent developments on quantitative frameworks for describing diffusive and bulk flow transport processes in and out of cells, with a more detailed focus on plasmodesmata, and outline open questions and challenges.

Biophysical Reviews' "Meet the Councilor Series"-a profile of Peter Pohl

It is my pleasure to write a few words to introduce myself to the readers of Biophysical Reviews as part of the "Meet the Councilor Series." Currently, I am serving the second period as IUPAB councilor after having been elected first in 2017. Initially, I studied Biophysics in Moscow (Russia) and later Medicine in Halle (Germany). My scientific carrier took me from the Medical School of the Martin Luther University of Halle-Wittenberg, via the Leibniz Institute for Molecular Pharmacology (Berlin) and the Institute for Biology at the Humboldt University (Berlin) to the Physics Department of the Johannes Kepler University in Linz (Austria). My key research interests lie in the molecular mechanisms of transport phenomena occurring at the lipid membrane, including (i) spontaneous and facilitated transport of water and other small molecules across membranes in reconstituted systems, (ii) proton migration along the membrane surface, (iii) protein translocation, and (iv) bilayer mechanics. Training of undergraduate, graduate, and postdoctoral researchers from diverse academic disciplines has been-and shall remain-a consistent part of my work.

Non-Fickian single-file pore transport

Single-file diffusion exhibits anomalously slow collective transport when particles are able to immobilize by binding and unbinding to the one-dimensional channel within which the particles diffuse. We have explored this system for short porelike channels using a symmetric exclusion process with fully stochastic dynamics. We find that for shorter channels, a non-Fickian regime emerges for slow binding kinetics. In this regime the average flux 〈Φ〉∼1/L^{3}, where L is the channel length in units of the particle size. We find that a two-state model describes this behavior well for sufficiently slow binding rates, where the binding rates determine the switching time between high-flux bursts of directed transport and low-flux leaky states. Each high-flux burst is Fickian with 〈Φ〉∼1/L. Longer systems are more often in a low-flux state, leading to the non-Fickian behavior.

Exploring cell membrane water exchange in aquaporin-4-deficient ischemic mouse brain using diffusion-weighted MRI

BACKGROUND

Aquaporin-4 is a membrane channel protein that is highly expressed in brain astrocytes and facilitates the transport of water molecules. It has been suggested that suppression of aquaporin-4 function may be an effective treatment for reducing cellular edema after cerebral infarction. It is therefore important to develop clinically applicable measurement systems to evaluate and better understand the effects of aquaporin-4 suppression on the living body.

METHODS

Animal models of focal cerebral ischemia were created by surgically occluding the middle cerebral artery of wild-type and aquaporin-4 knockout mice, after which multi-b-value multi-diffusion-time diffusion-weighted imaging measurements were performed. Data were analyzed with both the apparent diffusion coefficient (ADC) model and a compartmental water-exchange model.

RESULTS

ADCs were estimated for five different b value ranges. The ADC of aquaporin-4 knockout mice in the contralateral region was significantly higher than that of wild-type mice for each range. In contrast, aquaporin-4 knockout mice had significantly lower ADC than wild-type mice in ischemic tissue for each b-value range. Genotype-dependent differences in the ADC were particularly significant for the lowest ranges in normal tissue and for the highest ranges in ischemic tissue. The ADCs measured at different diffusion times were significantly different for both genotypes. Fitting of the water-exchange model to the ischemic region data found that the water-exchange time in aquaporin-4 knockout mice was approximately 2.5 times longer than that in wild-type mice.

CONCLUSIONS

Multi-b-value multi-diffusion-time diffusion-weighted imaging may be useful for in vivo research and clinical diagnosis of aquaporin-4-related diseases.

Molecular dynamics simulations reveal statistics and microscopic mechanisms of water permeation in membrane-embedded artificial water channel nanoconstructs

Understanding water transport mechanisms at the nanoscale level remains a challenge for theoretical chemical physics. Major advances in chemical synthesis have allowed us to discover new artificial water channels, rivaling with or even surpassing water conductance and selectivity of natural protein channels. In order to interpret experimental features and understand microscopic determinants for performance improvements, numerical approaches based on all-atom molecular dynamics simulations and enhanced sampling methods have been proposed. In this study, we quantify the influence of microscopic observables, such as channel radius and hydrogen bond connectivity, and of meso-scale features, such as the size of self-assembly blocks, on the permeation rate of a self-assembled nanocrystal-like artificial water channel. Although the absolute permeation rate extrapolated from these simulations is overestimated by one order of magnitude compared to the experimental measurement, the detailed analysis of several observed conductive patterns in large assemblies opens new pathways to scalable membranes with enhanced water conductance for the future design.

Adaptable and Multifunctional Ion-Conducting Aquaporins

Aquaporins function as water and neutral solute channels, signaling hubs, disease virulence factors, and metabolon components. We consider plant aquaporins that transport ions compared to some animal counterparts. These are candidates for important, as yet unidentified, cation and anion channels in plasma, tonoplast, and symbiotic membranes. For those individual isoforms that transport ions, water, and gases, the permeability spans 12 orders of magnitude. This requires tight regulation of selectivity via protein interactions and posttranslational modifications. A phosphorylation-dependent switch between ion and water permeation in AtPIP2;1 might be explained by coupling between the gates of the four monomer water channels and the central pore of the tetramer. We consider the potential for coupling between ion and water fluxes that could form the basis of an electroosmotic transducer. A grand challenge in understanding the roles of ion transporting aquaporins is their multifunctional modes that are dependent on location, stress, time, and development.

Characterizing the Water Wire in the Gramicidin Channel Found by Monte Carlo Sampling Using Continuum Electrostatics and in Molecular Dynamics Trajectories with Conventional or Polarizable Force Fields

Water molecules play a key role in all biochemical processes. They help define the shape of proteins, and they are reactant or product in many reactions and are released as ligands are bound. They facilitate the transfer of protons through transmembrane proton channel, pump and transporter proteins. Continuum electrostatics (CE) force fields used by program Multiconformation CE (MCCE) capture electrostatic interactions in biomolecules with an implicit solvent, which captures the averaged solvent water equilibrium properties. Hybrid CE methods can use explicit water molecules within the protein surrounded by implicit solvent. These hybrid methods permit the study of explicit hydrogen bond networks within the protein and allow analysis of processes such as proton transfer reactions. Yet hybrid CE methods have not been rigorously tested. Here, we present an explicit treatment of water molecules in the Gramicidin A (gA) channel using MCCE and compare the resulting distributions of water molecules and key hydration features against those obtained with explicit solvent Molecular Dynamics (MD) simulations with the nonpolarizable CHARMM36 and polarizable Drude force fields. CHARMM36 leads to an aligned water wire in the channel characterized by a large absolute net water dipole moment; the MCCE and Drude analysis lead to a small net dipole moment as the water molecules change orientation within the channel. The correct orientation is not as yet known, so these calculations identify an open question.

Native-like membrane models of E. coli polar lipid extract shed light on the importance of lipid composition complexity

BACKGROUND

Lipid-protein interactions stabilize protein oligomers, shape their structure, and modulate their function. Whereas in vitro experiments already account for the functional importance of lipids by using natural lipid extracts, in silico methods lack behind by embedding proteins in single component lipid bilayers. However, to accurately complement in vitro experiments with molecular details at very high spatio-temporal resolution, molecular dynamics simulations have to be performed in natural(-like) lipid environments.

RESULTS

To enable more accurate MD simulations, we have prepared four membrane models of E. coli polar lipid extract, a typical model organism, each at all-atom (CHARMM36) and coarse-grained (Martini3) representations. These models contain all main lipid headgroup types of the E. coli inner membrane, i.e., phosphatidylethanolamines, phosphatidylglycerols, and cardiolipins, symmetrically distributed between the membrane leaflets. The lipid tail (un)saturation and propanylation stereochemistry represent the bacterial lipid tail composition of E. coli grown at 37∘C until 3/4 of the log growth phase. The comparison of the Simple three lipid component models to the complex 14-lipid component model Avanti over a broad range of physiologically relevant temperatures revealed that the balance of lipid tail unsaturation and propanylation in different positions and inclusion of lipid tails of various length maintain realistic values for lipid mobility, membrane area compressibility, lipid ordering, lipid volume and area, and the bilayer thickness. The only Simple model that was able to satisfactory reproduce most of the structural properties of the complex Avanti model showed worse agreement of the activation energy of basal water permeation with the here performed measurements. The Martini3 models reflect extremely well both experimental and atomistic behavior of the E. coli polar lipid extract membranes. Aquaporin-1 embedded in our native(-like) membranes causes partial lipid ordering and membrane thinning in its vicinity. Moreover, aquaporin-1 attracts and temporarily binds negatively charged lipids, mainly cardiolipins, with a distinct cardiolipin binding site in the crevice at the contact site between two monomers, most probably stabilizing the tetrameric protein assembly.

CONCLUSIONS

The here prepared and validated membrane models of E. coli polar lipids extract revealed that lipid tail complexity, in terms of double bond and cyclopropane location and varying lipid tail length, is key to stabilize membrane properties over a broad temperature range. In addition, they build a solid basis for manifold future simulation studies on more realistic lipid membranes bridging the gap between simulations and experiments.

Water in Nanopores and Biological Channels: A Molecular Simulation Perspective

This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.

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.

Aquaporin-like water transport in nanoporous crystalline layered carbon nitride

Designing next-generation fuel cell and filtration devices requires the development of nanoporous materials that allow rapid and reversible uptake and directed transport of water molecules. Here, we combine neutron spectroscopy and first-principles calculations to demonstrate rapid transport of molecular H2O through nanometer-sized voids ordered within the layers of crystalline carbon nitride with a polytriazine imide structure. The transport mechanism involves a sequence of molecular orientation reversals directed by hydrogen-bonding interactions as the neutral molecules traverse the interlayer gap and pass through the intralayer voids that show similarities with the transport of water through transmembrane aquaporin channels in biological systems. The results suggest that nanoporous layered carbon nitrides can be useful for developing high-performance membranes.

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.

Functional stability of water wire-carbonyl interactions in an ion channel

Despite the well-characterized structural symmetry of the dimeric transmembrane antibiotic gramicidin A, we show that the symmetry is broken by selective hydrogen bonding between eight waters comprising a transmembrane water wire and a specific subset of the 26 pore-lining carbonyl oxygens of the gramicidin A channel. The ¹⁷O NMR spectroscopic resolution of the carbonyl resonances from the two subunits required the use of a world record high field magnet (35.2 T; 1,500 MHz for ¹H). Uniquely, this result documented the millisecond timescale stability of the water wire orientation within the gramicidin A pore that had been reported to have only subnanosecond stability. These ¹⁷O spectroscopic results portend wide applications in molecular biophysics and beyond.

Water wires are critical for the functioning of many membrane proteins, as in channels that conduct water, protons, and other ions. Here, in liquid crystalline lipid bilayers under symmetric environmental conditions, the selective hydrogen bonding interactions between eight waters comprising a water wire and a subset of 26 carbonyl oxygens lining the antiparallel dimeric gramicidin A channel are characterized by ¹⁷O NMR spectroscopy at 35.2 T (or 1,500 MHz for ¹H) and computational studies. While backbone ¹⁵N spectra clearly indicate structural symmetry between the two subunits, single site ¹⁷O labels of the pore-lining carbonyls report two resonances, implying a break in dimer symmetry caused by the selective interactions with the water wire. The ¹⁷O shifts document selective water hydrogen bonding with carbonyl oxygens that are stable on the millisecond timescale. Such interactions are supported by density functional theory calculations on snapshots taken from molecular dynamics simulations. Water hydrogen bonding in the pore is restricted to just three simultaneous interactions, unlike bulk water environs. The stability of the water wire orientation and its electric dipole leads to opposite charge-dipole interactions for K⁺ ions bound at the two ends of the pore, thereby providing a simple explanation for an ∼20-fold difference in K⁺ affinity between two binding sites that are ∼24 Å apart. The ¹⁷O NMR spectroscopy reported here represents a breakthrough in high field NMR technology that will have applications throughout molecular biophysics, because of the acute sensitivity of the ¹⁷O nucleus to its chemical environment.

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.

Artificial water channels enable fast and selective water permeation through water-wire networks

Artificial water channels are synthetic molecules that aim to mimic the structural and functional features of biological water channels (aquaporins). Here we report on a cluster-forming organic nanoarchitecture, peptide-appended hybrid[4]arene (PAH[4]), as a new class of artificial water channels. Fluorescence experiments and simulations demonstrated that PAH[4]s can form, through lateral diffusion, clusters in lipid membranes that provide synergistic membrane-spanning paths for a rapid and selective water permeation through water-wire networks. Quantitative transport studies revealed that PAH[4]s can transport >109 water molecules per second per molecule, which is comparable to aquaporin water channels. The performance of these channels exceeds the upper bound limit of current desalination membranes by a factor of ~104, as illustrated by the water/NaCl permeability-selectivity trade-off curve. PAH[4]'s unique properties of a high water/solute permselectivity via cooperative water-wire formation could usher in an alternative design paradigm for permeable membrane materials in separations, energy production and barrier applications.

Strong Electroosmotic Coupling Dominates Ion Conductance of 1.5 nm Diameter Carbon Nanotube Porins

Extreme confinement in nanometer-sized channels can alter fluid and ion transport in significant ways, leading to significant water flow enhancement and unusual ion correlation effects. These effects are especially pronounced in carbon nanotube porins (CNTPs) that combine strong confinement in the inner lumen of carbon nanotubes with the high slip flow enhancement due to smooth hydrophobic pore walls. We have studied ion transport and ion selectivity in 1.5 nm diameter CNTPs embedded in lipid membranes using a single nanopore measurement setup. Our data show that CNTPs are weakly cation selective at pH 7.5 and become nonselective at pH 3.0. Ion conductance of CNTPs exhibits an unusual 2/3 power law scaling with the ion concentration at both neutral and acidic pH values. Coupled Navier-Stokes and Poisson-Nernst-Planck simulations and atomistic molecular dynamics simulations reveal that this scaling originates from strong coupling between water and ion transport in these channels. These effects could result in development of a next generation of biomimetic membranes and carbon nanotube-based electroosmotic pumps.

PRDM9 forms a trimer by interactions within the zinc finger array

PRDM9 forms a trimer as a soluble protein and in complex with DNA mediated by the ZnF domain. Five ZnFs are already sufficient for multimerization and only one DNA molecule is complexed in the trimer.

PRDM9 is a trans-acting factor directing meiotic recombination to specific DNA-binding sites by its zinc finger (ZnF) array. It was suggested that PRDM9 is a multimer; however, we do not know the stoichiometry or the components inducing PRDM9 multimerization. In this work, we used in vitro binding studies and characterized with electrophoretic mobility shift assays, mass spectrometry, and fluorescence correlation spectroscopy the stoichiometry of the PRDM9 multimer of two different murine PRDM9 alleles carrying different tags and domains produced with different expression systems. Based on the migration distance of the PRDM9–DNA complex, we show that PRDM9 forms a trimer. Moreover, this stoichiometry is adapted already by the free, soluble protein with little exchange between protein monomers. The variable ZnF array of PRDM9 is sufficient for multimerization, and at least five ZnFs form already a functional trimer. Finally, we also show that only one ZnF array within the PRDM9 oligomer binds to the DNA, whereas the remaining two ZnF arrays likely maintain the trimer by ZnF–ZnF interactions.

Experimental and Simulation Studies of Aquaporin 0 Water Permeability and Regulation

We begin with the history of aquaporin zero (AQP0), the most prevalent membrane protein in the eye lens, from the early days when AQP0 was a protein of unknown function known as Major Intrinsic Protein 26. We progress through its joining the aquaporin family as a water channel in its own right and discuss how regulation of its water permeability by pH and calcium came to be discovered experimentally and linked to lens homeostasis and development. We review the development of molecular dynamics (MD) simulations of lipid bilayers and membrane proteins, including aquaporins, with an emphasis on simulation studies that have elucidated the mechanisms of water conduction, selectivity, and proton exclusion by aquaporins in general. We also review experimental and theoretical progress toward understanding why mammalian AQP0 has a lower water permeability than other aquaporins and the evolution of our present understanding of how its water permeability is regulated by pH and calcium. Finally, we discuss how MD simulations have elucidated the nature of lipid interactions with AQP0.

Intrinsic Membrane Permeability to Small Molecules

Spontaneous solute and solvent permeation through membranes is of vital importance to human life, be it gas exchange in red blood cells, metabolite excretion, drug/toxin uptake, or water homeostasis. Knowledge of the underlying molecular mechanisms is the sine qua non of every functional assignment to membrane transporters. The basis of our current solubility diffusion model was laid by Meyer and Overton. It correlates the solubility of a substance in an organic phase with its membrane permeability. Since then, a wide range of studies challenging this rule have appeared. Commonly, the discrepancies have their origin in ill-used measurement approaches, as we demonstrate on the example of membrane CO₂ transport. On the basis of the insight that scanning electrochemical microscopy offered into solute concentration distributions in immediate membrane vicinity of planar membranes, we analyzed the interplay between chemical reactions and diffusion for solvent transport, weak acid permeation, and enzymatic reactions adjacent to membranes. We conclude that buffer reactions must also be considered in spectroscopic investigations of weak acid transport in vesicular suspensions. The evaluation of energetic contributions to membrane translocation of charged species demonstrates the compatibility of the resulting membrane current with the solubility diffusion model. A local partition coefficient that depends on membrane penetration depth governs spontaneous membrane translocation of both charged and uncharged molecules. It is determined not only by the solubility in an organic phase but also by other factors like cholesterol concentration and intrinsic electric membrane potentials.

Cosolvent Impurities in SWCNT Nanochannel Confinement: Length Dependence of Water Dynamics Investigated with Atomistic Simulations

The advent of nanotechnology has seen a growing interest in the nature of fluid flow and transport under nanoconfinement. The present study leverages fully atomistic molecular dynamics (MD) simulations to study the effect of nanochannel length and intrusion of molecules of the organic solvent, hexafluoro-2-propanol (HFIP), on the dynamical characteristics of water within it. Favorable interactions of HFIP with the nanochannels comprised of single-walled carbon nanotubes traps them over time scales greater than 100 ns, and confinement confers small but distinguishable spatial redistribution between neighboring HFIP pairs. Water molecules within the nanochannels show clear signatures of dynamical slowdown relative to bulk water even for pure systems. The presence of HFIP causes further rotational and translational slowdown in waters when the nanochannel dimension falls below a critical length of 30 Å. The enhanced slowdown in the presence of HFIP is quantified from characteristic relaxation parameters and diffusion coefficients in the absence and presence of HFIP. It is finally seen that the net flow of water between the ends of the nanochannel shows a decreasing dependence with nanochannel length only when the number of HFIP molecules is small. These results lend insights into devising ways of modulating solvent properties within nanochannels with cosolvent impurities.

Artificial water channels: inspiration, progress, and challenges

Developing bioinspired artificial water channels may lead to the next-generation filtration membranes with ultra-high pore density and exclusive water permeability.

Positively charged residues at the channel mouth boost single-file water flow

Positively charged residues in the vicinity of the channel entrance or exit accelerate single-file water flow.

Water molecules lose two of their four bulk neighbours when entering single-file channels. This process may be sensitive to the presence of positive and negative charges at the channel mouth, since the costs for dehydrating cations and anions differ by a large margin. However, it is not known whether entrance charges affect the single channel water permeability (p_f). So far, p_f is only known to be governed by H-bond formation between permeating water molecules and wall-lining residues. Here we compare the p_f values of five different aquaporin species (AQP1, AQPZ, AQP4 wild type, and two phosphorylation mimicking AQP4 mutants) that offer the same number of hydrogen bond donating and receiving residues in their single-file region but display different entrance charges. The p_f measurements were performed with reconstituted lipid vesicles. We assessed (i) the osmotically induced vesicle deflation from the light scattering intensity in a stopped-flow device and (ii) the aquaporin abundance by fluorescence correlation spectroscopy. Substitution of serine at positions 111 and 180 in AQP4 for aspartic acid showed only a marginal effect on p_f, suggesting that negative entrance charges are of minor importance. In contrast, the total number of positively charged amino acid side chains at entrances and exits correlates with p_f: a total of three, four and seven charges of AQP4, AQPZ, and AQP1 translate into p_f values of 1.1, 1.8, and 3.2 × 10^–13 cm³ s^–1, respectively. Thus, positive interfacial charges boost the p_f value of AQP1 to three times the value of AQP4. Nevertheless, the number of hydrogen bond donating and receiving residues in the single-file region remains the major determinant of p_f. Their effect on p_f may be a hundredfold larger than that of interfacial charges.