Water transport in aquaporins: osmotic permeability matrix analysis of molecular dynamics simulations

Membrane tension-dependent conformational change of Isoleucine 106 of loop B diminishes water permeability in FaPIP2;1

Aquaporins (AQPs) are membrane proteins specialized in facilitating water transport across membranes. Mechanical stress is one of the various stimuli that regulate AQPs. Briefly, there are several studies that report a decrease in permeability upon an increase in membrane tension. However, the molecular details of this mechanosensitive (MS) response are still a matter of debate. Our work attempts to close that gap in knowledge by providing evidence of a conformational change that occurs inside the pore of the strawberry aquaporin FaPIP2;1. Via osmotic shock experiments and molecular dynamics (MD) simulations, we found that a residue of loop B, I106, is key to the blocking of the permeation pathway and such a change is almost exclusively found under membrane tensile stress. In detail, osmotic shock experiments exhibited a nonlinear increment in water fluxes for increasing osmolarities, evidencing a decrease in the FaPIP2;1 permeability. MD simulations under membrane tension showed the same trend, with a significant increase in states with a low water permeability. The latter was correlated with a conformational change in I106 that generates a permeation barrier of around 18 kJ mol-1, effectively closing the pore. This work constitutes the first report of a PIP type aquaporin reacting to tensile stress in the membrane. Our findings could pave the way to test whether this conformational change is also responsible for mechanical gating in the other MS aquaporins, both those already reported and those still waiting to be found.

Effect of AQP4 and its palmitoylation on the permeability of exogenous reactive oxygen species: Insights from computational study

Aquaporin 4 (AQP4) facilitates the transport of reactive oxygen species (ROS). Both cancer cells and the ionizing radiation microenvironment can induce posttranslational modifications (PTMs) in AQP4, which may affect its permeability to ROS. Because this ROS diffusion process is rapid, microscopic, and instantaneous within and outside cells, conventional experimental methods are inadequate for elucidating the molecular mechanisms involved. In this study, computational methods were employed to investigate the permeability of exogenous ROS mediated by radiation in AQP4 at a molecular scale. We constructed a simulation system incorporating AQP4 and AQP4-Cysp13 in a complex lipid environment with ROS. Long-timescale molecular dynamics simulations were conducted to assess the structural stability of both AQP4 and AQP4-Cysp13. Free energy calculations were utilized to determine the ROS transport capability of the two AQP4 proteins. Computational electrophysiology and channel structural analysis quantitatively evaluated changes in ROS transport capacity under various radiation-induced transmembrane voltage microenvironments. Our findings demonstrate the distinct transport capabilities of AQP4 channels for water molecules and various types of ROS and reveal a decrease in transport efficiency when AQP4 undergoes palmitoylation modification. In addition, we have simulated the radiation-induced alteration of cell membrane voltage, which significantly affected the ROS transport capacity. We propose that this research will enhance the understanding of the molecular mechanisms governing the transport of exogenous ROS by AQP4 and elucidate the influence of palmitoylation on ROS transport. This study will also help clarify how different structural features of AQP4 affect the transport of exogenous ROS mediated by radiotherapy, thereby providing a theoretical molecular basis for the development of new treatment strategies that combine with radiotherapy.

Impacts of external electric fields on the permeation of glycerol and water molecules through aquaglyceroporin-7: molecular dynamics simulation approach

The aquaglyceroporin-7 (AQP7) protein channels facilitate the permeation of glycerol and water molecules through cell membranes by passive diffusion and play a crucial role in cell physiology. Considering the wide-spirit usage of radiofrequency electromagnetic fields in our daily life, in this study, the effects of constant and GHz electric fields were investigated on the dynamics of glycerol and water molecules inside the AQP7. To this end, four different molecular simulation groups were carried out in the absence and presence of electric fields. The results reveal that the free energy profile of the glycerol permeation inside the channel is reduced in the presence of the field of 0.2 mV/nm and the oscillating field of 10 GHz. In addition, exposing the channel to the electric field of 0.2 mV/nm assisted the water transport through the channel with no considerable effect on channel stability. These observations provide a framework for understanding how such fields could alter normal operation of protein channels, which may lead to disease beginning or being used in disease treatment. Glycerol and water molecules permeation through the aquaglyceroporin-7 channel can be influenced by application of external electric fields.

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.

Multiple pore lining residues modulate water permeability of GlpF

The water permeability of aquaporins (AQPs) varies by more than an order of magnitude even though the pore structure, geometry, as well as the channel lining residues are highly conserved. However, channel gating by pH, divalent ions or phosphorylation was only shown for a minority of AQPs. Structural and in silico indications of water flux modulation by flexible side chains of channel lining residues have not been experimentally confirmed yet. Hence, the aquaporin "open state" is still considered to be a continuously open pore with water molecules permeating in a single-file fashion. Using protein mutations outside the selectivity filter in the aqua(glycerol)facilitator GlpF of Escherichia coli we, to the best of our knowledge, for the first time, modulate the position of the highly conserved Arg in the selectivity filter. This in turn enhances or reduces the unitary water permeability of GlpF as shown in silico by molecular dynamics (MD) simulations and in vitro with purified and reconstituted GlpF. This finding suggests that AQP water permeability can indeed be regulated by lipid bilayer asymmetry and the transmembrane potential. Strikingly, our long-term MD simulations reveal that not only the conserved Arg in the selectivity filter, but the position and dynamics of multiple other pore lining residues modulate water passage through GlpF. This finding is expected to trigger a wealth of future investigations on permeability and regulation of AQPs among others with the aim to tune water permeability for biotechnological applications.

Single-cell monitoring of dry mass and dry mass density reveals exocytosis of cellular dry contents in mitosis

Cell mass and composition change with cell cycle progression. Our previous work characterized buoyant mass dynamics in mitosis (Miettinen et al., 2019), but how dry mass and cell composition change in mitosis has remained unclear. To better understand mitotic cell growth and compositional changes, we develop a single-cell approach for monitoring dry mass and the density of that dry mass every ~75 s with 1.3% and 0.3% measurement precision, respectively. We find that suspension grown mammalian cells lose dry mass and increase dry mass density following mitotic entry. These changes display large, non-genetic cell-to-cell variability, and the changes are reversed at metaphase-anaphase transition, after which dry mass continues accumulating. The change in dry mass density causes buoyant and dry mass to differ specifically in early mitosis, thus reconciling existing literature on mitotic cell growth. Mechanistically, cells in early mitosis increase lysosomal exocytosis, and inhibition of lysosomal exocytosis decreases the dry mass loss and dry mass density increase in mitosis. Overall, our work provides a new approach for monitoring single-cell dry mass and dry mass density, and reveals that mitosis is coupled to extensive exocytosis-mediated secretion of cellular contents.

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.

Water Transport and Ion Diffusion Investigation of an Amphotericin B-Based Channel Applied to Forward Osmosis: A Simulation Study

The use of an Amphotericin B_Ergosterol (AmBEr) channel as an artificial water channel in forward osmosis filtration (FO) was studied via molecular dynamics (MD) simulation. Three channel models were constructed: a common AmBEr channel and two modified C3deOAmB_Ergosterol (C3deOAmBEr) channels with different diameters (12 Å and 18 Å). During FO filtration simulation, the osmotic pressure of salt-water was a driving force for water permeation. We examined the effect of the modified C3deOAmBEr channel on the water transport performance. By tracing the change of the number of water molecules along with simulation time in the saltwater region, the water permeability of the channel models could be calculated. A higher water permeability was observed for a modified C3deOAmBEr channel, and there was no ion permeation during the entire simulation period. The hydrated ions and water molecules were placed into the channel to explore the ion leakage behavior of the channels. The mean squared displacement (MSD) of ions and water molecules was obtained to study the ion leakage performance. The Amphotericin B-based channels showed excellent selectivity of water molecules against ions. The results obtained on an atomistic scale could assist in determining the properties and the optimal filtration applications for Amphotericin B-based channels.

Influences of electric fields on the operation of Aqy1 aquaporin channels: a molecular dynamics study

The dynamics of water molecules inside an Aquaporin channel, embedded within a stochastically fluctuating membrane, was modeled by means of the application of the molecular dynamics (MD) simulation method. We considered the effect of the existence and nonexistence of an external electric field, either constant or oscillating, on the stability of the channel. It was observed that the permeation of water molecules through the channel was increased when the channel was exposed to a constant electric field of strength -0.2 mV nm-1. Moreover, oscillating electric fields of 5 and 10 GHz frequencies, which is the range of field frequency generally present in our daily life, were applied to the channel, showing not significant effects on the stability of the channel and its important parts. In addition, we investigated the influence of the application of electric fields on the water molecule ordinations in the channels, and the results showed that the water molecule orientations were changed in response to the applied field.

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.

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.

Molecular dynamics study of nanoconfined TIP4P/2005 water: how confinement and temperature affect diffusion and viscosity

In the past few decades great effort has been devoted to the study of water confined in hydrophobic geometries at the nanoscale (tubes and slit pores) due to the multiple technological applications of such systems, ranging from drug delivery to water desalination devices. To our knowledge, neither numerical/theoretical nor experimental approaches have so far reached a consensual understanding of structural and transport properties of water under these conditions. In this work, we present molecular dynamics simulations of TIP4P/2005 water under different nanoconfinements (slit pores or nanotubes, with two degrees of hydrophobicity) within a wide temperature range. It has been found that water is more structured near the less hydrophobic walls, independently of the confining geometries. Meanwhile, we observe an enhanced diffusion coefficient of water in both hydrophobic nanotubes. Finally, we propose a confined Stokes-Einstein relation to obtain the viscosity from diffusivity, whose result strongly differs from the Green-Kubo expression that has been used in previous works. While viscosity computed with the Green-Kubo formula (applied for anisotropic and confined systems) strongly differs from that of the bulk, viscosity computed with the confined Stokes-Einstein relation is not so much affected by the confinement, independently of its geometry. We discuss the shortcomings of both approaches, which could explain this discrepancy.

Cooperativity and allostery in aquaporin 0 regulation by Ca2

Aquaporin 0 (AQP0) is essential for eye lens homeostasis as is regulation of its water permeability by Ca²⁺, which occurs through interactions with calmodulin (CaM), but the underlying molecular mechanisms are not well understood. Here, we use molecular dynamics (MD) simulations on the microsecond timescale under an osmotic gradient to explicitly model water permeation through the AQP0 channel. To identify any structural features that are specific to water permeation through AQP0, we also performed simulations of aquaporin 1 (AQP1) and a pure mixed lipid bilayer under the same conditions. The relative single-channel water osmotic permeability coefficients (p_f) calculated from all of our simulations are in reasonable agreement with experiment. Our simulations allowed us to characterize the dynamics of the key structural elements that modulate the diffusion of water single-files through the AQP0 and AQP1 pores. We find that CaM binding influences the collective dynamics of the whole AQP0 tetramer, promoting the closing of both the extracellular and intracellular gates by inducing cooperativity between neighboring subunits.

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.

Human aquaporin 4 gating dynamics under axially oriented electric-field impulses: A non-equilibrium molecular-dynamics study

Human aquaporin 4 has been studied using non-equilibrium molecular dynamics simulations in the absence and presence of pulses of external electric fields. The pulses were 100 ns in duration and 0.005-0.015 V/Å in intensity acting along the pores' axes. Water diffusivity and the dipolar response of various residues of interest within the pores have been studied. Results show relatively little change in levels of water permeability per se within aquaporin channels during axially oriented field impulses, although care must be taken with regard to statistical certainty. However, the spatial variation of water permeability vis-à-vis electric-field intensity within the milieu of the channels, as revealed by heterogeneity in diffusivity-map gradients, indicates the possibility of somewhat enhanced diffusivity, owing to several residues being affected substantially by external fields, particularly for HIS 201 and 95 and ILE 93. This has the effect of increasing slightly intra-pore water diffusivity in the "pore-mouths" locale, albeit rendering it more spatially uniform overall vis-à-vis zero-field conditions (via manipulation of the selectivity filter).

Presence of Intra-helical Salt-Bridge in Loop E Half-Helix Can Influence the Transport Properties of AQP1 and GlpF Channels: Molecular Dynamics Simulations of In Silico Mutants

Major intrinsic protein (MIP) superfamily contains water-transporting AQP1 and glycerol-specific GlpF belonging to two major phylogenetic groups, namely aquaporins (AQPs) and aquaglyceroporins (AQGPs). MIP channels have six transmembrane helices (TM1 to TM6) and two half-helices (LB and LE). LE region contributes two residues to the aromatic/arginine (Ar/R) selectivity filter (SF) within the MIP channel. Bioinformatics analyses have shown that all AQGPs have an intra-helical salt-bridge (IHSB) in LE half-helix and all AQGPs and majority of AQPs have helix destabilizing Gly and/or Pro in the same region. In this paper, we mutated in silico the acidic and basic residues in GlpF to Ser and introduced salt-bridge interaction in AQP1 LE half-helix by substituting Ser residues at the equivalent positions with acidic and basic residues. We investigated the influence of IHSB in LE half-helix on the transport properties of GlpF and AQP1 mutant channels using molecular dynamics simulations. With IHSB abolished in LE half-helix, the GlpF mutant exhibited a significantly reduced water transport. In contrast, the introduction of IHSB in the two AQP1 mutants has increased water transport. Absence of salt-bridge in LE half-helix alters the SF geometry and results in a higher energy barrier for the solutes in the Ar/R selectivity filter. Presence/absence of IHSB in LE half-helix influences the channel transport properties and it is evident especially for the AQGPs. By modulating its helical flexibility, LE half-helix can perhaps play a regulatory role in transport either on its own or in conjunction with other extracellular regions.

Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function

Aquaporin TIP2;1 is a protein channel permeable to both water and ammonia. The structural origin of ammonia selectivity remains obscure, but experiments have revealed that a double mutation renders it impermeable to ammonia without affecting water permeability. Here, we aim to reproduce and explain these observations by performing an extensive mutational study using microsecond long molecular dynamics simulations, applying the two popular force fields CHARMM36 and Amber ff99SB-ILDN. We calculate permeabilities and free energies along the channel axis for ammonia and water. For one force field, the permeability of the double mutant decreases by a factor of 2.5 for water and 4 for ammonia, increasing water selectivity by a factor of 1.6. We attribute this effect to decreased entropy of water in the pore, due to the observed increase in pore-water interactions and narrower pore. Additionally, we observe spontaneous opening and closing of the pore on the cytosolic side, which suggests a gating mechanism for the pore. Our results show that sampling methods and simulation times are sufficient to delineate even subtle effects of mutations on structure and function and to capture important long-timescale events, but also underline the importance of improving models further.

Electropumping of Water Through Human Aquaporin 4 by Circularly Polarized Electric Fields: Dramatic Enhancement and Control Revealed by Non-Equilibrium Molecular Dynamics

An extensive suite of nonequilibrium molecular-dynamics (NEMD) simulations have been performed for ∼60 ns of human aquaporin 4 in externally applied circularly polarized (CP) electric fields, applied axially along channels. These external fields were 0.05 V/Å in intensity and 100 GHz in frequency. This has the effect of "electro-pumping" the water through the pores as prototypical biochannels, from conversion of molecules' spin angular momentum to linear momentum in the asymmetric heterogeneous-frictional environment of the pores, thus inducing overall net flow. Water's osmotic permeability was enhanced very substantially (doubled) vis-à-vis the zero-field case. This raises the tantalizing possibility of CP-field-mediated control of water permeability in aquaporins, or other biological (or biomimetic) channels as a potential viable and competitive water-treatment technology.

Computing osmotic permeabilities of aquaporins AQP4, AQP5, and GlpF from near-equilibrium simulations

Measuring or computing the single-channel permeability of aquaporins/aquaglyceroporins (AQPs) has long been a challenge. The measured values scatter over an order of magnitude but the corresponding Arrhenius activation energies converge in the current literature. Osmotic flux through an AQP was simulated as water current forced through the channel by kilobar hydraulic pressure or theoretically approximated as single-file diffusion. In this paper, we report large scale simulations of osmotic current under sub M gradient through three AQPs (water channels AQP4 and AQP5 and glycerol-water channel GlpF) using the mature particle mesh Ewald technique (PME) for which the established force fields have been optimized with known accuracy. These simulations were implemented with hybrid periodic boundary conditions devised to avoid the artifactitious mixing across the membrane in a regular PME simulation. The computed single-channel permeabilities at 5°C and 25°C are in agreement with recently refined experiments on GlpF. The Arrhenius activation energies extracted from our simulations for all the three AQPs agree with the in vitro measurements. The single-file diffusion approximations from our large-scale simulations are consistent with the current literature on smaller systems. From these unambiguous agreements among the in vitro and in silico studies, we observe the quantitative accuracy of the all-atom force fields of the current literature for water-channel biology. We also observe that AQP4, that is particularly rich in the central nervous system, is more efficient in water conduction and more temperature-sensitive than other water-only channels (excluding glycerol channels that also conduct water when not inhibited by glycerol).

Potential of Mean Force Calculations of Solute Permeation Across UT-B and AQP1: A Comparison between Molecular Dynamics and 3D-RISM

Membrane channels facilitate the efficient and selective flux of various solutes across biological membranes. A common approach to investigate the selectivity of a channel has been the calculation of potentials of mean force (PMFs) for solute permeation across the pore. PMFs have been frequently computed from molecular dynamics (MD) simulations, yet the three-dimensional reference interaction site model (3D-RISM) has been suggested as a computationally efficient alternative to MD. Whether the two methods yield comparable PMFs for solute permeation has remained unclear. In this study, we calculated potentials of mean force for water, ammonia, urea, molecular oxygen, and methanol across the urea transporter B (UT-B) and aquaporin-1 (AQP1), using 3D-RISM, as well as using MD simulations and umbrella sampling. To allow direct comparison between the PMFs from 3D-RISM and MD, we ensure that all PMFs refer to a well-defined reference area in the bulk or, equivalently, to a well-defined density of channels in the membrane. For PMFs of water permeation, we found reasonable agreement between the two methods, with differences of ≲3 kJ mol-1. In contrast, we found stark discrepancies for the PMFs for all other solutes. Additional calculations confirm that discrepancies between MD and 3D-RISM are not explained by the choice for the closure relation, the definition the reaction coordinate (center of mass-based versus atomic site-based), details of the molecule force field, or fluctuations of the protein. Comparison of the PMFs suggests that 3D-RISM may underestimate effects from hydrophobic solute-channel interactions, thereby, for instance, missing the urea binding sites in UT-B. Furthermore, we speculate that the orientational averages inherent to 3D-RISM might lead to discrepancies in the narrow channel lumen. These findings suggest that current 3D-RISM solvers provide reasonable estimates for the PMF for water permeation, but that they are not suitable to study the selectivity of membrane channels with respect to uncharged nonwater solutes.

Sub-nanometre mapping of the aquaporin-water interface using multifrequency atomic force microscopy

Aquaporins are integral membrane proteins that regulate the transport of water and small molecules in and out of the cell. In eye lens tissue, circulation of water, ions and metabolites is ensured by a microcirculation system in which aquaporin-0 (AQP0) plays a central role. AQP0 allows water to flow beyond the diffusion limit through lens membranes. AQP0 naturally arranges in a square lattice. The malfunction of AQP0 is related to numerous diseases such as cataracts. Despite considerable research into its structure, function and dynamics, the interface between the protein and the surrounding liquid and the effect of the lattice arrangement on the behaviour of water at the interface with the membrane are still not fully understood. Here we use a multifrequency atomic force microscopy (AFM) approach to map both the liquid at the interface with AQP0 and the protein itself with sub-nanometer resolution. Imaging using the fundamental eigenmode of the AFM cantilever probes mainly the interfacial water at the surface of the membrane. The results highlight a well-defined region that surrounds AQP0 tetramers and where water exhibits a higher affinity for the protein. Imaging in the second eigenmode is dominated by the mechanical response of the protein and provides sub-molecular details of the protein surface and the sub-surface structure. The relationship between modes and harmonics is also examined.

Human Aquaporin 4 Gating Dynamics under Perpendicularly-Oriented Electric-Field Impulses: A Molecular Dynamics Study

Human aquaporin 4 has been studied using molecular dynamics (MD) simulations in the absence and presence of pulses of external static electric fields. The pulses were 10 ns in duration and 0.012-0.065 V/Å in intensity acting along both directions perpendicular to the pores. Water permeability and the dipolar response of all residues of interest (including the selectivity filter) within the pores have been studied. Results showed decreased levels of water osmotic permeability within aquaporin channels during orthogonally-oriented field impulses, although care must be taken with regard to statistical certainty. This can be explained observing enhanced "dipolar flipping" of certain key residues, especially serine 211, histidine 201, arginine 216, histidine 95 and cysteine 178. These residues are placed at the extracellular end of the pore (serine 211, histidine 201, and arginine 216) and at the cytoplasm end (histidine 95 and cysteine 178), with the key role in gating mechanism, hence influencing water permeability.

Human Aquaporin-4 and Molecular Modeling: Historical Perspective and View to the Future

Among the different aquaporins (AQPs), human aquaporin-4 (hAQP4) has attracted the greatest interest in recent years as a new promising therapeutic target. Such a membrane protein is, in fact, involved in a multiple sclerosis-like immunopathology called Neuromyelitis Optica (NMO) and in several disorders resulting from imbalanced water homeostasis such as deafness and cerebral edema. The gap of knowledge in its functioning and dynamics at the atomistic level of detail has hindered the development of rational strategies for designing hAQP4 modulators. The application, lately, of molecular modeling has proved able to fill this gap providing a breeding ground to rationally address compounds targeting hAQP4. In this review, we give an overview of the important advances obtained in this field through the application of Molecular Dynamics (MD) and other complementary modeling techniques. The case studies presented herein are discussed with the aim of providing important clues for computational chemists and biophysicists interested in this field and looking for new challenges.

Mechanism of the αβ conformational change in F1-ATPase after ATP hydrolysis: free-energy simulations

One of the motive forces for F1-ATPase rotation is the conformational change of the catalytically active β subunit due to closing and opening motions caused by ATP binding and hydrolysis, respectively. The closing motion is accomplished in two steps: the hydrogen-bond network around ATP changes and then the entire structure changes via B-helix sliding, as shown in our previous study. Here, we investigated the opening motion induced by ATP hydrolysis using all-atom free-energy simulations, combining the nudged elastic band method and umbrella sampling molecular-dynamics simulations. Because hydrolysis requires residues in the α subunit, the simulations were performed with the αβ dimer. The results indicate that the large-scale opening motion is also achieved by the B-helix sliding (in the reverse direction). However, the sliding mechanism is different from that of ATP binding because sliding is triggered by separation of the hydrolysis products ADP and Pi. We also addressed several important issues: 1), the timing of the product Pi release; 2), the unresolved half-closed β structure; and 3), the ADP release mechanism. These issues are fundamental for motor function; thus, the rotational mechanism of the entire F1-ATPase is also elucidated through this αβ study. During the conformational change, conserved residues among the ATPase proteins play important roles, suggesting that the obtained mechanism may be shared with other ATPase proteins. When combined with our previous studies, these results provide a comprehensive view of the β-subunit conformational change that drives the ATPase.

Expression pattern of aquaporins in patients with primary nephrotic syndrome with edema

The association between the expression of aquaporins (AQPs) in kidney tissues and the occurrence of edema in nephrotic syndrome (NS) remains unclear. The current study aimed to investigate this association. A total of 54 patients with primary glomerular disease, diagnosed by renal biopsy, were divided into three groups: Control, NS without edema and NS with edema. The expression of AQP1, AQP2, AQP3 and AQP4 in kidney tissues from these patients was assessed using immunohistochemistry, and urinary AQP concentrations were quantified by ELISA. Comparison of the three groups was conducted using one way analysis of variance, independent samples t-test or the Chi-square test. AQP1 was strongly expressed in the proximal tubules. The proportion of the AQP1-positive area in kidney tissues from patients with NS with edema was significantly reduced, in comparison with the other two groups. By contrast, the proportion of the AQP2-positive area in the NS with edema group was significantly higher than that of the other two groups; significant differences were also observed between the control and NS without edema groups for this parameter. Urinary AQP2 concentrations in patients with NS (with and without edema) were significantly higher than that of the control group, and exhibited a significant positive correlation with kidney tissue AQP2 concentrations. The present study demonstrated the abnormal expression pattern of AQP1-AQP4 in the kidney tissues of patients with NS, providing a basis for an improved understanding of the role of AQP in the pathogenesis of NS.

Bio-Inspired Aquaporinz Containing Double-Skinned Forward Osmosis Membrane Synthesized through Layer-by-Layer Assembly

We demonstrated a novel AquaporinZ (AqpZ)-incorporated double-skinned forward osmosis (FO) membrane by layer-by-layer (LbL) assembly strategy. Positively charged poly(ethyleneimine) (PEI) and negatively charged poly(sodium 4-styrenesulfonate) (PSS) were alternately deposited on both the top and bottom surfaces of a hydrolyzed polyacrylonitrile (H-PAN) substrate. Subsequently, an AqpZ-embedded 1,2-dioleloyl-sn-glycero-3-phosphocholine (DOPC)/1,2-dioleoyl-3-trimethylammonium- propane (chloride salt) (DOTAP) supported lipid bilayer (SLB) was formed on PSS-terminated (T-PSS) membrane via vesicle rupture method. The morphology and structure of the biomimetic membranes were characterized by in situ atomic force microscopy (AFM), scanning electron microscope (SEM), Fourier transform infrared spectrometer using the attenuated total reflection technique (ATR-FTIR), and contact angle. Moreover, the FO performance of the resultant membrane was measured by using 2 M MgCl₂ solution as draw solution and deionized (DI) water as feed solution, respectively. The membrane with a protein-to-lipid weight ratio (P/L) of 1/50 exhibits 13.2 L/m²h water flux and 3.2 g/m²h reversed flux by using FO mode, as well as 15.6 L/m²h water flux and 3.4 L/m²h reversed flux for PRO mode (the draw solution is placed against the active layer). It was also shown that the SLB layer of the double-skinned FO membrane can increase the surface hydrophilicity and reduce the surface roughness, which leads to an improved anti-fouling performance against humic acid foulant. The current work introduced a new method of fabricating high performance biomimetic FO membrane by combining AqpZ and a double-skinned structure based on LbL assembly.

Impact of monoolein on aquaporin1-based supported lipid bilayer membranes

Aquaporin (AQP) based biomimetic membranes have attracted considerable attention for their potential water purification applications. In this paper, AQP1 incorporated biomimetic membranes were prepared and characterized. The morphology and structure of the biomimetic membranes were characterized by in situ atomic force microscopy (AFM), infrared absorption spectroscopy, fluorescence microscopy, and contact angle measurements. The nanofiltration performance of the AQP1 incorporated membranes was investigated at 4 bar by using 2 g l^-1 NaCl as feed solution. Lipid mobility plays an important role in the performance of the AQP1 incorporated supported lipid bilayer (SLB) membranes. We demonstrated that the lipid mobility is successfully tuned by the addition of monoolein (MO). Through in situ AFM and fluorescence recovery after photo-bleaching (FRAP) measurements, the membrane morphology and the molecular mobility were studied. The lipid mobility increased in the sequence DPPC < DPPC/MO (R_MO = 5/5) < DOPC/MO (R_MO = 5/5) < DOPC, which is consistent with the flux increment and salt rejection. This study may provide some useful insights for improving the water purification performance of biomimetic membranes.

Molecular dynamics simulations of the transport of reactive oxygen species by mammalian and plant aquaporins

BACKGROUND

Aquaporins are responsible for water transport across lipid membranes. They are also able to transport reactive oxygen species, playing an important role in redox signaling. Certain plant aquaporins have even the ability to be regulated by oxidative stress. However, the underlying mechanisms are still not fully understood.

METHODS

Here, molecular dynamics simulations were employed to determine the activation free energies related to the transport of reactive oxygen species through both mammalian and plant aquaporin models.

RESULTS AND CONCLUSIONS

Both aquaporins may transport hydrogen peroxide (H2O2) and the protonated form of superoxide radicals (HO2). The solution-to-pore transfer free energies were low for small oxy-radicals, suggesting that even highly reactive hydroxyl radicals (HO) might have access to the pore interior and oxidize amino acids responsible for channel selectivity. In the plant aquaporin, no significant change in water permeability was observed upon oxidation of the solvent-exposed disulfide bonds at the extracellular region. During the simulated time scale, the existence of a direct oxidative gating mechanism involving these disulfide bonds could not be demonstrated.

GENERAL SIGNIFICANCE

Simulation results may improve the understanding of redox signaling mechanisms and help in the interpretation of protein oxidative labeling experiments.

Challenging AQP4 druggability for NMO-IgG antibody binding using molecular dynamics and molecular interaction fields

Neuromyelitis optica (NMO) is a multiple sclerosis-like immunopathology disease affecting optic nerves and the spinal cord. Its pathological hallmark is the deposition of a typical immunoglobulin, called NMO-IgG, against the water channel Aquaporin-4 (AQP4). Preventing NMO-IgG binding would represent a valuable molecular strategy for a focused NMO therapy. The recent observation that aspartate in position 69 (D69) is determinant for the formation of NMO-IgG epitopes prompted us to carry out intensive Molecular Dynamics (MD) studies on a number of single-point AQP4 mutants. Here, we report a domino effect originating from the point mutation at position 69: we find that the side chain of T62 is reoriented far from its expected position leaning on the lumen of the pore. More importantly, the strength of the H-bond interaction between L53 and T56, at the basis of the loop A, is substantially weakened. These events represent important pieces of a clear-cut mechanistic rationale behind the failure of the NMO-IgG binding, while the water channel function as well as the propensity to aggregate into OAPs remains unaltered. The molecular interaction fields (MIF)-based analysis of cavities complemented MD findings indicating a putative binding site comprising the same residues determining epitope reorganization. In this respect, docking studies unveiled an intriguing perspective to address the future design of small drug-like compounds against NMO. In agreement with recent experimental observations, the present study is the first computational attempt to elucidate NMO-IgG binding at the molecular level, as well as a first effort toward a less elusive AQP4 druggability.

The mobility of single-file water molecules is governed by the number of H-bonds they may form with channel-lining residues

Channel geometry governs the unitary osmotic water channel permeability, p_f, according to classical hydrodynamics. Yet, p_f varies by several orders of magnitude for membrane channels with a constriction zone that is one water molecule in width and four to eight molecules in length. We show that both the p_f of those channels and the diffusion coefficient of the single-file waters within them are determined by the number N_H of residues in the channel wall that may form a hydrogen bond with the single-file waters. The logarithmic dependence of water diffusivity on N_H is in line with the multiplicity of binding options at higher N_H densities. We obtained high-precision p_f values by (i) having measured the abundance of the reconstituted aquaporins in the vesicular membrane via fluorescence correlation spectroscopy and via high-speed atomic force microscopy, and (ii) having acquired the vesicular water efflux from scattered light intensities via our new adaptation of the Rayleigh-Gans-Debye equation.

Layer-by-layer assembly of aquaporin Z-incorporated biomimetic membranes for water purification

We fabricated a biomimetic nanofiltration (NF) membrane by immobilizing an Aquaporin Z (AqpZ)-incorporated supported lipid bilayer (SLB) on a layer-by-layer (LbL) complex polyelectrolyte membrane to achieve excellent permeability and salt rejection with a high stability. The polyelectrolyte membranes were prepared by LbL assembly of poly(ethylenimine) (PEI) with positive charges and poly(sodium 4-styrenesulfonate) (PSS) with negative charges alternately on a porous hydrolyzed polyacrylonitrile (H-PAN) substrate. AqpZ-incorporated 1,2-dioleloyl-sn-glycero-3-phosphocholine (DOPC)/1,2-dioleoyl-3-trimethylammo-nium-propane (chloride salt) (DOTAP) vesicles with positive charges were deposited on the H-PAN/PEI/PSS polyelectrolytes membrane surface. The resulting biomimetic membrane exhibited a high flux of 22 L·m(-2)·h(-1) (LMH), excellent MgCl2 rejection of ∼97% and NaCl rejection of ∼75% under an operation pressure of 0.4 MPa. Due to the attractive electrostatic interaction between SLB and the polyelectrolyte membrane, the biomimetic membrane showed satisfactory stability and durability as well as stable NF flux and rejection for at least 36 h. In addition, the AqpZ-containing biomimetic membrane was immersed in a 0.24 mM (critical micellar concentration, CMC) Triton X-100 solution for 5 min. The flux and rejection were slightly influenced by the Triton X-100 treatment. The current investigation demonstrated that the AqpZ-incorporated biomimetic membranes fabricated by the LbL method led to excellent separation performances and robust structures that withstand a high operation pressure for a relatively long time.

[Optimal permeability of aquaporins: a question of shape?]

Aquaporins are transmembrane proteins, ubiquitous in the human body. Inserted into the cell membranes, they play an important role in filtration, absorption and secretion of fluids. However, the excellent compromise between selectivity and permeability of aquaporins remains elusive. In this review, we focus on the hourglass shape of aquaporins, and we investigate its influence on water permeability, using numerical calculations and a simple theoretical model. We show that there is an optimum opening angle that maximizes the hydrodynamic permeability, and whose value is close to the angles observed in aquaporins.

Cyclooxygenase-2 and vascular endothelial growth factor expressions are involved in ultrafiltration failure

BACKGROUND

Long-term peritoneal dialysis (PD) is associated with ultrafiltration failure (UFF). The aim of the study was to investigate changes in cyclooxygenase-2 (COX-2), vascular endothelial growth factor A (VEGF-A), and vascular endothelial growth factor C (VEGF-C) expressions in a rat model of UFF induced by PD solution.

METHODS

Sprague-Dawley rats were divided into six groups (n = 8/group): normal untreated control group, sham operation group, uremic group (nephrectomy without PD), uremic 2-wk PD group (PD solution for 2 wk), uremic 4-wk PD group (PD solution for 4 wk), and uremic 4-wk PD + celecoxib group (PD solution plus COX-2 inhibitor celecoxib 20 mg/kg for 4 wk). Peritoneal function was determined by peritoneal equilibration test. Peritoneal morphology was determined by hematoxylin and eosin and Masson staining. Microvessel and lymphatic microvessel formation was determined by immunohistochemistry. COX-2, VEGF-A, and VEGF-C expressions were determined by real-time polymerase chain reaction and immunohistochemistry.

RESULTS

Uremic rat model was successfully established. PD-induced peritoneal morphologic changes associated with UFF, characterized by inflammation, edema, and collagen accumulation. PD solution increased the density of microvessels marked by CD31 (microvessel density) and lymphatic microvessels marked by LYVE-1 (lymphatic vessel density) in peritoneum. COX-2, VEGF-A, and VEGF-C expression levels in the uremic 4-wk PD group were higher than those in the uremic group (all P < 0.05). All these changes were partially reversed by celecoxib. VEGF-A and VEGF-C protein expressions were positively correlated with microvessel density and lymphatic vessel density formation.

CONCLUSIONS

COX-2 could increase VEGF-A and VEGF-C expressions in peritoneal tissue, resulting in increased formation of peritoneal microvessels and lymphatic microvessels, playing pivotal roles in the development of UFF.

Functional rotation induced by alternating protonation states in the multidrug transporter AcrB: all-atom molecular dynamics simulations

The multidrug transporter AcrB actively exports a wide variety of noxious compounds using proton-motive force as an energy source in Gram-negative bacteria. AcrB adopts an asymmetric structure comprising three protomers with different conformations that are sequentially converted during drug export; these cyclic conformational changes during drug export are referred to as functional rotation. To investigate functional rotation driven by proton-motive force, all-atom molecular dynamics simulations were performed. Using different protonation states for the titratable residues in the middle of the transmembrane domain, our simulations revealed the correlation between the specific protonation states and the side-chain configurations. Changing the protonation state for Asp408 induced a spontaneous structural transition, which suggests that the proton translocation stoichiometry may be one proton per functional rotation cycle. Furthermore, our simulations demonstrate that alternating the protonation states in the transmembrane domain induces functional rotation in the porter domain, which is primarily responsible for drug transport.

Optimizing water permeability through the hourglass shape of aquaporins

The ubiquitous aquaporin channels are able to conduct water across cell membranes, combining the seemingly antagonist functions of a very high selectivity with a remarkable permeability. Whereas molecular details are obvious keys to perform these tasks, the overall efficiency of transport in such nanopores is also strongly limited by viscous dissipation arising at the connection between the nanoconstriction and the nearby bulk reservoirs. In this contribution, we focus on these so-called entrance effects and specifically examine whether the characteristic hourglass shape of aquaporins may arise from a geometrical optimum for such hydrodynamic dissipation. Using a combination of finite-element calculations and analytical modeling, we show that conical entrances with suitable opening angle can indeed provide a large increase of the overall channel permeability. Moreover, the optimal opening angles that maximize the permeability are found to compare well with the angles measured in a large variety of aquaporins. This suggests that the hourglass shape of aquaporins could be the result of a natural selection process toward optimal hydrodynamic transport. Finally, in a biomimetic perspective, these results provide guidelines to design artificial nanopores with optimal performances.