Pore Hydration Research Articles

STIM1 activates CRAC channels through rotation of the pore helix to open a hydrophobic gate

Store-operated Ca2+ release-activated Ca2+ (CRAC) channels constitute a major pathway for Ca2+ influx and mediate many essential signalling functions in animal cells, yet how they open remains elusive. Here, we investigate the gating mechanism of the human CRAC channel Orai1 by its activator, stromal interacting molecule 1 (STIM1). We find that two rings of pore-lining residues, V102 and F99, work together to form a hydrophobic gate. Mutations of these residues to polar amino acids produce channels with leaky gates that conduct ions in the resting state. STIM1-mediated channel activation occurs through rotation of the pore helix, which displaces the F99 residues away from the pore axis to increase pore hydration, allowing ions to flow through the V102-F99 hydrophobic band. Pore helix rotation by STIM1 also explains the dynamic coupling between CRAC channel gating and ion selectivity. This hydrophobic gating mechanism has implications for CRAC channel function, pharmacology and disease-causing mutations.

Tracking Pore Hydration within the Red-Activatable Channelrhodopsin ReaChR by Site-Directed Labeling with Infrared-Active Azido Probes

Tracking Pore Hydration within the Red-Activatable Channelrhodopsin ReaChR by Site-Directed Labeling with Infrared-Active Azido Probes

Pore Hydration States of KcsA Potassium Channels in Membranes

Water-filled hydrophobic cavities in channel proteins serve as gateways for transfer of ions across membranes, but their properties are largely unknown. We determined water distributions along the conduction pores in two tetrameric channels embedded in lipid bilayers using neutron diffraction: potassium channel KcsA and the transmembrane domain of M2 protein of influenza A virus. For the KcsA channel in the closed state, the distribution of water is peaked in the middle of the membrane, showing water in the central cavity adjacent to the selectivity filter. This water is displaced by the channel blocker tetrabutyl-ammonium. The amount of water associated with the channel was quantified, using neutron diffraction and solid state NMR. In contrast, the M2 proton channel shows a V-shaped water profile across the membrane, with a narrow constriction at the center, like the hourglass shape of its internal surface. These two types of water distribution are therefore very different in their connectivity to the bulk water. The water and protein profiles determined here provide important evidence concerning conformation and hydration of channels in membranes and the potential role of pore hydration in channel gating.

Microstructure Observations of Natural Gas Hydrate Occurrence in Porous Media Using Microfocus X-ray Computed Tomography

Natural gas hydrates are globally considered a potential alternative form of energy suitable for sustainable development. The microstructure of natural gas hydrates in sediments governs their seismic and acoustic exploration, stability of seafloors, and gas production from hydrate deposits. To investigate the microstructure and occurrence of natural gas hydrates in pores, natural gas hydrate-bearing porous media were directly observed using microfocus X-ray computed tomography (CT). The spatial distributions of free gas, natural gas hydrates, water, and grains were identified. The results indicated the preference of natural gas hydrates to form primarily within pore spaces and not to cement the adjacent grains, which was described by the floating model. Moreover, the migration of gas and water within pore spaces during hydrate formation appeared random, and natural gas hydrates were found to nucleate preferentially at the gas–water interface. The values of porosity and hydrate saturation obtained via reco...

A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation.

Nicotinic acetylcholine receptors (nAchRs) are ligand-gated ion channels that regulate chemical transmission at the neuromuscular junction. Structural information is available at low resolution from open and closed forms of an eukaryotic receptor, and at high resolution from other members of the same structural family, two prokaryotic orthologs and an eukaryotic GluCl channel. Structures of human channels however are still lacking. Homology modeling and Molecular Dynamics simulations are valuable tools to predict structures of unknown proteins, however, for the case of human nAchRs, they have been unsuccessful in providing a stable open structure so far. This is due to different problems with the template structures: on one side the homology with prokaryotic species is too low, while on the other the open eukaryotic GluCl proved itself unstable in several MD studies and collapsed to a dehydrated, non-conductive conformation, even when bound to an agonist. Aim of this work is to obtain, by a mixing of state-of-the-art homology and simulation techniques, a plausible prediction of the structure (still unknown) of the open state of human α7 nAChR complexed with epibatidine, from which it is possible to start structural and functional test studies. To prevent channel closure we employ a restraint that keeps the transmembrane pore open, and obtain in this way a stable, hydrated conformation. To further validate this conformation, we run four long, unbiased simulations starting from configurations chosen at random along the restrained trajectory. The channel remains stable and hydrated over the whole runs. This allows to assess the stability of the putative open conformation over a cumulative time of 1 μs, 800 ns of which are of unbiased simulation. Mostly based on the analysis of pore hydration and size, we suggest that the obtained structure has reasonable chances to be (at least one of the possible) structures of the channel in the open conformation.

Influence of lipids on the hydrophobic barrier within the pore of the TWIK-1 K2P channel

Several recent ion channel structures have revealed large side portals, or ‘fenestrations’ at the interface between their transmembrane helices that potentially expose the ion conduction pathway to the lipid core of the bilayer. In a recent study we demonstrated that functional activity of the TWIK-1 K2P channel is influenced by the presence of hydrophobic residues deep within the inner pore. These residues are located near the fenestrations in the TWIK-1 structure and promote dewetting of the pore by forming a hydrophobic barrier to ion conduction. During our previous MD simulations, lipid tails were observed to enter these fenestrations. In this addendum to that study, we investigate lipid contribution to the dewetting process. Our results demonstrate that lipid tails from both the upper and lower leaflets can occupy the fenestrations and partially penetrate into the pore. The lipid tails do not sterically occlude the pore, but there is an inverse correlation between the presence of water within the hydrophobic barrier and the number of lipids tails within the lining of the pore. However, dewetting still occurs in the absence of lipids tails, and pore hydration appears to be determined primarily by those side-chains lining the narrowest part of the pore cavity.

Property Optimization of Inorganic Silicon Aluminum Polymer Based on Quadratic Regression and Orthogonal Design

Because of the dosage of metakaolin and ash fly had a big impact on the performance optimization of inorganic silicon aluminum polymer, using of metakaolin and ash fly can optimize the pore structure and hydration products of inorganic silicon aluminum polymer paste, how to determine the dosage of metakaolin and ash fly of inorganic silicon aluminum polymer reasonably and directly has become a problem in this research needed to be resolved instantly at hand. The current study investigated the relationship between the amounts of metakaolin and fly ash added and the compressive strength of the inorganic silicon aluminum polymer paste, and then established relevant mathematical model using a quadratic regression quadrature combination design. Previous studies have shown that the addition of 13.56% metakaolin and 3% fly ash would be the optimal plan, and that 57.4 MPa would be the maximum value of the compressive strength of the cement paste of inorganic silicon aluminum polymer that could be obtained. Keywords: Inorganic silicon aluminum polymer; Property Optimization; Quadratic Regression and Orthogonal Design

Water permeability in hydrate‐bearing sediments: A pore‐scale study

AbstractPermeability is a critical parameter governing methane flux and fluid flow in hydrate‐bearing sediments; however, limited valid data are available due to experimental challenges. Here we investigate the relationship between apparent water permeability (k′) and hydrate saturation (Sh), accounting for hydrate pore‐scale growth habit and meso‐scale heterogeneity. Results from capillary tube models rely on cross‐sectional tube shapes and hydrate pore habits, thus are appropriate only for sediments with uniform hydrate distribution and known hydrate pore character. Given our pore network modeling results showing that accumulating hydrate in sediments decreases sediment porosity and increases hydraulic tortuosity, we propose a modified Kozeny‐Carman model to characterize water permeability in hydrate‐bearing sediments. This model agrees well with experimental results and can be easily implemented in reservoir simulators with no empirical variables other than Sh. Results are also relevant to flow through other natural sediments that undergo diagenesis, salt precipitation, or bio‐clogging.

Altering the Open vs. Closed State Balance of the GLIC Ligand-Gated Ion Channel through Mutagenesis Enables Molecular Simulation of the Reversible Gating Process

The prokaryotic Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) is an important template for studies of Cys-loop receptors in the human central nervous system. It is also a key model system to understand the transitions and stabilization of different conformations of membrane proteins through allosteric modulation - a ligand that opens the channel can either stabilize the open state, or destabilize the closed one. Capturing these processes on the molecular level will not only enable us to understand gating, but also make it possible to predict functional responses rather than merely binding properties. Over the last years, we have studied mutants of the GLIC channel that make it more similar to the human Cys-loop receptors both experimentally and in simulations, and shown how this provides evidence for a dual allosteric modulation mechanism with separate inhibitory and potentiating binding sites. Here, I will present our new results on mutations in the central GLIC pore. By modifying the hydrophobicity of one or several residues in the pore it is possible to alter the pore hydration level, which in turn has paramount effects on the conformation - molecular simulations show that it is possible to stabilize the channel either in the open or closed conformation independent of pH. By using ensemble molecular dynamics simulations covering several tens of microseconds, we show that it is possible to reversibly simulate transitions between conformations that are shown to actually conduct ions or block the current in simulations. In vivo electrophysiology and single-channel recordings on the mutants confirm this influence on the kinetics, and provide us with a way to couple molecular-level dynamics and kinetics to the experimentally observed equilibrium and transitions between conformations.

Relating rejection of trace organic contaminants to membrane properties in forward osmosis: Measurements, modelling and implications

This study elucidates the relationship between membrane properties and the rejection of trace organic contaminants (TrOCs) in forward osmosis (FO). An asymmetric cellulose triacetate (CTA) and a thin-film composite (TFC) polyamide FO membrane were used for this investigation. The effective average pore radius (rp), selective barrier thickness over porosity parameter (l/ε), surface charge, support layer structural parameter (S), pure water permeability coefficient (A) and salt (NaCl) permeability coefficient (B) of the two membranes were systematically characterised. Results show that measured rejection of TrOCs as a function of permeate water flux can be well described by the pore hindrance transport model. This observation represents the first successful application of this model, which was developed for pressure-driven nanofiltration, to an osmotically-driven membrane process. The rejection of charged TrOCs by the CTA and TFC membranes was high and was governed by both electrostatic repulsion and steric hindrance. The TFC membrane exhibited higher rejection of neutral TrOCs with low molecular weight than the CTA membrane, although the estimated pore size of the TFC membrane (0.42 nm) was slightly larger than that of the CTA membrane (0.37 nm). This higher rejection of neutral TrOCs by the TFC membrane is likely attributed to its active layer properties, namely a more effective active layer structure, as indicated by a larger l/ε parameter, and pore hydration induced by the negative surface charge.

Water retention curve for hydrate‐bearing sediments

AbstractThe water retention curve plays a central role in numerical algorithms that model hydrate dissociation in sediments. The determination of the water retention curve for hydrate‐bearing sediments faces experimental difficulties, and most studies assume constant water retention curves regardless of hydrate saturation. This study employs network model simulation to investigate the water retention curve for hydrate‐bearing sediments. Results show that (1) hydrate in pores shifts the curve to higher capillary pressures and the air entry pressure increases as a power function of hydrate saturation; (2) the air entry pressure is lower in sediments with patchy rather than distributed hydrate, with higher pore size variation and pore connectivity or with lower specimen slenderness along the flow direction; and (3) smaller specimens render higher variance in computed water retention curves, especially at high water saturation Sw > 0.7. Results are relevant to other sediment pore processes such as bioclogging and mineral precipitation.

Equilibrium of Ethane Hydrate Formation in Carbon Pores

The formation of hydrates in carbon pores was utilized to store natural gas, and ethane is the second major component of natural gas; therefore, ethane hydrate formation in carbon pores is studied in comparison with that of methane. Ethane is a major raw material of ethylene in the petrochemical industry; therefore, its mixture with ethylene is of importance and the formation condition of ethane hydrates was compared also with that of ethylene. The equilibrium isotherms of ethane on wet carbons with different water contents as well as the isotherms for different temperatures were collected, from which the formation pressures of ethane hydrates as well as the enthalpy change of ethane hydrate formation were determined. It was shown that the largest volumetric capacity for ethane storage is observed at the water load that just about fully fills pore spaces. Ethane hydrates were formed in wet activated carbons at about same pressures as in water media and the formation pressure is much lower than that required for methane hydrates formation.

日本海東縁海底下に分布する砂層の孔隙特性と年代 : MD179航海

In 2010 the MD179 project was undertaken aiming at recovery of deep seated gas hydrate, methane induced carbonate, and deep sediments older than 300 ka. Sediment samples were obtained in the Umitaka Spur, Joetsu Channel, Toyama Trough, Japan Basin, Nishi Tsugaru and Okushiri Ridge areas. Small amounts of sandy sediment have been retrieved as thin intercalations in Pleistocene and Holocene muddy layers, where trace fossils and strong bioturbations are commonly observed.Those sandy sediments consist of very fine- to fine-grained sand grains, and are sometimes tuffaceous. Pore-size distribution measurements and thin-section observations of these sands were undertaken, which indicated that porosities of muddy sediments are around 50 % but those of arenites range from 42 to 52%. Mean pore sizes and permeabilities of those arenites are larger than those of mudstones. While the presence of gas hydrate in intergranular pores of sands has not been confirmed, the soupy occurrence in recovered sediments may strongly indicate the presence of hydrate filling the intergranular pore system of sands. Such arenites have been recognized till now in the Mallik, NW Territory Canada, as well as in the Nankai Trough areas, which are expected common even in the subsurface sandy sediments at the eastern margin of Japan Sea. Concentration of gas hydrate may need primary intergranular pores large enough for gas hydrate to occur within host sediments likely deposited in the sedimentary environment such as deep sea channels. Small amounts of sandy sediment were retrieved as thin intercalations in Pleistocene silty layers, because supplying sediments may not be abundant due to sea level fluctuation during Pleistocene ice age. As time of deposition of coarse-grained sediments can be recognized by the thermoluminescence (TL) dating method, sandy sediments are usually tuffaceous and contain a small amount of quartz grains, and TL dating has been completed only for seven samples, which indicate 48 to 980 ka in age. This study was performed as a part of the MH21 Research Consortium.

Two Distinct Transport Mechanisms in AmtB and RhCG Proteins

The Amt/Rh family of membrane proteins facilitates the diffusion of ammonium across cellular membranes. Functional data show that Amt proteins, notably found in plants, transport ammonium ion (NH4+) while human rhesus (Rh) proteins transport ammonia (NH3). Comparison between the X-ray structures of the prokaryotic AmtB and the human RhCG reveals important differences at the level of their pore. Despite these important functional and structural differences between Amt and Rh proteins, studies of the AmtB transporter have led to the conclusion that proteins of both sub-families work according to the same mechanism and all transport ammonia. We performed molecular dynamics simulations of the AmtB and RhCG proteins under different conditions. Our free energy calculations suggest that the probability of finding NH3 molecules in the pore of AmtB is negligible in comparison to water and refute a single file diffusion of ammonia in AmtB. The pore lumen of RhCG is found to be more hydrophobic due to the presence of a phenylalanine conserved among Rh proteins. Simulations of RhCG also reveal that one of the signature histidine residues is occasionally exposed to the extra-cellular bulk, which is never observed in AmtB. These quite different hydration patterns are consistent with the idea that permeation in Amt and Rh proteins are not functionally equivalent and take place according to two distinct mechanisms. In both cases, after binding to the histidine dyad, ammonium deprotonates and diffuse down the pore as ammonia. Hydration of the pore in Amt proteins allows proton diffusion, which results in electrogenic transport. Such mechanism cannot take place in Rh proteins due to lack of pore hydration. Our QM/MM simulations rather show that the excess proton is released back to the extracellular bulk through a network of H-bonds, resulting in net NH3 transport.

Mechanism of expansion of mortars immersed in sodium sulfate solutions

The mechanisms behind the expansion of samples immersed in solutions containing sulfate ions have been controversial. Expansion is believed to originate in the formation of ettringite, but it is not possible to find any direct correlation between these two processes or to relate expansion purely to the increase in solid volume. Crystallization pressure is considered to be the most likely mechanism. A key aspect of this mechanism is the existence of supersaturation in the solution with respect to the growing crystal and it is not possible to directly measure the composition of the pore solution at different points within the specimen.In this paper we present a refinement of the crystallization pressure hypothesis to explain sulfate related expansion. We provide evidence that expansion is related to the transformation of monosulfate crystals embedded in the C-S-H to ettringite. Initially incoming sulfate reacts with aluminate containing hydrates in large pores to give ettringite without expansion. During this process the composition of the solution is buffered by the precipitation of solids so the rate of ingress does not depend strongly on the solution composition. After all this “freely available” aluminate has reacted, the concentration of sulfate ions in the pore solution increases, as indicated by the rise of sulfate absorbed on C-S-H. When the solution concentration reaches a critical level it provides the driving force for the precipitation of ettringite crystals in small pores within the C-S-H. Due to the confinement and the supersaturation of the solution this formation of ettringite leads to expansion of the paste.

Hydrate formation and growth in pores

Gas hydrates consist of guest gas molecules encaged in water cages. Methane hydrate forms in marine and permafrost sediments. In this study, we use optical, mechanical and electrical measurements to monitor hydrate formation and growth in small pores to better understand the hydrate pore habit in hydrate-bearing sediments. Hydrate formation in capillary tubes exposes the complex and dynamic interactions between nucleation, gas diffusion and gas solubility. The observation of hydrate growth in a droplet between transparent plates shows that the hydrate shell does not grow homogeneously but advances in the form of lobes that invade the water phase; in fact, the hydrate shell must be discontinuous and possibly cracked to justify the relatively fast growth rates observed in these experiments. Volume expansion during hydrate formation causes water to flow out of menisci; expelled water either spreads on the surface of water-wet substrates and forms a thin hydrate sheet, or remains next to menisci when substrates are oil-wet. Hydrate formation is accompanied by ion exclusion, yet, there is an overall increase in electrical resistance during hydrate formation. Hydrate growth may become salt-limited in trapped water conditions; in this case, aqueous brine and gas CH4 may be separated by hydrate and the three-phase system remains stable within the pore space of sediments.

Impact of nano-geothermal silica waste and chloride content on pore solution, microstructure, and hydration products in Portland cement pastes

An investigation was carried out on pastes of Portland cement partially substituted by a geothermal silica waste (GSW), which was obtained as a byproduct from a power plant that uses geothermal underground resources. The waste is predominantly nanometric amorphous silica with sodium and potassium chlorides. Pastes containing 0, 10, and 20% GSW and 0, 10, and 20% chlorides by weight of GSW were cured at 20 and 60 °C in order to evaluate the phases formed in the presence of chlorides by means of scanning electron microscopy. The calcium hydroxide consumption was followed using X-ray diffraction. Pore solution tests were performed utilizing a leaching method, which is an alternative technique that could provide an easier and more efficient analysis method compared to the conventional pore expression methodology requiring high pressures and special equipment. The results indicated that the blended cements showed an intense consumption of calcium hydroxide by the pozzolanic reaction and a more compact matrix of hydration products. Furthermore, the high concentration of chlorides provided by the GSW affected the pore solution, reducing the pH, and increasing the concentration of sodium and potassium ions. These were related to the formation of Friedel′s salt, which could be correlated with the reduction in chloride content in the aqueous phase.

Microstructure of High Strength Concrete Mercury Intrusion Porosimetry and Thermogravimetry Analysis

Microstructural properties such as pore structure and hydration play a decisive role in determining the properties of a concrete. This paper presents the investigation on pore structure and hydration process of high strength concrete. Pore structure study was conducted using mercury intrusion porosimetry and hydration progress was monitored using thermogravimetry analysis on various blended combinations of cementitious materials incorporating fly ash and silica fume as partial cement replacement. It was found that silica fume refined the pore structure efficiently and reduced the calcium hydroxide content as early as 1 day. All ternary blended systems containing fly ash and silica fume exhibited lower calcium hydroxide content and refined pore structure in comparison to their respective blended pastes.

A Phase Equilibrium Model for Gas Hydrates Considering Pore-Size Distribution of Sediments

The phase equilibrium condition for gas hydrates has been an important and difficult subject in gas hydrate-related research. In this paper, the mechanism of the effect of pore-size distribution on the phase equilibrium is first explored and the concept of effective pore radius is proposed. Using information on the pore-size distribution of sediments, a relationship between hydrate saturation and effective pore radius is developed. Combined with the van der Waals-Platteeuw model, this relationship was then used to develop a new phase equilibrium model for gas hydrates in sediments, which can properly account for the effect of pore-size distribution. In contrast to the traditional models, this new model does not represent a curve on the p-T plane but instead addresses the relationship between the temperature, pressure, and hydrate saturation. Such a feature allows the new model to take into account the effect of pore-size distribution on the phase equilibrium while treating the formation and/or dissolution processes of gas hydrates in pores more realistically. The simulated results were compared with the experimental data available in literature showing that the new model gives better results compared with the other traditional models. Given the temperature and the pore pressure, the hydrate saturation can be determined using the proposed model. Therefore, the new model can be used to estimate the amount of hydrate resources in the field.

Phase Behavior and 13C NMR Spectroscopic Analysis of the Mixed Methane + Ethane + Propane Hydrates in Mesoporous Silica Gels

In this study, the phase behavior and quantitative determination of hydrate composition and cage occupancy for the mixed CH(4) + C(2)H(6) + C(3)H(8) hydrates were closely investigated through the experimental measurement of three-phase hydrate (H)-water-rich liquid (L(W))-vapor (V) equilibria and (13)C NMR spectra. To examine the effect of pore size and salinity, we measured hydrate phase equilibria for the quaternary CH(4) (90%) + C(2)H(6) (7%) + C(3)H(8) (3%) + water mixtures in silica gel pores of nominal diameters of 6.0, 15.0, and 30.0 nm and for the quinary CH(4) (90%) + C(2)H(6) (7%) + C(3)H(8) (3%) + NaCl + water mixtures of two different NaCl concentrations (3 and 10 wt %) in silica gel pores of a nominal 30.0 nm diameter. The value of hydrate-water interfacial tension for the CH(4) (90%) + C(2)H(6) (7%) + C(3)H(8) (3%) hydrate was found to be 47 ± 4 mJ/m(2) from the relation of the dissociation temperature depression with the pore size of silica gels at a given pressure. At a specified temperature, three-phase H-L(W)-V equilibrium curves of pore hydrates were shifted to higher pressure regions depending on pore sizes and NaCl concentrations. From the cage-dependent (13)C NMR chemical shifts of enclathrated guest molecules, the mixed CH(4) (90%) + C(2)H(6) (7%) + C(3)H(8) (3%) gas hydrate was confirmed to be structure II. The cage occupancies of each guest molecule and the hydration number of the mixed gas hydrates were also estimated from the (13)C NMR spectra.