Central Pore Research Articles

Comparing the Effectiveness of SO2 with CO2 for Replacing Hydrocarbons from Nanopores

Molecular dynamic simulation is employed to investigate the fluid distribution of pure hydrocarbons, i.e., C1, C2, nC3, nC4, and nC5, in a hydrocarbon-wetting nanopore. SO2 and CO2 are then introduced into this nanopore to explore how SO2 and CO2 affect the hydrocarbon adsorption in an organic pore. Adsorption selectivity and replacement efficiency of SO2 over hydrocarbons are subsequently calculated and compared with those of CO2. The performance of SO2 and CO2 in enhancing hydrocarbon recovery from nanopores is thus evaluated. After introducing SO2 or CO2 into the “hydrocarbon-saturated” pore, the density of hydrocarbons in the adsorption layer decreases, while the density in the pore center increases. It suggests that both SO2 and CO2 can replace the adsorbed hydrocarbons from the pore surface. In addition, higher adsorption capacity is observed for CO2 than that for C1 but smaller than those of the heavier hydrocarbons, i.e., C2, nC3, nC4, and nC5. Comparatively, SO2 exhibits a stronger adsorption cap...

Self-Assembly of C3 Symmetric Rigid Macrolactams into Very Polar and Porous Trigonal Crystals.

Cyclohexane and cyclotri-β-alanyl have been used as scaffolds for the design of new C3 -symmetric rings incorporating conjugated alkenes and dienes. All three C3 -symmetric lactams share the same triangular shape and their crystal system is trigonal. They all belong to the R3 space group, R3m, R3 and R3c, for the increasingly large 12-, 18- and 24-membered rigid rings, respectively. All lactams stack on top of each other, through H-bonds and van der Waals noncovalent interactions, leading to endless supramolecular cylinders and tubes. The largest member of the family leads to tubes, the central pores of which is wide enough to let water in. A common feature of all the lactams is their very large dipole, of around 9 D, according to DFT calculations. Surprisingly, all the resulting cylinders and tubes pack side by side in the crystals, with all the dipoles pointing to the same direction. As a result, all three crystals are anisotropic and appear to be the first members of a new kind of highly polar crystals.

Experimental study on convective boiling of micro-pin-finned channels with parallel arrangement fins for FC-72 dielectric fluid

The boiling convective heat transfer of dielectric fluid of FC-72 in a microchannel with etched micro fins is experimentally studied. The microchannel test surface is a square of 10 mm size with a height of 100 μm. The surface of the microchannel is covered with parallel-nucleated fins of a cubic size of 100 μm. The fins are nucleated with the central pore size of 60 μm and an opening of 45 μm. The fins are arranged in the equal space of 400 μm. There is a planar electrical element below the microchannel, which produces an adjustable surface heat flux below the channel. The dielectric liquid enters the test microchannel and flows over the test surface and the fins. In the experiments, the mass velocity (94–275 kg/m2 s) and heat flux (0–6 W/cm2) are tested with a saturation temperature of either 35 or 50 °C. The heat transfer, the outlet vapor quality, and the pressure drop across the microchannel are measured and reported. The boiling behavior of FC-72 over the etched fins is also investigated using photos. The results show that the liquid first go through some superheat states and then the boiling phase change starts. When the boiling heat transfer occurs, a significant pressure-drop can be observed across the microchannel, but the surface temperature difference would also drop significantly. In the case of very low mass velocity of 94 kg/m2 s, the minimum superheat temperature-difference of 4.7 °C is observed.

The plant stomatal lineage at a glance.

Stomata are structures on the surfaces of most land plants that are required for gas exchange between plants and their environment. In Arabidopsis thaliana, stomata comprise two kidney bean-shaped epidermal guard cells that flank a central pore overlying a cavity in the mesophyll. These guard cells can adjust their shape to occlude or facilitate access to this pore, and in so doing regulate the release of water vapor and oxygen from the plant, in exchange for the intake of carbon dioxide from the atmosphere. Stomatal guard cells are the end product of a specialized lineage whose cell divisions and fate transitions ensure both the production and pattern of cells in aerial epidermal tissues. The stomatal lineage is dynamic and flexible, altering stomatal production in response to environmental change. As such, the stomatal lineage is an excellent system to study how flexible developmental transitions are regulated in plants. In this Cell Science at a Glance article and accompanying poster, we will summarize current knowledge of the divisions and fate decisions during stomatal development, discussing the role of transcriptional regulators, cell-cell signaling and polarity proteins. We will highlight recent work that links the core regulators to systemic or environmental information and provide an evolutionary perspective on stomata lineage regulators in plants.

Effect of inhibitors on oxygen permeability of wild type and knockout mouse red blood cells

We now recognize that the paradigm that all gases cross red blood cell (RBC) membranes by dissolving in and diffusing through the lipid phase is not correct. Work on human RBCs genetically deficient in aquaporin‐1 (AQP1) or the Rh complex (mainly RhAG) showed that these two proteins account for ~90% of membrane CO2 permeability (PM,CO2), and that 4,4′‐diisothiocyanatostilbene‐2,2′‐disulfonate (DIDS) reduces PM,CO2. We used stopped‐flow (SF) analysis of hemoglobin (Hb) absorbance spectra as we mixed oxygenated RBCs with an extracellular O2 scavenger, and determined the rate constant of Hb deoxygenation (kHbO2). Because kHbO2 depends on Hb kinetics as well as diffusion of O2 to the extracellular space, we used a mathematical model to estimate effects on membrane O2 permeability (PM,O2). We examined the effects of DIDS and chloromercuribenzenesulfonate (pCMBS), agents that decrease PM,CO2. We find that, in RBCs from wild type (WT) mice, pCMBS reduces kHbO2 by 64% (est. PM,O2 by ~84%) and DIDS, by 41% (est. PM,O2 by ~67%). Because pCMBS and DIDS likely act by targeting membrane proteins (rather than lipids), we hypothesized that O2, at least in part, crosses RBC membranes via the same membrane proteins that conduct CO2. Therefore, we examined RBCs from mice genetically deficient in AQP1, RhAG, or both, ± inhibitors. Deletion of AQP1 lowers kHbO2 by 11% (est. PM,O2 by ~27%); RhAG, by 16% (est. PM,O2 by ~35%); the double knockout (dKO), by 33% (est. PM,O2 by ~59%). The combination dKO + pCMBS lowers kHbO2 (vs. WT without inhibitors) by 77% (est. PM,O2 by ~91%), whereas dKO + DIDS lowers kHbO2 by 52% (est. PM,O2 by ~76%). The effects of pCMBS on estimated PM,O2 are very similar when we compare dKO vs. RhAG−/−, or when we compare WT vs. AQP1−/−. Thus, the deletion of AQP1 may have little effect on the sensitivity of PM,O2 to pCMBS—consistent with the hypothesis that AQP1 conducts O2 only via pathways other than the mercury‐sensitive monomeric pores (e.g., via the hydrophobic central pore). In summary, our data suggest that AQP1 and RhAG account for nearly 60% of RBC O2 permeability, and point towards the existence of other O2 channels that account for at least 30%.Support or Funding InformationSupported by ONR N00014‐15‐1‐2060, ONR N00014‐16‐1‐2535 to WFB and NIH K01‐DK107787 to ROThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Hydrogen exchange reveals Hsp104 architecture, structural dynamics, and energetics in physiological solution

Hsp104 is a large AAA+ molecular machine that can rescue proteins trapped in amorphous aggregates and stable amyloids by drawing substrate protein into its central pore. Recent cryo-EM studies image Hsp104 at high resolution. We used hydrogen exchange mass spectrometry analysis (HX MS) to resolve and characterize all of the functionally active and inactive elements of Hsp104, many not accessible to cryo-EM. At a global level, HX MS confirms the one noncanonical interprotomer interface in the Hsp104 hexamer as a marker for the spiraled conformation revealed by cryo-EM and measures its fast conformational cycling under ATP hydrolysis. Other findings enable reinterpretation of the apparent variability of the regulatory middle domain. With respect to detailed mechanism, HX MS determines the response of each Hsp104 structural element to the different bound adenosine nucleotides (ADP, ATP, AMPPNP, and ATPγS). They are distinguished most sensitively by the two Walker A nucleotide-binding segments. Binding of the ATP analog, ATPγS, tightly restructures the Walker A segments and drives the global open-to-closed/extended transition. The global transition carries part of the ATP/ATPγS-binding energy to the somewhat distant central pore. The pore constricts and the tyrosine and other pore-related loops become more tightly structured, which seems to reflect the energy-requiring directional pull that translocates the substrate protein. ATP hydrolysis to ADP allows Hsp104 to relax back to its lowest energy open state ready to restart the cycle.

In Silico Analysis of the Subtype Selective Blockage of KCNA Ion Channels through the µ-Conotoxins PIIIA, SIIIA, and GIIIA.

Understanding subtype specific ion channel pore blockage by natural peptide-based toxins is crucial for developing such compounds into promising drug candidates. Herein, docking and molecular dynamics simulations were employed in order to understand the dynamics and binding states of the µ-conotoxins, PIIIA, SIIIA, and GIIIA, at the voltage-gated potassium channels of the KV1 family, and they were correlated with their experimental activities recently reported by Leipold et al. Their different activities can only adequately be understood when dynamic information about the toxin-channel systems is available. For all of the channel-bound toxins investigated herein, a certain conformational flexibility was observed during the molecular dynamic simulations, which corresponds to their bioactivity. Our data suggest a similar binding mode of µ-PIIIA at KV1.6 and KV1.1, in which a plethora of hydrogen bonds are formed by the Arg and Lys residues within the α-helical core region of µ-PIIIA, with the central pore residues of the channel. Furthermore, the contribution of the K+ channel’s outer and inner pore loops with respect to the toxin binding. and how the subtype specificity is induced, were proposed.

Characterization of Residues in the 5-HT3 Receptor M4 Region That Contribute to Function.

5-HT3 receptors are members of the family of pentameric ligand gated ion channels (pLGICs). Each subunit has four transmembrane α-helices (M1-M4), with M4 being most distant from the central pore. Residues in this α-helix interact with adjacent lipids and the neighboring M1 and M3 helices, contributing to both receptor assembly and channel function. This study probes the role of each M4 receptor residue in the 5-HT3A receptor using mutagenesis and subsequent expression in HEK293 cells, probing functional parameters using fluorescence membrane potential sensitive dye. The data show that only one residue in M4 (Y441) and two flanking residues (D434 and W459) result in nonfunctional receptors when substituted with Ala: D434A and W459A-containing receptors ablate expression, while Y441A-containing receptor do not, suggesting the latter is involved in channel gating. Most other altered residues have wild-type-like properties, which is inconsistent with data from other pLGICs. Substitution of Y441 and W459 with other aromatics restores function, suggesting the π ring is important. Further substitutions indicate interactions of Y441 with D238 in M1, W459 with F144 in the Cys loop, and D434 with R251 in M2, data consistent with recently published structures. These regions are critical for transducing binding into gating, and thus interactions of these residues can explain their importance in the function of the 5-HT3 receptor. We also conclude that the small number of critical M4 residues compared to related receptors supports the hypothesis that M4 does not behave identically in all pLGICs.

Application of a Bioactive/Bioresorbable Three-Dimensional Porous Uncalcined and Unsintered Hydroxyapatite/Poly-D/L-lactide Composite with Human Mesenchymal Stem Cells for Bone Regeneration in Maxillofacial Surgery: A Pilot Animal Study.

A novel three-dimensional (3D) porous uncalcined and unsintered hydroxyapatite/poly-d/l-lactide (3D-HA/PDLLA) composite demonstrated superior biocompatibility, osteoconductivity, biodegradability, and plasticity, thereby enabling complex maxillofacial defect reconstruction. Mesenchymal stem cells (MSCs)—a type of adult stem cell—have a multipotent ability to differentiate into chondrocytes, adipocytes, and osteocytes. In a previous study, we found that CD90 (Thy-1, cluster of differentiation 90) and CD271 (low-affinity nerve growth factor receptor) double-positive cell populations from human bone marrow had high proliferative ability and differentiation capacity in vitro. In the present study, we investigated the utility of bone regeneration therapy using implantation of 3D-HA/PDLLA loaded with human MSCs (hMSCs) in mandibular critical defect rats. Microcomputed tomography (Micro-CT) indicated that implantation of a 3D-HA/PDLLA-hMSC composite scaffold improved the ability to achieve bone regeneration compared with 3D-HA/PDLLA alone. Compared to the sufficient blood supply in the mandibular defection superior side, a lack of blood supply in the inferior side caused delayed healing. The use of Villanueva Goldner staining (VG staining) revealed the gradual progression of the nucleated cells and new bone from the scaffold border into the central pores, indicating that 3D-HA/PDLLA loaded with hMSCs had good osteoconductivity and an adequate blood supply. These results further demonstrated that the 3D-HA/PDLLA-hMSC composite scaffold was an effective bone regenerative method for maxillofacial boney defect reconstruction.

Structure of amyloid \u03b225\u201335 in lipid environment and cholesterol-dependent membrane pore formation

The amyloid β (Aβ) peptide and its shorter variants, including a highly cytotoxic Aβ25–35 peptide, exert their neurotoxic effect during Alzheimer’s disease by various mechanisms, including cellular membrane permeabilization. The intrinsic polymorphism of Aβ has prevented the identification of the molecular basis of Aβ pore formation by direct structural methods, and computational studies have led to highly divergent pore models. Here, we have employed a set of biophysical techniques to directly monitor Ca2+-transporting Aβ25–35 pores in lipid membranes, to quantitatively characterize pore formation, and to identify the key structural features of the pore. Moreover, the effect of membrane cholesterol on pore formation and the structure of Aβ25–35 has been elucidated. The data suggest that the membrane-embedded peptide forms 6- or 8-stranded β-barrel like structures. The 8-stranded barrels may conduct Ca2+ ions through an inner cavity, whereas the tightly packed 6-stranded barrels need to assemble into supramolecular structures to form a central pore. Cholesterol affects Aβ25–35 pore formation by a dual mechanism, i.e., by direct interaction with the peptide and by affecting membrane structure. Collectively, our data illuminate the molecular basis of Aβ membrane pore formation, which should advance both basic and clinical research on Alzheimer’s disease and membrane-associated pathologies in general.

Challenging asymmetric cements as indicators of vadose diagenesis: “pseudo-gravitational” cements from the lower Pliensbachian of the Traras Mountains in NW Algeria

Asymmetric, pendant cements are considered good indicators for early lithification in the vadose zone. In the present study, asymmetric cements are recorded in thin-sections of a Lower Jurassic limestone from the Traras Mountains (northwest Algeria). Geopetal fabrics, however, indicate that these seemingly “pendant cements” are, in some places, oriented upwards, i.e., they have grown in the opposite direction from that expected, or they grew from grains towards the pore centers. These observations disprove their origin as gravitational cements precipitated from pendant water droplets on the undersides of grains as in the vadose zone. In contrast, a formation in the marine phreatic zone seems more probable. Under high-energy conditions, and after an early lithification stage with isopachous cements in the subtidal zone, strong tidally driven horizontal pore-water flow allowed sufficient seawater to pass through the slightly cemented but still highly permeable rock. Those grain sides, which were oriented towards the pore center, where faster flowing water prevailed, were more exposed to CaCO3-supersaturated percolating seawater and therefore the cements precipitated here show their greatest thickness. In relatively more protected areas around the margins of the pores, asymmetric cements are rarely developed. The resulting rock exhibits an unusual, heterogeneous cementation with preferential centripetal nucleation areas.

Functional Characterization of Gating in a Bacterial Cyclic Nucleotide-Gated Channel

Cyclic nucleotide-gated (CNG) channels produce the initial electrical signal in mammalian vision and olfaction. The transmembrane (TM) region contains a voltage-sensing domain and a pore domain. The cytoplasmic region is comprised of a C-linker domain followed by a cyclic nucleotide-binding domain (CNBD). CNG channels assemble as a tetramer with a central pore. cAMP and cGMP bind to the CNBD and produce an allosteric conformational rearrangement that opens the pore. The rearrangement occurring at the CNBD is well characterized due in large part to structural and biochemical experiments conducted on the purified C-linker/CNBD fragment from the related hyperpolarization-activated, cyclic nucleotide-gated channel, HCN2. However, the rearrangement occurring in the rest of the channel (C-linker and TM region) is not understood. Therefore, we are interested in developing a model system for structural and functional studies of gating in full-length CNG channels. SthK is a bacterial CNG channel that has the potential to serve as an ideal model system for studying CNG channel gating. It can be expressed in E. coli and purified in large quantities, and its resting-state structure has recently been published. However, SthK is reported to exhibit a low open probability (Po) even in saturating cAMP. This property limits its usefulness in studying the allosteric opening transition. Here, we express SthK in giant E. coli spheroplasts. We patch-clamped these spheroplasts and recorded both single-channel and macroscopic currents to characterize SthK gating in a bacterial membrane. Furthermore, we introduced mutations and show that they increased the Po while preserving SthK's biochemical tractability.

Structural Bases for Chemical and Mechanical Gating in the Piezo1 Channel

Mechanosensitive Piezo channels possess a propeller-like structure with a central cation-selective pore and three putative force-sensing blades encompassing several helical bundles called Piezo repeats. How membrane stretch and chemical agonists modulate Piezo channels is unknown. Here, using all-atom molecular dynamic stimulations and experimental assays, we localize the binding site of Yoda1, a small molecule Piezo1 activator, and identify stretch-induced conformational rearrangements of the blades. Yoda1 binding uncouples two adjacent Piezo repeats, facilitating stretch-induced blade motions, and alters long-range residue-residue contacts between pore and blades, as evidenced by Yoda1-induced channel activation of a mechanically-insensitive mutant. In addition, cation-selective fenestrations allow potassium, not chloride, ions to enter a pore vestibule. Our work reveals the structural bases of cationic selectivity, chemical modulation and mechanical sensing in a mammalian Piezo channel.

Energetics of Nucleotides Translocation through HIV-1 CA Hexamer

The HIV-1 capsid is a protein shell of the virus genome and other viral proteins. Viral reverse transcription is initiated inside the capsid and nucleoside triphosphates (NTPs) are synthesized into cDNA using viral RNA as a template, which requires NTPs translocation from cytoplasm into the capsid. Recently, it was reported that the center pore of HIV-1 capsid hexamer is a potential nucleotide channel to fuel cDNA synthesis and the R18 ring in the pore plays an essential role in recruiting nucleotides. However, the molecular mechanism of nucleotide translocate through the capsid hexamer is still unclear. Here, we designed and performed a series of all-atom molecular dynamic simulations sampling over 100 microseconds to study the translocation of the nucleoside triphosphates (NTPs) and inositol hexakisphosphate (IP6) through the central cavity of a CA hexamer. The latter was recently found to be a cellular cofactor of HIV-1 Gag assembly and maturation. The potential-of-mean-forces (PMFs) of the nucleoside triphosphates (NTPs) and inositol hexakisphosphate (IP6) translocation were calculated by employing Hamiltonian replica exchange (HREX)/Umbrella sampling (US) method. The single nucleotide translocation results suggested that nucleotides binding inside channel is energetically favorable and thus a passive translocation of single nucleotide seems unlikely. On the other hand, a translocation pathway involving two dATPs or a dATP and an IP6 molecule was found in the 2D-PMF results. Together, a cooperative translocation mechanism for nucleotide translocation through HIV-1 CA hexamer was proposed and tested experimentally.

TMC1 Forms the Pore of the Mechanosensitive Transduction Channels in Inner Ear Hair Cells

The TMC1 and TMC2 proteins are critical components of the mechanotransduction complex in vertebrate inner-ear hair cells. To understand TMC proteins, we sought insight into the structural properties of TMC1. First, we performed a variety of tests—including size-exclusion chromatography, chemical crosslinking, multi-angle light scattering and cryo electron microscopy— all of which suggest that TMC1 assembles as a dimer. Further, TMC predicted secondary structure and hydrophobicity suggest an architecture with ten transmembrane domains. The dimeric stoichiometry, and topology similarity between TMCs and the TMEM16 family of anion channels and lipid scramblases, suggest that TMCs may have a similar fold. We used I-TASSER to align TMC1 with TMEM16A, for which the atomic structure has been solved. TMEM16A dimerizes at an interface involving the tenth transmembrane domain, and each subunit of the dimer has an separate ion conducting pore, bounded by transmembrane domains S4-S7—a configuration strikingly different from well-known ion channels with a central pore bounded by three to six subunits. To ask whether S4-S7 of TMC1 might also enclose a functional pore, we designed and prepared AAV constructs of TMC1, bearing cysteine mutations, for expression in inner ear hair cells of Tmc1/2-null mice. Through our collaboration with Holt lab, we found that cysteine-modification reagents, when applied acutely, altered mechanosensory currents through these mutant channels in expected ways. Our data together provide evidence that TMC1 forms the pore of sensory transduction channels in auditory hair cells with a permeation pathway lined by residues on S4-S7.

Microscopic Insights into Biological Relevance of Membrane Channels in Gas Transport across Lipid Membranes

Membrane transport of small, non-polar gas molecules, such as O2 and CO2, is among fundamental processes of living cells. Because of their size and chemical properties, these molecules may unimpededly transit through the lipid phase of the membrane. However, varying degrees of gas permeability in membranes with different lipid compositions have been reported experimentally, suggesting involvement of protein channels, particularly aquaporins (AQPs), in gas transport across membranes. To account for membrane heterogeneity and to probe potential roles of AQPs in gas transport, we performed extensive MD simulations of gas diffusion through lipid membranes. The systems simulated included POPC bilayers embedded with an AQP tetramer (i.e., AQP1, AQP5 or AQP7), and protein-free lipid bilayer mixtures of POPC, cholesterol (CHL) and sphingomyelin (SM) or DPPC. Each of them contained an excess amount (125 molecules) of a gas species and was simulated for several hundred nanoseconds. Since the gas molecules were allowed to diffuse freely, their permeability coefficients were directly estimated by measuring their flow through the lipid and protein phases. The results showed that gas molecules diffused through the membrane via monomeric water and hydrophobic central pores of AQPs, and via the lipid phase. For fluid-like membranes (e.g., 100% POPC) which exhibited high gas permeability, AQPs would not facilitate the permeation. Highly-ordered or gel-like membranes (e.g., 100% SM and 50:50 SM:CHL or DPPC:CHL), on the other hand, exhibited reduced gas permeability as low as or even lower than through AQPs, suggesting that in such conditions, AQPs would become imminent in facilitating gas transport. Consistently with experimentally observed low gas permeability in high SM-CHL containing membranes, such as those of erythrocytes and ocular lens, our study suggests biological significance of protein-facilitated gas permeation across membranes.

Measurements and modeling of high-pressure adsorption of CH4 and CO2 on shales

The Simplified Local Density (SLD) model has been widely used to study the adsorption of gases on activated carbon, coal and shale. However, previous studies mainly focused on the experimental data fitting and the adsorption prediction based on model regression parameters. Few studies have been conducted to investigate the fluid distribution in the pores, which is of great significance for the study of the adsorption mechanism. In this study, high pressure adsorption experiments coupled with SLD model were impressed on the study of adsorption characterizations of shales from Sichuan Basin, China. The results showed that the SLD model could fit the adsorption of gas on shale well, and the average absolute deviations were within 10%. The gas was adsorbed around the pore wall when the pore size was large. As the pore size decreased, the gas molecules in the pore center also began to be adsorbed and finally all the gas in the pores were in an adsorbed state when the pore size was decreased to a certain value. According to the adsorption potential energy curves of CH4 and CO2 gas, CO2 was preferentially adsorbed relative to CH4 when the pore size was larger than 0.42 nm, which was consistent with the experimental results; while when the pore size is less than 0.42 nm, CH4 was preferentially adsorbed. This may be due to that in smaller pores, the repulsion of the pores to CO2 was greater than CH4, making it more difficult for CO2 to enter the pores. The adsorbed phase density was a function of temperature, pressure and pore size. The temperature only changed the magnitude of the adsorbed phase density, while the pore size not only changed the magnitude, but also changed the tendency of the adsorbed phase density with pressure. A temperature dependency model was finally established. Adsorption at a wider range of temperatures can be predicted basing on the model.

Na and Cl immobilization by size controlled calcium silicate hydrate nanometer pores

The movement of water and ions in the calcium silicate hydrate (C-S-H) gel pores determines the durability for the material. In this study, molecular dynamics was utilized to study aqueous NaCl solution capillary transport through the C-S-H gel pore with pore size of 3.5 nm, 2.5 nm, 1.5 nm and 1 nm. The penetration depth for the solution advancing frontier with menisci shape follows a parabolic relation as the function of time, matching well with classic LW capillary adsorption theory. The progressively reduction for the solution/C-S-H contact angle reflects the hydrophilic nature of the C-S-H surface. With decreasing of C-S-H gel pore size, the ions are filtered by the small C-S-H gel pore, with water invading deeply in the gel pore, and chloride and sodium ions remaining in the region of gel pore channel entry. The ultra-slow transport mechanism for ions in the nanometer channel has been further explained by the local structure and dynamics of ions hydrated ultra-confined in the gel pore. While the silicate chains in C-S-H surface can provide non-bridging oxygen sites to associate with the sodium ions by Na-Os connection, the courter calcium ions in C-S-H surface can capture the chloride ions, forming the ionic pair. Both Na-Os and Ca-Cl pairs have longer resident time that the unstable H-bond connection between water and solid oxygen. Furthermore, the transition region with slow mobility is formed at the channel entry region due to the coupling immobilization effect by both surfaces normal and parallel to the transport pathway. The presence of transition zones results in the necking of channel entry, which inhibits the ions with larger hydration shell from penetration. Additionally, at channel with size less than 2 nm, the Ca-Cl and Na-Cl ionic pairs accumulate to cluster and are highly concentrated in the center of the gel pore, blocking transport pathway for water molecules and ions.

Structure and mechanism of the ESCRT pathway AAA+ ATPase Vps4.

The progression of ESCRT (Endosomal Sorting Complexes Required for Transport) pathways, which mediate numerous cellular membrane fission events, is driven by the enzyme Vps4. Understanding of Vps4 mechanism is, therefore, of fundamental importance in its own right and, moreover, it is highly relevant to the understanding of many related AAA+ ATPases that function in multiple facets of cell biology. Vps4 unfolds its ESCRT-III protein substrates by translocating them through its central hexameric pore, thereby driving membrane fission and recycling of ESCRT-III subunits. This mini-review focuses on recent advances in Vps4 structure and mechanism, including ideas about how Vps4 translocates and unfolds ESCRT-III subunits. Related AAA+ ATPases that share structural features with Vps4 and likely utilize an equivalent mechanism are also discussed.

Adsorption and Diffusion of Benzene in Mg-MOF-74 with Open Metal Sites.

We performed molecular simulations to investigate the adsorption and diffusion of benzene in metal-organic framework Mg-MOF-74. At 300 K and 20 Pa, the saturated loading of benzene reaches 8.2 mmol/g, almost twice of (12,12) single-walled carbon nanotube with a similar pore size, and 93% of the benzene molecules in Mg-MOF-74 can desorb at 390 K. The energy analysis indicates that the van der Waals contribution still dominates 70-80% of the total fluid-wall interaction energy compared with the Coulombic contribution. We further analyzed the structure of benzene confined in Mg-MOF-74 by the molecular snapshots, pair correlation functions, orientational order parameters, and local density profiles. It is found that low temperature and high pressure make the structure of adsorbed benzene more similar to that of the liquid benzene. Moreover, the benzene molecules in the contact adsorption layer lie flat on the surface of adsorbent, whereas those molecules near the pore center have no particular orientations. Due to the existence of open metal sites, the structures of adsorbed benzene are more compact and ordered than those of bulk liquid benzene. Consequently, the self-diffusion coefficient of saturated benzene in Mg-MOF-74 at 300 K is significantly lower than that of bulk liquid benzene and confined liquid benzene in slit pores and disordered carbons by 4-5 orders of magnitude. We investigated the separation and diffusion of benzene/cyclohexane in the mixture in Mg-MOF-74 and found that the pores almost completely adsorbed benzene, although its self-diffusion coefficient was slightly lower than that of cyclohexane.