Mechanism Of Pore Formation Research Articles

Glu289 residue in the pore-forming motif of Vibrio cholerae cytolysin is important for efficient β-barrel pore formation

Vibrio cholerae cytolysin (VCC) is a potent membrane-damaging β-barrel pore-forming toxin. Upon binding to the target membranes, VCC monomers first assemble into oligomeric prepore intermediates and subsequently transform into transmembrane β-barrel pores. VCC harbors a designated pore-forming motif, which, during oligomeric pore formation, inserts into the membrane and generates a transmembrane β-barrel scaffold. It remains an enigma how the molecular architecture of the pore-forming motif regulates the VCC pore-formation mechanism. Here, we show that a specific pore-forming motif residue, E289, plays crucial regulatory roles in the pore-formation mechanism of VCC. We find that the mutation of E289A drastically compromises pore-forming activity, without affecting the structural integrity and membrane-binding potential of the toxin monomers. Although our single-particle cryo-EM analysis reveals WT-like oligomeric β-barrel pore formation by E289A-VCC in the membrane, we demonstrate that the mutant shows severely delayed kinetics in terms of pore-forming ability that can be rescued with elevated temperature conditions. We find that the pore-formation efficacy of E289A-VCC appears to be more profoundly dependent on temperature than that of the WT toxin. Our results suggest that the E289A mutation traps membrane-bound toxin molecules in the prepore-like intermediate state that is hindered from converting into the functional β-barrel pores by a large energy barrier, thus highlighting the importance of this residue for the pore-formation mechanism of VCC.

Effect of solid support and membrane tension on adsorption and lateral interaction of amphipathic peptides.

A wide class of antimicrobial amphipathic peptides is aimed to selectively form through pores in bacterial membranes. The partial incorporation of the peptides into the lipid monolayer leads to elastic deformation of the membrane. The deformation influences both the adsorption of the peptides and their lateral interaction. Detailed study of pore formation mechanisms requires an accurate determination of the surface concentration of the peptides at their given bulk concentration. Widely used methods to register the adsorption are atomic force microscopy (AFM), surface plasmon resonance refractometry (SPRR), and inner field compensation (IFC). AFM and SPRR utilize membranes deposited onto a solid support, while IFC operates with model membranes under substantial lateral tension. Here, we theoretically studied the effect of the solid support and lateral tension on the elastic deformations of the membrane induced by partially incorporated amphipathic peptides and thus on the peptide adsorption energy and lateral interaction. We demonstrated that, under conditions typical for AFM, SPRR, and IFC, the adsorption energy can increase by up to 1.5 kBT per peptide leading to about 4 times decreased surface concentration as compared to free-standing tensionless membranes. In addition, the effective lateral size of the peptide molecule increases by about 10%, which can have an impact on the quantitative description of the adsorption isotherms. Our results allow estimating the effects of the solid support and lateral tension on the adsorption and interaction of amphipathic peptides at the membrane surface and taking them into account in interpretation of experimental observations.

Microstructural evolution of early-stage oxide film on 15–15Ti austenitic stainless steel under 500 ℃ steam

The microstructural evolution with time and dissolved oxygen of the oxide film formed on 15–15Ti austenitic stainless steel during the early oxidation stage in steam at 500 ℃ was studied using multiple test instruments such as transmission electron microscopy (TEM). A triplex oxide structure with an outer Fe-rich layer, an inner Cr-rich layer, and a Ni-rich transition layer was confirmed for all samples. The relationship between corrosion resistance and oxide structure is discussed. One mechanism for pore formation in the inner oxide layer of austenitic steel is proposed based on the spatial distribution and migration behavior of Ni during oxidation.

Synergetic effect of graphene oxide and poly(MMA-co-GMA) copolymer on PSF ultrafiltration membrane for the remediation of potential environmental contaminants

• GO/poly(MMA-co-GMA)/PSF membrane was synthesized by phase inversion method. • GO as a nanofiller showed great influence on pore formation mechanism in membrane. • O/w emulsion flux for GO/poly(MMA-co-GMA)/PSF membrane was six fold to the pristine membrane. • GO/poly(MMA-co-GMA)/PSF membrane exhibited an excellent fouling resistant property. A novel hydrophilic polysulfone (PSF) membranes integrated with graphene oxide (GO) and bifunctional based poly(methyl methacrylate-co-glycidyl methacrylate) (poly(MMA-co-GMA)) copolymer were prepared. The functional groups of synthesized GO, poly(MMA-co-GMA) and PSF membranes were justified using FTIR spectroscopy. The variety of physicochemical analysis helped to demonstrate the presence GO (1.5 wt%) and poly(MMA-co-GMA) (0–2 wt%) and also its impact on morphology and performance of the membranes. Embedding of the pristine GO, affected the pore forming mechanism due to which the modified membrane exhibited uniform finger-like pores as a result of its hydrophilic filler property. PGC-1 membrane was endowed with maximum pore density, porosity and permeability. There was a significant decline in CA and the amount of BSA adsorbed from 81.2° and 0.22 mg/cm 2 for pristine membrane to 59.7° and 0.06 mg/cm 2 , respectively for PGC-2 membrane. By increasing the amount of the copolymer from 0 wt% to 2 wt% the irreversible fouling and total fouling were decreased, which resulted to high flux recovery ratio ( F r r ) for the modified PSF membrane. Besides, the o/w emulsion flux obtained for PGC-2 membrane was 6 times greater than that of the unmodified PSF membrane signifying that the foulants were unable to affect the modified membrane. In general, PSF/GO/poly(MMA-co-GMA) membrane with improved fouling resistance and high separation efficiency open up a way for its great potential for protein separation, oil/water emulsion separation and various other similar domains.

Organic matter occurrence and pore-forming mechanisms in lacustrine shales in China

The evolution of pore structure in shales is affected by both the thermal evolution of organic matter (OM) and by inorganic diagenesis, resulting in a wide variety of pore structures. This paper examines the OM distribution in lacustrine shales and its influence on pore structure, and describes the process of porosity development. The principal findings are: (i) Three distribution patterns of OM in lacustrine shales are distinguished; laminated continuous distribution, clumped distribution, and stellate scattered distribution. The differences in total organic carbon (TOC) content, free hydrocarbon content (S1), and OM porosity among these distribution patterns are discussed. (ii) Porosity is negatively correlated with TOC and plagioclase content and positively correlated with quartz, dolomite, and clay mineral content. (iii) Pore evolution in lacustrine shales is characterized by a sequence of decreasing-increasing-decreasing porosity, followed by continuously increasing porosity until a relatively stable condition is reached. (iv) A new model for evaluating porosity in lacustrine shales is proposed. Using this model, the organic and inorganic porosity of shales in the Permian Lucaogou Formation are calculated to be 2.5%–5% and 1%–6.3%, respectively, which correlate closely with measured data. These findings may provide a scientific basis and technical support for the sweet spotting in lacustrine shales in China.

Correlation of powder degradation, energy absorption and gas pore formation in laser-based powder bed fusion process of AlSi10Mg0.4

Gas pore formation observed during laser-based powder bed fusion is yet not fully understood. This study is a comprehensive investigation of the mechanisms of hydrogen pore formation in the powder bed fusion process of AlSi10Mg0.4 via laser beam. The influence of varying process parameters such as hatch distance, layer thickness and build plate temperature as well as the impact of virgin and long-term reused powder on part porosity and melt pool characteristics is investigated in detail. A novel, very efficient method to characterize powder aging by the correlation of powder gray value measurements with the oxygen content is presented. The relation between powder aging and the change of the absorption coefficient reveals the origin of gas formation as being intimately related to the energy input. Vacuum heat treatment of as-built parts indicates the potential of hydrogen removal in a postprocessing step with the prospect of welding additively manufactured aluminum parts.

Cryo-EM elucidates mechanism of action of bacterial pore-forming toxins

Pore-forming toxins (PFTs) rupture plasma membranes and kill target cells. PFTs are secreted as soluble monomers that undergo drastic structural rearrangements upon interacting with the target membrane and generate transmembrane oligomeric pores. A detailed understanding of the molecular mechanisms of the pore-formation process remains unclear due to limited structural insights regarding the transmembrane oligomeric pore states of the PFTs. However, recent advances in the field of cryo-electron microscopy (cryo-EM) have led to the high-resolution structure determination of the oligomeric pore forms of diverse PFTs. Here, we discuss the pore-forming mechanisms of various PFTs, specifically the mechanistic details contributed by the cryo-EM-based structural studies.

Implications of conformational flexibility, lipid binding, and regulatory domains in cell-traversal protein CelTOS for apicomplexan migration

Malaria and other apicomplexan-caused diseases affect millions of humans, agricultural animals, and pets. Cell traversal is a common feature used by multiple apicomplexan parasites to migrate through host cells and can be exploited to develop therapeutics against these deadly parasites. Here, we provide insights into the mechanism of the Cell-traversal protein for ookinetes and sporozoites (CelTOS), a conserved cell-traversal protein in apicomplexan parasites and malaria vaccine candidate. CelTOS has previously been shown to form pores in cell membranes to enable traversal of parasites through cells. We establish roles for the distinct protein regions of Plasmodium vivax CelTOS and examine the mechanism of pore formation. We further demonstrate that CelTOS dimer dissociation is required for pore formation, as disulfide bridging between monomers inhibits pore formation, and this inhibition is rescued by disulfide-bridge reduction. We also show that a helix-destabilizing amino acid, Pro127, allows CelTOS to undergo significant conformational changes to assemble into pores. The flexible C terminus of CelTOS is a negative regulator that limits pore formation. Finally, we highlight that lipid binding is a prerequisite for pore assembly as mutation of a phospholipids-binding site in CelTOS resulted in loss of lipid binding and abrogated pore formation. These findings identify critical regions in CelTOS and will aid in understanding the egress mechanism of malaria and other apicomplexan parasites as well as have implications for studying the function of other essential pore-forming proteins.

Enzymatic poly(gallic acid)-grafted α-l-lysine inhibits Staphylococcus aureus and Escherichia coli strains with no cytotoxicity for human cells.

The α-l-Lysine (LL) grafting onto the enzymatic poly(gallic acid) (PGAL) produces a helicoidal brush-like antimicrobial polymer containing outer positive-charged moieties. Best results are found with ca. 16mol% α-LL-grafting for the inhibition of gram-positive Staphylococcus aureus and gram-negative Escherichia coli strains. Membrane permeability, confocal and scanning electron microscopy studies suggest a pore-formation and translocation mechanisms by initial electrostatic interaction of positive charged polymer at the negatively charged bacterial membranes. The attained polymer displays high concentration of hemolysis (Hc) in erythrocytes, and no lymphocyte mitochondrial activity. Interestingly, PGAL-LL is not cytotoxic on human dermal fibroblast. The antioxidant activity after the LL hybridization is also demonstrated by DPPH, ORAC, FRAP and hydroxyl radical scavenging, which enhances the preservation of human cells in addition to antimicrobial for this polymer.

Preparation and pore-forming mechanism of MgO–Al2O3–CaO-based porous ceramics using phosphorus tailings

A simple strategy for preparing MgO–Al2O3–CaO-based porous ceramics (MACPC) with high strength and ultralow thermal conductivity has been proposed in this work based on the raw material of phosphorus tailings. The effects of phosphorus tailings content, carbon black addition and heat treatment temperature on the properties of MACPC were studied, and their pore-forming mechanism during sintering was revealed. The results showed that the main phase composition of MACPC was magnesia alumina spinel and calcium aluminate after sintering at 1225 °C. Furthermore, the MACPC exhibited excellent comprehensive properties when 60 wt% phosphorus tailings and 40 wt% alumina were added, whose apparent porosity was 62.8%, cold compressive strength was 14.8 MPa, and the thermal conductivity was 0.106 W/(m·K) at 800 °C. The synchronously enhanced strength and thermal insulation properties of MACPC were related to the formation of uniformly distributed micropores (<2 μm) and passages in the matrix, which originated from the decomposition of phosphorus tailings and the burnt out of carbon black during the sintering process. The preparation of MACPC with high temperature resistance and excellent mechanical and thermal insulation properties with the raw material of phosphorus tailings provided an effective method for the high-value utilization of phosphorus tailings.

Molecular and Kinetic Models for Pore Formation of Bacillus thuringiensis Cry Toxin.

Cry proteins from Bacillus thuringiensis (Bt) and other bacteria are pesticidal pore-forming toxins. Since 2010, when the ABC transporter C2 (ABCC2) was identified as a Cry1Ac protein resistant gene, our understanding of the mode of action of Cry protein has progressed substantially. ABCC2 mediates high Cry1A toxicity because of its high activity for helping pore formation. With the discovery of ABCC2, the classical killing model based on pore formation and osmotic lysis became nearly conclusive. Nevertheless, we are still far from a complete understanding of how Cry proteins form pores in the cell membrane through interactions with their host gut membrane proteins, known as receptors. Why does ABCC2 mediate pore formation with high efficiency unlike other Cry1A-binding proteins? Is the “prepore” formation indispensable for pore formation? What is the mechanism underlying the synergism between ABCC2 and the 12-cadherin domain protein? We examine potential mechanisms of pore formation via receptor interactions in this paper by merging findings from prior studies on the Cry mode of action before and after the discovery of ABC transporters as Cry protein receptors. We also attempt to explain Cry toxicity using Cry–receptor binding affinities, which successfully predicts actual Cry toxicity toward cultured cells coexpressing ABC transporters and cadherin.

Pore Formation Mechanism of A-Beta Peptide on the Fluid Membrane: A Combined Coarse-Grained and All-Atomic Model.

In Alzheimer’s disease, ion permeability through the ionic channel formed by Aβ peptides on cellular membranes appears to underlie neuronal cell death. An understanding of the formation mechanism of the toxic ionic channel by Aβ peptides is very important, but remains unclear. Our simulation results demonstrated the dynamics and mechanism of channel formation by Aβ1-28 peptides on the DPPC and POPC membrane by the coarse-grained method. The ionic channel formation is driven by the gyration of the radius and solvent accessible molecular surface area of Aβ1-28 peptides. The ionic channel formation mechanism was explored by the free energy profile based on the distribution of the gyration of the radius and solvent accessible molecular surface area of Aβ1-28 peptides on the fluid membrane. The stability and water permeability of the ionic channel formed by Aβ peptides was investigated by all-atomic model simulation. Our simulation showed that the ionic channel formed by Aβ1-28 peptides is very stable and has a good water permeability. This could help us to understand the pore formation mechanism by Aβ1-28 peptides on the fluidic membrane. It also provides us with a guideline by which to understand the toxicity of Aβ1-28 peptides’ pores to the cell.

Enhancing the abrasion resistance of hydrophobic coatings by flower bush-like micro rough structure of alumina

The anti-fouling design of ceramics is of great significance in improving their effectiveness and range of applications. Generally, constructing a micro rough structure coated with a low surface energy polymer substance is an effective strategy for creating a super-hydrophobic layer on ceramic surfaces. However, to be operated under certain wear conditions, the abrasion resistance of hydrophobic materials constructed by conventional methods is far from the requirements for application. Inspired by the multi-scale porous structure of the flower bush, a flower bush-like multi-scale micro rough structure (FMMS) has been constructed on ceramics using alumina pellets as petals. Compared with single-scale micro rough structures and non-connected pore micro rough structures, this structure enabled hydrophobic coatings which accelerated failure once worn, to attain an excellent contact angle (CA) of 143° and a sliding angle (SA) of 8.7° after a 100th abrasion test, demonstrating that the FMMS can significantly improve the mechanical stability of the coating. The hydrophobic model designed for the FMMS indicates that the excellent performance of the structure was achieved by a multi-scale protection mechanism for the hydrophobic material and a multi-scale pore-forming mechanism for the surface, and this provides a new idea for the design of highly abrasion-resistant super-hydrophobic surfaces on ceramics.

Preparation and properties of porous ZrB2 ceramics via combining in-situ boro/carbothermal reduction and partial sintering approach

In this manuscript, high performance porous ZrB2 ceramics were firstly fabricated via a novel and facile method combining in-situ boro/carbothermal reduction (BCTR) reaction (at 1300 °C for 2 h) and partial sintering technique (at 1900 °C for 1 h) using ZrO2, B4C, and carbon black as material precursors. The porosity, linear shrinkage, mechanical properties, and thermal conductivity of the porous ZrB2 ceramics can be regulated by varying particle size of ZrO2 and B4C powders. B4C and carbon black performed as reducing agent and pore-foaming agent for in-situ synthesis porous ZrB2 ceramics. The as-obtained porous ZrB2 ceramics with pore size in the 2–26 μm range exhibited low linear shrinkage of 0.5–7.8%, high porosity of 65–72%, relatively high compressive strength of 3–28 MPa and low thermal conductivity of 3–9 W m−1K−1. Effect of CO partial pressure on synthesizing ZrB2 and pore formation mechanism were also discussed in details. The comprehensive properties of as-obtained porous ZrB2 ceramics make them as candidate porous materials for thermal insulation applications.

Repurposing N-Doped Grape Marc for the Fabrication of Supercapacitors with Theoretical and Machine Learning Models.

Porous carbon derived from grape marc (GM) was synthesized via carbonization and chemical activation processes. Extrinsic nitrogen (N)-dopant in GM, activated by KOH, could render its potential use in supercapacitors effective. The effects of chemical activators such as potassium hydroxide (KOH) and zinc chloride (ZnCl2) were studied to compare their activating power toward the development of pore-forming mechanisms in a carbon electrode, making them beneficial for energy storage. GM carbon impregnated with KOH for activation (KAC), along with urea as the N-dopant (KACurea), exhibited better morphology, hierarchical pore structure, and larger surface area (1356 m2 g−1) than the GM carbon activated by ZnCl2 (ZnAC). Moreover, density functional theory (DFT) investigations showed that the presence of N-dopant on a graphite surface enhances the chemisorption of O adsorbates due to the enhanced charge-transfer mechanism. KACurea was tested in three aqueous electrolytes with different ions (LiOH, NaOH, and NaClO4), which delivered higher specific capacitance, with the NaOH electrolyte exhibiting 139 F g−1 at a 2 mA current rate. The NaOH with the alkaline cation Na+ offered the best capacitance among the electrolytes studied. A multilayer perceptron (MLP) model was employed to describe the effects of synthesis conditions and physicochemical and electrochemical parameters to predict the capacitance and power outputs. The proposed MLP showed higher accuracy, with an R2 of 0.98 for capacitance prediction.

Storage space development and hydrocarbon occurrence model controlled by lithofacies in the Eocene Jiyang Sub-basin, East China: Significance for shale oil reservoir formation

Complex mineral composition, multiple depositional processes, and strong reservoir heterogeneity cause the complexity and uniqueness of a lacustrine shale oil reservoir. Understanding the storage space development and hydrocarbon occurrence model should facilitate the analysis of the shale oil reservoir and hydrocarbon accumulation in lacustrine shales. In this study, the storage space development model for different lithofacies and the modes of hydrocarbon occurrence in different storage space were analyzed in the Es4s–Es3x shale in the Jiyang Sub-basin, East China, based on thin-section and field emission scanning electron microscopy (FE-SEM) observations, X-ray diffraction (XRD) analysis, physical property testing, and geochemical analysis. Inorganic pores, particularly recrystallization intercrystalline pores in calcite, are the key matrix pores for lacustrine shale oil. However, the types and abundance of storage space are noticeably different in various lithofacies. The hydrocarbon occurrence is mainly manifested in three states: (A) free state in interlaminar fractures, structural fractures, and abnormal pressure fractures; (B) adsorbed state in organic pores, intercrystalline pores in pyrite, and floccule pores; and (C) free state in large pore spaces, including dissolution pores and recrystallization intercrystalline pores, which can form a continuous hydrocarbon accumulation. The hydrocarbon generation potential and thermal maturity are closely associated with the lithofacies and mineral composition. The matching mechanisms of pore formation as well as hydrocarbon generation, migration, and accumulation are favorable. Among the various lithofacies, the organic-rich calcareous shale has abundant storage space, high porosity, total organic carbon content, and hydrocarbon potential, making it a “sweet spot” for shale oil exploration.

Pore formation mechanism and oxidation resistance of porous CoAl3 intermetallic prepared by rapid thermal explosion

Porous CoAl3 is a candidate material in the field of catalytic due to its high porosity, good thermostability and quasicrystal structure. However, its rapid preparation are still a challenge, and the oxidation resistance need to be further investigated. In this work, we have rapidly prepared porous CoAl3 by thermal explosion (TE) reaction and studied its oxidation process. The results show that two exothermic peaks at 616 °C and 646 °C, corresponding to the solid-phase diffusion and TE reaction, respectively. The heat released from the two reactions led to the expansion of the compact, which reached a maximum of 104% at 800 °C, and the corresponding open porosity reached at 53%. The pore sources include the original pores during the green compact pressing process, the Kirkendall pores generated by the solid-phase diffusion process and the in-situ pores generated by the Al consumption after the TE occurs. The cyclic oxidation of porous CoAl3 at 700 °C for 130 h only increased the weight by 1.52%, forming a continuous protective oxide film on the surface of the skeleton. It has been found that porous CoAl3 can combine the oxidation resistance of Co–Al monoliths alloys and the high porosity of porous materials, which have potential applications in the field of catalysis such as methanation at 600–700 °C.

Influence of Beam Figure on Porosity of Electron Beam Welded Thin-Walled Aluminum Plates.

Welded aluminum components in the aerospace industry are subject to more stringent safety regulations than in other industries. Electron beam welding as a highly precise process fulfills this requirement. The welding of aluminum poses a challenge due to its high tendency to pore formation. To gain a better understanding of pore formation during the process, 1.5 mm thick aluminum AW6082 plates were welded using specially devised beam figures in different configurations. The obtained welds were examined with radiographic testing to evaluate the size, distribution, and the number of pores. Cross-sections of the welds were investigated with light microscopy and an electron probe microanalyzer to decipher the potential mechanisms that led to porosity. The examined welds showed that the porosity is influenced in various ways by the used figures, but it cannot be completely avoided. Chemical and microstructural analyzes have revealed that the main mechanism for pore formation was the evaporation of the alloying elements Mg and Zn. This study demonstrates that the number of pores can be reduced and their size can be minimized using a proper beam figure and energy distribution.

Gasdermin-A3 pore formation propagates along variable pathways

Gasdermins are main effectors of pyroptosis, an inflammatory form of cell death. Released by proteolysis, the N-terminal gasdermin domain assembles large oligomers to punch lytic pores into the cell membrane. While the endpoint of this reaction, the fully formed pore, has been well characterized, the assembly and pore-forming mechanisms remain largely unknown. To resolve these mechanisms, we characterize mouse gasdermin-A3 by high-resolution time-lapse atomic force microscopy. We find that gasdermin-A3 oligomers assemble on the membrane surface where they remain attached and mobile. Once inserted into the membrane gasdermin-A3 grows variable oligomeric stoichiometries and shapes, each able to open transmembrane pores. Molecular dynamics simulations resolve how the membrane-inserted amphiphilic β-hairpins and the structurally adapting hydrophilic head domains stabilize variable oligomeric conformations and open the pore. The results show that without a vertical collapse gasdermin pore formation propagates along a set of multiple parallel but connected reaction pathways to ensure a robust cellular response.

Cooperative antimicrobial action of melittin on lipid membranes: A coarse-grained molecular dynamics study

We conducted a series of coarse-grained molecular dynamics (CG-MD) simulations to investigate the complicated actions of melittin, which is an antimicrobial peptide (AMP) derived from honey bee venom, on a lipid membrane. To accurately simulate the AMP action, we developed and used a protein CG model as an extension of the pSPICA force field (FF), which was designed to reproduce several thermodynamic quantities and structural properties. At a low peptide-to-lipid (P/L) ratio (1/102), no defect was detected. At P/L = 1/51, toroidal pore formation was observed due to collective insertion of multiple melittin peptides from the N-termini. The pore formation was initiated by a local increase in membrane curvature in the vicinity of the peptide aggregate. At a higher P/L ratio (1/26), two more modes were detected, seemingly not controlled by the P/L ratio but by a local arrangement of melittin peptides: 1. Pore formation accompanied by lipid extraction by melittin peptides:a detergent-like mechanism. 2. A rapidly formed large pore in a significantly curved membrane: bursting. Thus, we observed three pore formation modes (toroidal pore formation, lipid extraction, and bursting) depending on the peptide concentration and local arrangement. These observations were consistent with experimental observations and hypothesized melittin modes. Through this study, we found that the local arrangements and population of melittin peptides and the area expansion rate by membrane deformation were key to the initiation of and competition among the multiple pore formation mechanisms.