Pore Lining Research Articles

Free Energy Analysis of Peptide-Induced Pore Formation in Lipid Membranes by Bridging Atomistic and Coarse-Grained Simulations.

Antimicrobial peptides (AMPs) are attractive materials for combating the antimicrobial resistance crisis because they can kill target microbes by directly disrupting cell membranes. Although thousands of AMPs have been discovered, their molecular mechanisms of action are still poorly understood. One broad mechanism for membrane disruption is the formation of membrane-spanning hydrophilic pores which can be stabilized by AMPs. In this study, we use molecular dynamics simulations to investigate the thermodynamics of pore formation in model single-component lipid membranes in the presence of one of three AMPs: aurein 1.2, melittin and magainin 2. To overcome the general challenge of modeling long time scale membrane-related behaviors, including AMP binding, clustering, and pore formation, we develop a generalizable methodology for sampling AMP-induced pore formation. This approach involves the long equilibration of peptides around a pore created with a nucleation collective variable by performing coarse-grained simulations, then backmapping equilibrated AMP-membrane configurations to all-atom resolution. We then perform all-atom simulations to resolve free energy profiles for pore formation while accurately modeling the interplay of lipid-peptide-solvent interactions that dictate pore formation free energies. Using this approach, we quantify free energy barriers for pore formation without direct biases on peptides or whole lipids, allowing us to investigate mechanisms of pore formation for these 3 AMPs that are a consequence of unbiased peptide diffusion and clustering. Further analysis of simulation trajectories then relates variations in pore lining by AMPs, AMP-induced lipid disruptions, and salt bridges between AMPs to the observed pore formation free energies and corresponding mechanisms. This methodology and mechanistic analysis have the potential to generalize beyond the AMPs in this study to improve our understanding of pore formation by AMPs and related antimicrobial materials.

Cryo-EM structures of pannexin 1 and 3 reveal differences among pannexin isoforms.

Pannexins are single-membrane large-pore channels that release ions and ATP upon activation. Three isoforms of pannexins 1, 2, and 3, perform diverse cellular roles and differ in their pore lining residues. In this study, we report the cryo-EM structure of pannexin 3 at 3.9 Å and analyze its structural differences with pannexin isoforms 1 and 2. The pannexin 3 vestibule has two distinct chambers and a wider pore radius in comparison to pannexins 1 and 2. We further report two cryo-EM structures of pannexin 1, with pore substitutions W74R/R75D that mimic the pore lining residues of pannexin 2 and a germline mutant of pannexin 1, R217H at resolutions of 3.2 Å and 3.9 Å, respectively. Substitution of cationic residues in the vestibule of pannexin 1 results in reduced ATP interaction propensities to the channel. The germline mutant R217H in transmembrane helix 3 (TM3), leads to a partially constricted pore, reduced ATP interaction and weakened voltage sensitivity. The study compares the three pannexin isoform structures, the effects of substitutions of pore and vestibule-lining residues and allosteric effects of a pathological substitution on channel structure and function thereby enhancing our understanding of this vital group of ATP-release channels.

Molecular Dynamics Simulations of Claudin-10a and -10b Ion Channels: With Similar Architecture, Different Pore Linings Determine the Opposite Charge Selectivity.

Claudin polymers constitute the tight junction (TJ) backbone that forms paracellular barriers, at least for bigger solutes. While some claudins also seal the barrier for small electrolytes, others form ion channels. For cation-selective claudin-15 and claudin-10b, structural models of channels embedded in homo-polymeric strands have been suggested. Here, we generated a model for the prototypic anion-selective claudin-10a channel. Based on previously established claudin-10b models, dodecamer homology models of claudin-10a embedded in two membranes were analyzed by molecular dynamics simulations. The results indicate that both claudin-10 isoforms share the same strand and channel architecture: Sidewise unsealed tetrameric pore scaffolds are interlocked with adjacent pores via the β1β2 loop of extracellular segment 1. This leads to TJ-like strands with claudin subunits arranged in four joined rows in two opposing membranes. Several but not all cis- and trans-interaction modes are indicated to be conserved among claudin-10a, -10b, and -15. However, pore-lining residues that differ between claudin-10a and -10b (i.e., R33/I35, A34/D36, K69/A71, N54/D56, H60/N62, R62/K64) result in opposite charge selectivity of channels. This was supported by electric field simulations for both claudins and is consistent with previous electrophysiological studies. In summary, for the first time, a structural and mechanistic model of complete and prototypic paracellular anion channels is provided. This improves understanding of epithelial paracellular transport.

Genome-wide identification and characterisation of Aquaporins in Rosa chinensis

ABSTRACT Aquaporins (AQPs) are small integral membrane proteins that facilitate the efficient transport of small solutes like water, metalloids, urea, and CO2 across the membrane. Plant aquaporins are known to be involved in vital physiological processes like seed germination, stomatal movement, cell elongation, and reproductive growth. In the present study, 36 AQPs were identified through genome-wide computational analysis performed in the rose genome. Subsequent phylogenetic analysis classified the AQPs into five subfamilies, including 10 Plasma membrane intrinsic proteins (PIPs), 8 Tonoplast intrinsic proteins (TIPs), 9 Nodulin intrinsic proteins (NIPs), 3 Small intrinsic proteins (SIPs), and 6 uncharacterised intrinsic proteins (XIPs). Based on the prediction of silicon solute specificity, one of the NIPs is predicted to be a silicon transporter. Structural analysis revealed the characteristic six trans-membrane domains and two-half alpha helix harbouring two conserved NPA motifs in the majority of the predicted AQPs. The protein tertiary structures predicted with homology-based modelling were used to study the pore lining remains and to predict the solute transport activity of the AQPs. Expression profiling of the rose AQPs showed tissue-specific expression of many members. The data provided here will help in understanding the AQP-based solute transport system in roses and other related species.

A mitigation strategy for productivity impairment in sandstone reservoirs with varying clay mineralogy

The interaction between drilling fluids and oil and gas reservoir formations can result in the reduction or blockage of the micropore structural network, leading to a consequent decrease in permeability. Due to the negative economic impact of formation damage on hydrocarbon production, formulating drilling fluids with characteristics that minimise formation damage has been a major focus of the petroleum industry and researchers since the 1970s–1980s. Formation damage can significantly affect the ultimate productivity in hydrocarbon-bearing formations, especially in sandstone reservoirs with varying clay mineralogy such as kaolinite, smectite, illite, and mixed layer (illite + smectite) clay mineralogy in the micropore structural networks. These clay minerals are highly unstable/reactive and often appear as pore lining, pore bridging, and pore-filling along the walls of the micropore structural, inevitably coming into contact with drilling fluids (both solids and filtrates) that have invaded the micropore structure. Existing studies on the understanding of the relationship between drilling fluid formulation and formation damage mechanisms have not adequately addressed the role of individual species of clay minerals and their varying physicochemical properties during the formulation of drilling fluids for sandstone reservoirs with varying clay minerals. Instead, clay minerals are often treated as a whole or a single group. The work presented in this paper aims to examine and quantifies the impact of three drilling fluids (PAC-UL water-based, potassium formate, and halide drilling fluids) on productivity impairment in kaolinitic sandstone reservoirs and in kaolinitic and mixed-layer (illitic + smectitic) sandstone reservoirs. To achieve this, a high-temperature, high-pressure (HTHP) formation damage testing facility was designed and built to determine the initial and return permeability of selected hydrocarbon reservoirs using core samples. The formation damage mechanisms resulting from the interaction of the reservoir rocks with different formulations of drilling fluids are fully characterized using a combination of scanning electron microscopy, energy dispersive X-ray and micro-computed tomography. For all three drilling fluid formulations, the results showed an enhanced return permeability of the kaolinitic sandstone after interaction with the specially formulated halide drilling fluid.

3D printed piezoelectric porous structure with enhanced output performance and stress-electricity response for road energy harvesting

With the continuous innovation of intelligent interaction and energy technology, piezoelectric devices have attracted immense attention due to their unique stress-electricity response and conversion characteristics. Nevertheless, the limited structural variety and the lack of theoretical basis greatly limit the performance breakthrough and application prospect of these devices. Herein, a series of novel piezoelectric enhanced porous structures with excellent output performance was designed and prepared by powder bed fusion of polymers using a laser beam (PBF-LB/P). Using theoretical analysis and analog simulation, the influence mechanism of porous structure size characteristics (pore shape and line thickness) on piezoelectric performance was established. As a proof-of-concept, a piezoelectric road energy harvester based on cross-shaped structure was successfully constructed and optimized. The enhanced piezoelectric properties included an open-circuit voltage of 60.5 V and a short-circuit current of 654.2 nA, which were better than those of most reported piezoelectric parts. In addition, the energy harvester also exhibited outstanding piezoelectric response and energy supply efficiency in different stress modes and actual road environment. Hence, this work not only contributes a new route to develop novel piezoelectric structures, but also greatly enriches the application scenarios and functions of piezoelectric devices.

Structural assessment of OsNIP2;1 highlighted critical residues defining solute specificity and functionality of NIP class aquaporins

IntroductionNodulin-26-like intrinsic proteins (NIPs) are integral membrane proteins belonging to the aquaporin family, that facilitate the transport of neutral solutes across the bilayer. The OsNIP2;1 a member of NIP-III class of aquaporins is permeable to beneficial elements like silicon and hazardous arsenic. However, the atomistic cross-talk of these molecules traversing the OsNIP2;1 channel is not well understood. ObjectiveDue to the lack of genomic variation but the availability of high confidence crystal structure, this study aims to highlight structural determinants of metalloid permeation through OsNIP2;1. MethodsThe molecular simulations, combined with site-directed mutagenesis were used to probe the role of specific residues in the metalloid transport activity of OsNIP2;1. ResultsWe drew energetic landscape of OsNIP2;1, for silicic and arsenous acid transport. Potential Mean Force (PMF) construction illuminate three prominent energetic barriers for metalloid passage through the pore. One corresponds to the extracellular molecular entry in the channel, the second located on ar/R filter, and the third size constriction in the cytoplasmic half. Comparative PMF for silicic acid and arsenous acid elucidate a higher barrier for silicic acid at the cytoplasmic constrict resulting in longer residence time for silicon. Furthermore, our simulation studies explained the importance of conserved residues in loop-C and loop-D with a direct effect on pore dynamics and metalloid transport. Next we assessed contribution of predicted key residues for arsenic uptake, by functional complementation in yeast. With the aim of reducing arsenic uptake while maintaining beneficial elements uptake, we identified novel OsNIP2;1 mutants with substantial reduction in arsenic uptake in yeast. ConclusionWe provide a comprehensive assessment of pore lining residues of OsNIP2;1 with respect to metalloid uptake. The findings will expand mechanistic understanding of aquaporin’s metalloid selectivity and facilitate variant interpretation to develop novel alleles with preference for beneficial metalloid species and reducing hazardous ones.

Conformational changes in the human Cx43/GJA1 gap junction channel visualized using cryo-EM

Connexin family proteins assemble into hexameric hemichannels in the cell membrane. The hemichannels dock together between two adjacent membranes to form gap junction intercellular channels (GJIChs). We report the cryo-electron microscopy structures of Cx43 GJICh, revealing the dynamic equilibrium state of various channel conformations in detergents and lipid nanodiscs. We identify three different N-terminal helix conformations of Cx43—gate-covering (GCN), pore-lining (PLN), and flexible intermediate (FIN)—that are randomly distributed in purified GJICh particles. The conformational equilibrium shifts to GCN by cholesteryl hemisuccinates and to PLN by C-terminal truncations and at varying pH. While GJIChs that mainly comprise GCN protomers are occluded by lipids, those containing conformationally heterogeneous protomers show markedly different pore sizes. We observe an α-to-π-helix transition in the first transmembrane helix, which creates a side opening to the membrane in the FIN and PLN conformations. This study provides basic structural information to understand the mechanisms of action and regulation of Cx43 GJICh.

Cysteine mutagenesis reveals novel structure-function features within the predicted transmembrane domain of chloride intracellular ion channel 1 (CLIC1).

Chloride intracellular ion channels (CLICs) are a unique class of metamorphic proteins that exists as soluble proteins and can auto-insert into the membrane to form an ion channel. The soluble structure of all the CLICs is well established but the structural information on the membrane form is lacking. CLICs are known to have a single putative transmembrane (PTM) region and proteins oligomerize to a tetramer to form a functional channel. CLIC1 is a sensor of oxidative stress, overexpressed in different types of cancer, and involved in diabetes, cell viability, and angiogenesis. The PTM region of CLIC1 encompasses residue 24-46, where cysteine at position 24 is a critical redox-sensitive residue. However, the precise arrangement of the residues in the pore region is not known. Hence, to identify the key residue involved in the gating mechanism and ion selectivity, the putative residues lining the pore region were mutated using site-directed mutagenesis. We incorporated the substituted cysteine accessibility method (SCAM) and recorded the channel activity of the mutants in the whole-cell and inside-out configurations. The ion selectivity was measured by perfusing with different anions (chloride, bromide, fluoride, and phosphate). The open channel probability (Po) is significantly higher in R29C mutant (0.88) compared to WT (0.21), suggesting R29C residue is involved in CLIC1 gating. Similarly, the CLIC1 is highly selective for chloride ions as compared to other anions, and the selective filer is located between V33C and K37C residues. We probed substituted cysteine residues with cadmium and identified that the T40C showed a reduction in Po and amplitude. Our results have delineated the pore lining of the CLIC1 and identified the residues involved in its gating and regulating the chloride selectivity.

Effect of Authigenic Chlorite on the Pore Structure of Tight Clastic Reservoir in Songliao Basin.

Authigenic chlorite is a common clay mineral in clastic rock reservoirs, and it has an important influence on the pore structure of tight clastic rock reservoirs. In this paper, the tight clastic reservoirs in the Lower Cretaceous Yingcheng Formation in the Longfengshan subsag in the Changling fault depression in the Songliao Basin were investigated. Polarized light microscopy, scanning electron microscopy (SEM), X-ray diffraction (XRD), high-pressure mercury injection (HPMI), and low temperature nitrogen adsorption (LTNA) were used to study the influence of authigenic chlorite on the pore structure of tight clastic reservoirs. The results show that the authigenic chlorite in the study area was mainly generated in the form of pore linings. The formation of the authigenic chlorite was mainly controlled by the parent rock type and the sedimentary microfacies in the provenance area. The hydrolysis and dissolution of the iron- and magnesium-rich intermediate-mafic magmatic rocks and the high-energy, open, weakly alkaline reducing environment in the delta-front underwater distributary channel were the key factors controlling the formation of the authigenic chlorite in the study area. The pore-lining chlorite slowed down compaction and inhibited quartz overgrowth, protecting the original pores. Moreover, there are a large number of intercrystalline pores in the chlorite, which provided channels for the flow of acidic water and thus the formation of secondary pores, playing a positive role in the physical properties of the tight clastic rock reservoirs. However, the pore-filling chlorite also blocked the pore throats, playing a negative role in the physical properties of the tight clastic rock reservoirs. The tight clastic rock reservoirs with pore-lining chlorite generally had low displacement pressures and large pore throat radii. The morphology of the nano-scale pores was mainly parallel plate-shaped slit pores. There were many primary pores and a small number of secondary pores in the reservoir. Some of the pores were connected by narrow-necked or curved sheet-like throats, and the pore structure was relatively good. A higher relative content of chlorite led to a larger nano-scale pore throat radius, a smaller specific surface area, a smoother pore surface, and stronger homogeneity. Authigenic chlorite played a positive role in the formation of the tight clastic reservoirs in the study area.

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.

The Relationship between Chlorite and Reservoir Quality in the Huagang Formation, Xihu Depression, China

Low permeability tight gas resources account for 90% of the Xihu Sag. Under the background of extensive development of low permeability and tight reservoirs, the key to economic and effective development is to find sweet reservoir formation. To clarify the origin and distribution of a sweet reservoir in the study area, it is important to study the formation and evolution mechanisms of chlorite. In this study, based on the analysis of thin section, X-ray diffraction and SEM, through the analysis of the key factors in the formation of authigenic chlorite of the Huagang Formation in the middle and north of the central inversion structural belt, we reasoned the formation and evolution process of chlorite in the whole life cycle. According to the sedimentary diagenetic response characteristics of chlorite, two types of favorable sedimentary facies belts of chlorite are identified. The results showed that the development of pore-lined chlorite is a natural advantage of reservoirs in the East China Sea. Chlorite is formed under the joint action of three factors: the source of iron and magnesium ions, the alkaline environment in the early diagenetic stage and the open fluid field. After the formation of pore-lined chlorite, the sweet spots developed under the protection of four mechanisms: inhibiting quartz cementation, enhancing compression resistance, protecting macropore throat and primary pores, and promoting secondary intergranular dissolved pores. When the content of chlorite in the pore lining is high (relative content > 35%), the lining thickness is moderate (4–10 μm). A high degree of wrapping and good crystallization are conducive to the formation and preservation of sweet spots.

Molecular characterization and structural dynamics of Aquaporin1 from walking catfish in lipid bilayers

Aquaporin's (AQPs) are the major superfamily of small integral membrane proteins that facilitates transportation of water, urea, ammonia, glycerol and ions across biological cell membranes. Despite of recent advancements made in understanding the biology of Aquaporin's, only few isoforms of aquaporin 1 (AQP1) some of the teleost fish species have been characterized at molecular scale. In this study, we made an attempt to elucidate the molecular mechanism of water transportation in AQP1 from walking catfish (Clarias batrachus), a model species capable of breathing in air and inhabits in challenging environments. Using state-of-the-art computational modelling and all-atoms molecular dynamics simulation, we explored the structural dynamics of full-length aquaporin 1 from walking catfish (CbAQP1) in lipid mimetic bilayers. Unlike AQP1 of human and bovine, structural ensembles of CbAQP1 from MD revealed discrete positioning of pore lining residues at the intracellular end. Snapshots from MD simulation displayed differential dynamics of aromatic/arginine (ar/R) filter and extracellular loop C bridging transmembrane (TM) helix H3 and H4. Distinct conformation of large extracellular loops, loop bridging TM2 domain and HB helix along with positioning of selectivity filter lining residues controls the permeability of water across the bilayer. Moreover, the identified unique and conserved lipid binding sites with 100% lipid occupancy signifies lipid mediated structural dynamics of CbAQP1. All-together, this is the first ever report on structural-dynamics of aquaporin 1 in walking catfish which will be useful to understand the molecular basis of transportation of water and other small molecules under varying degree of hyperosmotic environment.

High-Performance Biomimetic Water Channel: The Constructive Interplay of Interaction Parameters and Hydrophilic Doping Levels.

In this study, we introduce a superfast biomimetic water channel mimicking the hydrophobicity scales of the Aquaporin (AQP) pore lining. Molecular dynamics simulation is used to scrutinize the impact of hydrophilic doping level in the nanotube and the water-wall interaction strength on water permeability. In the designed biomimetic channel, the constructive interplay of Lennard-Jones (LJ) ε parameters and hydrophilic doping levels increased the possibility of ultrafast water transport. Moreover, a unique set of LJ parameters is discovered for each biomimetic channel with different hydrophilic doping levels, enhancing water permeation. Inside high-performance biomimetic channels, water distribution surprisingly implies a varying pore geometry that narrows down in the middle, mimicking the pattern obtained from GplF pore analysis, evoking the narrow pore induced by the aromatic/arginine selectivity filter. This exciting accordance occurred as a result of tailoring specific hydrophilic arrays within the hydrophobic channel backbone by mimicking the AQP pore interior. The main takeaway of hydrophilic doping arrays implanted within the hydrophobic nanotube is to break the large barrier in the water-wall vdW energy profile into multiple reduced ones to increase water conduction. Consequently, the "water jumping" phenomenon in the middle of the biomimetic channel occurs under specific circumstances. The biomimetic channel with the highest value of water permeability of about 13.67 ± 0.66 × 10-13 cm3·s-1 exhibits the best mechanism for artificial water channels (AWCs), serving superfast water transport considering the low entrance barrier and weak water-wall interaction.

Concrete protection by combined hygroscopic and hydrophilic crystallization waterproofing applied to fresh concrete

Crystallization-based waterproofing is a multi-functional technology which combines hygroscopic and hydrophilic crystallization pore blocking with hydrophobic pore lining. This paper presents experimental findings of investigating dual-crystallization waterproofing engineered treatment (DCE) onto fresh concrete. The DCE has the potential to provide an effective solution to various concrete durability problems associated with all water phases of vapor, liquid and solid. The characteristics of treated and untreated concrete specimens have been investigated experimentally according to ASTM procedures. The DCE system is able to reduce moisture penetration through concrete thus enhances concrete durability. The DCE is able to increase concrete resistance against chloride ion penetration and to reduce damages from freezing and thawing cycles, scaling and ASR. Additionally, the application of DCE technology improves water retention for better cement hydration leading to an enhancement of surface characteristics (adhesion strength and surface smoothness).

Side‐Chain Polarity of Amino Acids within the Kir7.1 Channel Pore Lining Determine Permeability and Function

Background Inwardly rectifying potassium (K+) channels (Kir) maintain membrane potential and K+ homeostasis across many tissues. Mutations in the KCNJ13 gene encoding for Kir7.1 protein, in the retinal pigmented epithelium (RPE), cause pediatric blindness. One point mutation in the KCNJ13 gene c.458C>T Threonine (T) to Isoleucine (I) at amino acid position 153 lines the inner pore of the tetrameric protein. We sought to elucidate the impact of pore region amino-acid hydrophobicity and side-chain length on the channel function. Hypothesis Amino acid side-chain polarity and length at position T153 are important determinants of Kir7.1 channel structure/function. Methods HEK293 cells in culture were transfected with GFP tagged wildtype (WT) Kir7.1, T153I, T153G, T153A, T153L, T153C, or T153S plasmid DNA. Live-cell imaging, using the Nikon-C2 confocal system, mapped the expression of GFP fused protein. Hoescht and WGA-Alexa 594 labeled the nucleus and plasma membrane, respectively. Off-line image analysis was performed with Nikon NIS Elements. Whole-cell patch-clamp electrophysiology with either extracellular Ringer's or Rb+ determined channel function. Extracellular K+-gradient was used to determine chord conductance. Data analyzed using the Clampfit program. Results Live-cell imaging indicated that Kir7.1 WT and all mutants studied are trafficked to the membrane. The IV plot for the Kir7.1 WT showed inward current measured at -150 mV with a mean amplitude of -863.67 ± 142.44 pA (n = 8) compared to Ile -68.54 ± 10.49 pA (n = 9, P = 2.79x10-5). Extracellular K+ dependent chord conductance further confirmed that T153I is nonfunctional. The current amplitude rank order for the mutant channel K+ permeability was Cys > WT > Ser > Gly > Ile > Ala> Leu. The membrane potential, measured as zero-current potential, was -57.75 ± 3.23 mV (n = 8) for the WT compared to-5.46 ± 6.01 mV (n = 9, P = 2.27x10-6) for the disease mutant with a rank order of Cys > WT > Ser > Leu > Gly > Ile > Ala. Rb+ ion, selectively permeates through Kir7.1 channel with a Rb+-current fold-change of7.28 ± 1.63 (n = 8) for WT versus 6.48 ± 2.78 (n = 9, P=0.81) for the disease mutant. The rank order of Rb+-current fold-change was Leu > Ser > WT > Ile > Cys > Gly > Ala. Conclusion Even though all the mutant channels traffick normally to the membrane, T153I was non-functional as determined by K+ ion permeability. Upon testing a more permeable ion, Rb+, it was deemed that T153I is actually dysfunctional. Based on the rank order, a substitution of polar amino acid at position 153 is required for Kir7.1 channel function. Permeability of all the mutant channels except T153A to Rb+ indicates that channel function is dependent on size of the cation. Since aa position T153 is within the inner pore-lining of the channel, a hydrophobic aa might alter protein-lipid interaction to affect channel function. Additionally, short-chain amino acids may further alter protein-protein interactions within the channel.

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.

Free energy of hydrophilic and hydrophobic pores in lipid bilayers by free energy perturbation of a restraint.

The free energy of pore formation in lipid bilayers has been previously calculated using a variety of reaction coordinates. Here, we use free energy perturbation of a cylindrical lipid exclusion restraint to compute the free energy profile as a function of pore radius in dimyristoylphosphatidylcholine (DMPC) and dioleoylphosphatidylcholine (DOPC) bilayers. Additionally restraining the headgroups to lie on the membrane surface allows us to also calculate the free energy profile of hydrophobic pores, i.e., cylindrical pores lined by acyl chains. For certain pore radii, the free energy of wetting of hydrophobic pores is calculated using the density bias method. It is found that wetting of hydrophobic pores becomes thermodynamically favorable at 5.0 Å for DMPC and 6.5 Å for DOPC, although significant barriers prevent spontaneous wetting of the latter on a nanosecond time scale. The free energy of transformation of hydrophilic pores to hydrophobic ones is also calculated using free energy perturbation of headgroup restraints along the bilayer normal. This quantity, along with wetting and pore growth free energies, provides complete free energy profiles as a function of radius. Pore line tension values for the hydrophilic pores obtained from the slope of the free energy profiles are 37.6 pN for DMPC and 53.7 pN for DOPC. The free energy profiles for the hydrophobic pores are analyzed in terms of elementary interfacial tensions. It is found that a positive three-phase line tension is required to explain the results. The estimated value for this three-phase line tension (51.2 pN) lies within the expected range.

Petrography and authigenic chlorite in the Siegenian reservoir rocks, Berkine Basin, eastern Algerian Sahara

In Berkine Basin, the Siegenian stage is constituted by clayey sandstones and it contains several reservoir levels especially in the perimeter of Zemlet El Arbi, where the sandstone levels can reach 30 m of thickness. The Siegenian reservoir shows a tidal deposit environment, it is located at depths greater than 3200 m, its average thickness is 200 m in the south and it decreases to 30 m because it is strongly affected by Hercynian orogeny mainly in the northwest of the studied area. Petrographic and X-ray diffraction studies indicate the presence of authigenic chlorite, which is the most important cement in Siegenian sandstones. Chlorite appears in different forms: grain coating, pore lining, pore filling and rarely in the form of oolite. It often has a great impact on petrophysical reservoir qualities by inhibiting authigenic quartz overgrowth in porous space and preserving porosity. Other diagenetic phenomena observed are mechanical compaction, alteration and dissolution of feldspars and biotite, precipitation of clay minerals (smectite, berthierine, chlorite, kaolinite and illite) and precipitation of secondary silica, carbonates, pyrite and haematite.

SEM-EDX study on authigenic clay minerals in sandstone of Jatiluhur formation

The presence of authigenic clay minerals is usually found in sandstones where these minerals grow in the environment itself. Authigenic clay minerals provide benefits to sandstones, especially to determine the quality of porosity and permeability in sandstones. The samples in this study were collected from an outcrop of measured section at Cipamingkis’ River. The main goal of this study was to understand the presence of authigenic clay minerals in sandstones caused by the diagenetic process using Scanning Electron Microscope and Energy Dispersive X-Ray (SEM – EDX method. The results of this study were kaolinite, smectite, and illite found in very dominant amounts in sandstones as pore linings, pore fillings, replacement, and vug fillings.