Inflammation-Induced Claudin-2 Upregulation Limits Pancreatitis Progression by Enhancing Tight Junction-Controlled Pancreatic Ductal Transport.

Pancreatitis is an inflammatory disease of the pancreas that can arise due to various factors, including environmental risks such as diet, alcohol, and smoking, as well as genetic predispositions. In some cases, pancreatitis may progress and become chronic, leading to irreversible damage and impaired pancreatic function. Genome-wide association studies (GWAS) have identified polymorphisms at the X-linked locus as risk factors for both sporadic and alcohol-related chronic pancreatitis.

Computational Models of Claudin Assembly in Tight Junctions and Strand Properties.

Claudins are one of the major components of tight junctions (TJs) that polymerize within the cell membrane and form interactions between cells. Some claudins seal the paracellular space, limiting paracellular flux, while others form selectively permeable ion channels that control the paracellular permeability of small ions. Claudin strands are known to be dynamic and reshape within TJs to accommodate large-scale movements and rearrangements of epithelial tissues.

Molecular dynamics analyses of CLDN15 pore size and charge selectivity.

The Claudin-15 (CLDN15) channel is important for nutrient, electrolyte, and water transport in the gastrointestinal tract. We used cell culture studies and molecular dynamics simulations to elucidate its structure and permeability mechanisms. We provide a model that underscores the crucial role of the D55 residue in the CLDN15 selectivity filter, which interacts with permeating cations.

Phase Separation and Ion Diffusion in Ionic Liquid, Organic Solvent, and Lithium Salt Electrolyte Mixtures.

The highly desirable characteristics of ternary mixtures of ionic liquids, organic solvents, and metal salts make them a promising candidate for use in various electrothermal energy storage and conversion systems. In this study, using large-scale classical molecular dynamics simulations, we looked into 10 different ternary electrolyte mixtures using combinations of [EMIM], [BMIM], and [OMIM] cations with [NO], [BF], [PF], [ClO], [TFO], and [NTf] anions, tetraglyme, and Li salt to study the effect of ionic liquid composition on the phase behavior of ternary electrolyte mixtures. We uncovered that in these electrolytes, phase separation is mainly a function of pairwise binding energy of the constituents of the mixture.

Thermodynamics and Kinetics in Anisotropic Growth of One-Dimensional Midentropy Nanoribbons.

One-dimensional (1D) materials demonstrate anisotropic in-plane physical properties that enable a wide range of functionalities in electronics, photonics, valleytronics, optoelectronics, and catalysis. Here, we undertake an in-depth study of the growth mechanism for equimolar midentropy alloy of (NbTaTi)S nanoribbons as a model system for 1D transition metal trichalcogenide structures. To understand the thermodynamic and kinetic effects in the growth process, the energetically preferred phases at different synthesis temperatures and times are investigated, and the phase evolution is inspected at a sequence of growth steps.

Molecular mechanism of claudin-15 strand flexibility: A computational study.

Claudins are one of the major components of tight junctions that play a key role in the formation and maintenance of the epithelial barrier function. Tight junction strands are dynamic and capable of adapting their structure in response to large-scale tissue rearrangement and cellular movement. Here, we present molecular dynamics simulations of claudin-15 strands of up to 225 nm in length in two parallel lipid membranes and characterize their mechanical properties.

Role of TM3 in claudin-15 strand flexibility: A molecular dynamics study.

Claudins are cell-cell adhesion proteins within tight junctions that connect epithelial cells together. Claudins polymerize into a network of strand-like structures within the membrane of adjoining cells and create ion channels that control paracellular permeability to water and small molecules. Tight junction morphology and barrier function is tissue specific and regulated by claudin subtypes.

Multicomponent Phase Separation in Ternary Mixture Ionic Liquid Electrolytes.

We investigate the phase behavior of ternary mixtures of ionic liquid, organic solvent, and lithium salt by molecular dynamics simulations. We find that at room temperature, the electrolyte separates into distinct phases with specific compositions; an ion-rich domain that contains a fraction of solvent molecules and a second domain of pure solvent. The phase separation is shown to be entropy-driven and is independent of lithium salt concentration.

Computational Modeling of Claudin Structure and Function.

Tight junctions form a barrier to control passive transport of ions and small molecules across epithelia and endothelia. In addition to forming a barrier, some of claudins control transport properties of tight junctions by forming charge- and size-selective ion channels. It has been suggested claudin monomers can form or incorporate into tight junction strands to form channels.

New Class of Electrocatalysts Based on 2D Transition Metal Dichalcogenides in Ionic Liquid.

The optimization of traditional electrocatalysts has reached a point where progress is impeded by fundamental physical factors including inherent scaling relations among thermokinetic characteristics of different elementary reaction steps, non-Nernstian behavior, and electronic structure of the catalyst. This indicates that the currently utilized classes of electrocatalysts may not be adequate for future needs. This study reports on synthesis and characterization of a new class of materials based on 2D transition metal dichalcogenides including sulfides, selenides, and tellurides of group V and VI transition metals that exhibit excellent catalytic performance for both oxygen reduction and evolution reactions in an aprotic medium with Li salts.

Molecular determination of claudin-15 organization and channel selectivity.

Tight junctions are macromolecular structures that traverse the space between adjacent cells in epithelia and endothelia. Members of the claudin family are known to determine tight junction permeability in a charge- and size-selective manner. Here, we use molecular dynamics simulations to build and refine an atomic model of claudin-15 channels and study its transport properties.

A lithium-oxygen battery with a long cycle life in an air-like atmosphere.

Lithium-air batteries are considered to be a potential alternative to lithium-ion batteries for transportation applications, owing to their high theoretical specific energy. So far, however, such systems have been largely restricted to pure oxygen environments (lithium-oxygen batteries) and have a limited cycle life owing to side reactions involving the cathode, anode and electrolyte. In the presence of nitrogen, carbon dioxide and water vapour, these side reactions can become even more complex.

Modeling and Analysis of Intercalant Effects on Circular DNA Conformation.

The large-scale conformation of DNA molecules plays a critical role in many basic elements of cellular functionality and viability. By targeting the structural properties of DNA, many cancer drugs, such as anthracyclines, effectively inhibit tumor growth but can also produce dangerous side effects. To enhance the development of innovative medications, rapid screening of structural changes to DNA can provide important insight into their mechanism of interaction.

Stable and Selective Humidity Sensing Using Stacked Black Phosphorus Flakes.

Black phosphorus (BP) atomic layers are known to undergo chemical degradation in humid air. Yet in more robust configurations such as films, composites, and embedded structures, BP can potentially be utilized in a large number of practical applications. In this study, we explored the sensing characteristics of BP films and observed an ultrasensitive and selective response toward humid air with a trace-level detection capability and a very minor drift over time.

Bimodal Phonon Scattering in Graphene Grain Boundaries.

Graphene has served as the model 2D system for over a decade, and the effects of grain boundaries (GBs) on its electrical and mechanical properties are very well investigated. However, no direct measurement of the correlation between thermal transport and graphene GBs has been reported. Here, we report a simultaneous comparison of thermal transport in supported single crystalline graphene to thermal transport across an individual graphene GB.

A structural rearrangement of the Na+/K+-ATPase traps ouabain within the external ion permeation pathway.

With the use of the energy of ATP hydrolysis, the Na+/K+-ATPase is able to transport across the cell membrane Na+ and K+ against their electrochemical gradients. The enzyme is strongly inhibited by ouabain and its derivatives, some that are therapeutically used for patients with heart failure (cardiotonic steroids). Using lanthanide resonance energy transfer, we trace here the conformational changes occurring on the external side of functional Na+/K+-ATPases induced by the binding of ouabain.

Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations.

A computational method is developed to allow molecular dynamics simulations of biomembrane systems under realistic ionic gradients and asymmetric salt concentrations while maintaining the conventional periodic boundary conditions required to minimize finite-size effects in an all-atom explicit solvent representation. The method, which consists of introducing a nonperiodic energy step acting on the ionic species at the edge of the simulation cell, is first tested with illustrative applications to a simple membrane slab model and a phospholipid membrane bilayer. The nonperiodic energy-step method is then used to calculate the reversal potential of the bacterial porin OmpF, a large cation-specific β-barrel channel, by simulating the I-V curve under an asymmetric 10:1 KCl concentration gradient.

An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations.

Developing an understanding of the mechanism of voltage-gated ion channels in molecular terms requires knowledge of the structure of the active and resting conformations. Although the active-state conformation is known from x-ray structures, an atomic resolution structure of a voltage-dependent ion channel in the resting state is not currently available. This has motivated various efforts at using computational modeling methods and molecular dynamics (MD) simulations to provide the missing information.

Molecular dynamics investigation of the ω-current in the Kv1.2 voltage sensor domains.

Voltage sensor domains (VSD) are transmembrane proteins that respond to changes in membrane voltage and modulate the activity of ion channels, enzymes, or in the case of proton channels allow permeation of protons across the cell membrane. VSDs consist of four transmembrane segments, S1-S4, forming an antiparallel helical bundle. The S4 segment contains several positively charged residues, mainly arginines, located at every third position along the helix.

Constant electric field simulations of the membrane potential illustrated with simple systems.

Advances in modern computational methods and technology make it possible to carry out extensive molecular dynamics simulations of complex membrane proteins based on detailed atomic models. The ultimate goal of such detailed simulations is to produce trajectories in which the behavior of the system is as realistic as possible. A critical aspect that requires consideration in the case of biological membrane systems is the existence of a net electric potential difference across the membrane.

Ouabain binding site in a functioning Na+/K+ ATPase.

The Na(+)/K(+) ATPase is an almost ubiquitous integral membrane protein within the animal kingdom. It is also the selective target for cardiotonic derivatives, widely prescribed inhibitors for patients with heart failure. Functional studies revealed that ouabain-sensitive residues distributed widely throughout the primary sequence of the protein.

On the sensing mechanism in carbon nanotube chemiresistors.

There has been recent controversy whether the response seen in carbon nanotube (CNT) chemiresistors is associated with a change in the resistance of the individual nanotubes or changes in the resistance of the junctions. In this study, we carry out a network analysis to understand the relative contributions of the nanotubes and the junctions to the change in resistance of the nanotube network. We find that the dominant mode of detection in nanotube networks changes according to the conductance level (defect level) in the nanotubes.

Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel.

The atomic models of the Kv1.2 potassium channel in the active and resting state, originally presented elsewhere, are here refined using molecular dynamics simulations in an explicit membrane-solvent environment. With a minor adjustment of the orientation of the first arginine along the S4 segment, the total gating charge of the channel determined from >0.

Molecular dynamics simulations of membrane channels and transporters.

Membrane transport constitutes one of the most fundamental processes in all living cells with proteins as major players. Proteins as channels provide highly selective diffusive pathways gated by environmental factors, and as transporters furnish directed, energetically uphill transport consuming energy. X-ray crystallography of channels and transporters furnishes a rapidly growing number of atomic resolution structures, permitting molecular dynamics (MD) simulations to reveal the physical mechanisms underlying channel and transporter function.

Dynamics of K+ ion conduction through Kv1.2.

The crystallographic structure of a potassium channel, Kv1.2, in an open state makes it feasible to simulate entire K(+) ion permeation events driven by a voltage bias and, thereby, elucidate the mechanism underlying ion conduction and selectivity of this type of channel. This Letter demonstrates that molecular dynamics simulations can provide movies of the overall conduction of K(+) ions through Kv1.