Surface potentials and the calculated selectivity of ion channels

Asymmetric Lipid Bilayers and Potassium Channels Embedded Therein in the Contact Bubble Bilayer

Cell membranes are highly intricate systems comprising numerous lipid species and membrane proteins, where channel proteins, lipid molecules, and lipid bilayers, as continuous elastic fabric, collectively engage in multi-modal interplays. Owing to the complexity of the native cell membrane, studying the elementary processes of channel-membrane interactions necessitates a bottom-up approach starting from forming simplified synthetic membranes. This is the rationale for establishing an in vitro membrane reconstitution system consisting of a lipid bilayer with a defined lipid composition and a channel molecule. Recent technological advancements have facilitated the development of asymmetric membranes, and the contact bubble bilayer (CBB) method allows single-channel current recordings under arbitrary lipid compositions in asymmetric bilayers. Here, we present an experimental protocol for the formation of asymmetric membranes using the CBB method. The KcsA potassium channel is a prototypical model channel with huge structural and functional information and thus serves as a reporter of membrane actions on the embedded channels. We demonstrate specific interactions of anionic lipids in the inner leaflet. Considering that the local lipid composition varies steadily in cell membranes, we `present a novel lipid perfusion technique that allows rapidly changing the lipid composition while monitoring the single-channel behavior. Finally, we demonstrate a leaflet perfusion method for modifying the composition of individual leaflets. These techniques with custom synthetic membranes allow for variable experiments, providing crucial insights into channel-membrane interplay in cell membranes.

Revealing the single-channel characteristics of OprD (OccAB1) porins from hospital strains of Acinetobacter baumannii

Nowadays, reports of antimicrobial resistance (AMR) against many antibiotics are increasing because of their misapplication. With this rise, there is a serious decrease in the discovery and development of new types of antibiotics amid an increase in multi-drug resistance. Unfermented Acinetobacter baumannii from gram-negative bacteria, which is one of the main causes of nosocomial infections and multi-drug resistance, has 4 main kinds of antibiotic resistance mechanism: inactivating antibiotics by enzymes, reduced numbers of porins and changing of their target or cellular functions due to mutations, and efflux pumps. In this study, characterization of the possible mutations in OprD (OccAB1) porins from hospital strains of A. baumannii were investigated using single channel electrophysiology and compared with the standard OprD isolated from wild type ATCC 19,606. For this aim, 5 A. baumannii bacteria samples were obtained from patients infected with A. baumannii, after which OprD porins were isolated from these A. baumannii strains. OprD porins were then inserted in an artificial lipid bilayer and the current-voltage curves were obtained using electrical recordings through a pair of Ag/AgCl electrodes. We observed that each porin has a characteristic conductance and single channel recording, which then leads to differences in channel diameter. Finally, the single channel data have been compared with the gene sequences of each porin. It was interesting to find out that each porin isolated has a unique porin diameter and decreased anion selectivity compared to the wild type.

Electrification of water interface

The surface charge of a water interface determines many fundamental processes in physical chemistry and interface science, and it has been intensively studied for over a hundred years. We summarize experimental methods to characterize the surface charge densities developed so far: electrokinetics, double-layer force measurements, potentiometric titration, surface-sensitive nonlinear spectroscopy, and surface-sensitive mass spectrometry. Then, we elucidate physical ion adsorption and chemical electrification as examples of electrification mechanisms. In the end, novel effects on surface electrification are discussed in detail. We believe that this clear overview of state of the art in a charged water interface will surely help the fundamental progress of physics and chemistry at interfaces in the future.

C-Glucosylation as a tool for the prevention of PAINS-induced membrane dipole potential alterations

The concept of Pan-Assay Interference Compounds (PAINS) is regarded as a threat to the recognition of the broad bioactivity of natural products. Based on the established relationship between altered membrane dipole potential and transmembrane protein conformation and function, we investigate here polyphenols' ability to induce changes in cell membrane dipole potential. Ultimately, we are interested in finding a tool to prevent polyphenol PAINS-type behavior and produce compounds less prone to untargeted and promiscuous interactions with the cell membrane. Di-8-ANEPPS fluorescence ratiometric measurements suggest that planar lipophilic polyphenols-phloretin, genistein and resveratrol-act by decreasing membrane dipole potential, especially in cholesterol-rich domains such as lipid rafts, which play a role in important cellular processes. These results provide a mechanism for their labelling as PAINS through their ability to disrupt cell membrane homeostasis. Aiming to explore the role of C-glucosylation in PAINS membrane-interfering behavior, we disclose herein the first synthesis of 4-glucosylresveratrol, starting from 5-hydroxymethylbenzene-1,3-diol, via C-glucosylation, oxidation and Horner-Wadsworth-Emmons olefination, and resynthesize phloretin and genistein C-glucosides. We show that C-glucosylation generates compounds which are no longer able to modify membrane dipole potential. Therefore, it can be devised as a strategy to generate bioactive natural product derivatives that no longer act as membrane dipole potential modifiers. Our results offer a new technology towards rescuing bioactive polyphenols from their PAINS danger label through C-C ligation of sugars.

Divalent Cation Modulation of Ion Permeation in TMEM16 Proteins

Intracellular divalent cations control the molecular function of transmembrane protein 16 (TMEM16) family members. Both anion channels (such as TMEM16A) and phospholipid scramblases (such as TMEM16F) in this family are activated by intracellular Ca²⁺ in the low µM range. In addition, intracellular Ca²⁺ or Co²⁺ at mM concentrations have been shown to further potentiate the saturated Ca²⁺-activated current of TMEM16A. In this study, we found that all alkaline earth divalent cations in mM concentrations can generate similar potentiation effects in TMEM16A when applied intracellularly, and that manipulations thought to deplete membrane phospholipids weaken the effect. In comparison, mM concentrations of divalent cations minimally potentiate the current of TMEM16F but significantly change its cation/anion selectivity. We suggest that divalent cations may increase local concentrations of permeant ions via a change in pore electrostatic potential, possibly acting through phospholipid head groups in or near the pore. Monovalent cations appear to exert a similar effect, although with a much lower affinity. Our findings resolve controversies regarding the ion selectivity of TMEM16 proteins. The physiological role of this mechanism, however, remains elusive because of the nearly constant high cation concentrations in cytosols.

Choline and NMDG directly reduce outward currents: reduced outward current when these substances replace Na+ is alone not evidence of Na+-activated K+ currents

Choline chloride is often, and N-methyl-d-glucamine (NMDG) sometimes, used to replace sodium chloride in studies of sodium-activated potassium channels. Given the high concentrations used in sodium replacement protocols, it is essential to test that it is not the replacement substances themselves, as opposed to the lack of sodium, that cause any observed effects. We therefore compared, in lobster stomatogastric neurons and leech Retzius cells, the effects of applying salines in which choline chloride replaced sodium chloride, and in which choline hydroxide or sucrose was added to normal saline. We also tested, in stomatogastric neurons, the effect of adding NMDG to normal saline. These protocols allowed us to measure the direct effects (i.e., effects not due to changes in sodium concentration or saline osmolarity or ionic strength) of choline on stomatogastric and leech currents, and of NMDG on stomatogastric currents. Choline directly reduced transient and sustained depolarization-activated outward currents in both species, and NMDG directly reduced transient depolarization-activated outward currents in stomatogastric neurons. Experiments with lower choline concentrations showed that adding as little as 150 mM (stomatogastric) or 5 mM (leech) choline reduced at least some depolarization-activated outward currents. Reductions in outward current with choline chloride or NMDG replacement alone are thus not evidence of sodium-activated potassium currents. NEW & NOTEWORTHY We show that choline or N-methyl-d-glucamine (NMDG) directly (i.e., not due to changes in extracellular sodium) decrease outward currents. Prior work studying sodium-activated potassium channels in which sodium was replaced with choline or NMDG without an addition control may therefore be artifactual.

New Theoretical Model of Nerve Conduction in Unmyelinated Nerves

Nerve conduction in unmyelinated fibers has long been described based on the equivalent circuit model and cable theory. However, without the change in ionic concentration gradient across the membrane, there would be no generation or propagation of the action potential. Based on this concept, we employ a new conductive model focusing on the distribution of voltage-gated sodium ion channels and Coulomb force between electrolytes. Based on this new model, the propagation of the nerve conduction was suggested to take place far before the generation of action potential at each channel. We theoretically showed that propagation of action potential, which is enabled by the increasing Coulomb force produced by inflowing sodium ions, from one sodium ion channel to the next sodium channel would be inversely proportionate to the density of sodium channels on the axon membrane. Because the longitudinal number of sodium ion channel would be proportionate to the square root of channel density, the conduction velocity of unmyelinated nerves is theoretically shown to be proportionate to the square root of channel density. Also, from a viewpoint of equilibrium state of channel importation and degeneration, channel density was suggested to be proportionate to axonal diameter. Based on these simple basis, conduction velocity in unmyelinated nerves was theoretically shown to be proportionate to the square root of axonal diameter. This new model would also enable us to acquire more accurate and understandable vision on the phenomena in unmyelinated nerves in addition to the conventional electric circuit model and cable theory.

Modeling the light-induced electric potential difference ΔΨ across the thylakoid membrane based on the transition state rate theory

In photosynthesis, electron transport-coupled proton movement initiates the formation of the light-induced electric potential difference, ΔΨ, across the thylakoid membrane (TM). Ions are transported across the TM to counterbalance the charge of protons accumulated in the lumen. The objective of this work is to construct range of mathematical models for simulation of ΔΨ, using the transition state rate theory (TSRT) for description of movement of ions through the channels. The TSRT considers either single-ion (TSRT-SI) or multi-ion occupancy (TSRT-MI) in the channels. Movement of ions through the channel pore is described by means of energy barriers and binding sites; ions move in and out of vacant sites with rate constants that depend on the barrier heights and well depths, as well as on the interionic repulsion in TSRT-MI model. Three energy motifs are used to describe the TSRT-SI model: two-barrier one-site (2B1S), three-barrier two-site (3B2S), and four-barrier three-site (4B3S). The 3B2S energy motif is used for the TSRT-MI model. The accumulation of cations due to the TM surface negative fixed charges is also taken into account. A model employing the electro-diffusion theory instead of the TSRT is constructed for comparison. The dual wavelength transmittance signal (ΔA515-560nm) measuring the electrochromic shift (ECS) provides a proxy for experimental light-induced ΔΨ. The simulated ΔΨ traces qualitatively agree with the measured ECS traces. The models can simulate different channel conducting regimes and assess their impact on ΔΨ. The ionic flux coupling in the TSRT-MI model suggests that an increase in the internal or external K⁺ concentration may block the outward or the inward Mg²⁺ current, respectively.

Ion channels of the nuclear membrane of hippocampal neurons

Rise in Ca(2+) concentration in the nucleus affects gene transcription and has been implicated in neuroprotection, transcription-dependent neuronal plasticity, and pain modulation, but the mechanism of regulation of nuclear Ca(2+) remains poorly understood. The nuclear envelope is a part of the endoplasmic reticulum and may be one of the sources of nuclear Ca(2+) . Here, we studied ion channels in the nuclear membrane of hippocampal neurons using the patch-clamp technique. We have found that the nuclear membrane of CA1 pyramidal and dentate gyrus granule (DG), but not CA3 pyramidal neurons, was enriched in functional inositol 1,4,5-trisphosphate receptors/Ca(2+) -release channels (IP3 Rs) localized mainly in the inner nuclear membrane. A single nuclear ryanodine receptor (RyR) has been detected only in DG granule neurons. Nuclei of the hippocampal neurons also expressed a variety of spontaneously active cation and anion channels specific for each type of neuron. In particular, large-conductance ion channels selective for monovalent cations (LCC) were coexpressed with IP3 Rs. These data suggest that: (1) the nuclear membranes of hippocampal neurons contain distinct sets of ion channels, which are specific for each type of neuron; (2) IP3 Rs, but not RyRs are targeted to the inner nuclear membrane of CA1 pyramidal and DG granule, but they were not found in the nuclear membranes of CA3 pyramidal neurons; (3) the nuclear envelope of these neurons is specialized to release Ca(2+) into the nucleoplasm which may amplify Ca(2+) signals entering the nucleus from the cytoplasm or generate Ca(2+) transients on its own; (4) LCC channels are an integral part the of Ca(2+) -releasing machinery providing a route for counterflow of К(+) and thereby facilitating Ca(2+) movement in and out of the Ca(2+) store.

Molecular dynamics simulations of cardiolipin bilayers

Cardiolipin is a key lipid component in the inner mitochondrial membrane, where the lipid is involved in energy production, cristae structure, and mechanisms in the apoptotic pathway. In this article we used molecular dynamics computer simulations to investigate cardiolipin and its effect on the structure of lipid bilayers. Three cardiolipin/POPC bilayers with different lipid compositions were simulated: 100, 9.2, and 0% cardiolipin. We found strong association of sodium counterions to the carbonyl groups of both lipid types, leaving in the case of 9.2% cardiolipin virtually no ions in the aqueous compartment. Although binding occurred primarily at the carbonyl position, there was a preference to bind to the carbonyl groups of cardiolipin. Ion binding and the small headgroup of cardiolipin gave a strong ordering of the hydrocarbon chains. We found significant effects in the water dipole orientation and water dipole potential which can compensate for the electrostatic repulsion that otherwise should force charged lipids apart. Several parameters relevant for the molecular structure of cardiolipin were calculated and compared with results from analyses of coarse-grained simulations and available X-ray structural data.

Spontaneously active and InsP3-activated ion channels in cell nuclei from rat cerebellar Purkinje and granule neurones

Increases in Ca(2+) concentration in the nucleus of neurones modulate gene transcription and may be involved in activity-dependent long-term plasticity, apoptosis, and neurotoxicity. Little is currently known about the regulation of Ca(2+) in the nuclei of neurones. Investigation of neuronal nuclei is hampered by the cellular heterogeneity of the brain where neurones comprise no more than 10% of the cells. The situation is further complicated by large differences in properties of different neurones. Here we report a method for isolating nuclei from identified central neurones. We employed this technique to study nuclei from rat cerebellar Purkinje and granule neurones. Patch-clamp recording from the nuclear membrane of Purkinje neurones revealed numerous large-conductance channels selective for monovalent cations. The nuclear membrane of Purkinje neurones also contained multiple InsP(3)- activated ion channels localized exclusively in the inner nuclear membrane with their receptor loci facing the nucleoplasm. In contrast, the nuclear membrane of granule neurones contained only a small number of mainly anion channels. Nuclear InsP(3) receptors (InsP(3)Rs) were activated by InsP(3) with EC(50) = 0.67 microm and a Hill coefficient of 2.5. Ca(2+) exhibited a biphasic effect on the receptors elevating its activity at low concentrations and inhibiting it at micromolar concentrations. InsP(3) in saturating concentrations did not prevent the inhibitory effect of Ca(2+), but strongly increased InsP(3)R activity at resting Ca(2+) concentrations. These data are the first evidence for the presence of intranuclear sources of Ca(2+) in neurones. Ca(2+) release from the nuclear envelope may amplify Ca(2+) transients penetrating the nucleus from the cytoplasm or generate Ca(2+) transients in the nucleus independently of the cytoplasm.

Electrostatic potentials and fields in the vicinity of engineered nanostructures

We have developed a method for calculating the electrostatic potentials and fields in the vicinity of geometrically complex engineered nanostructures composed of varying materials in electrolytes of arbitrary pH and ionic strength. The method involves direct summation of charged Debye-Hückel spheres composing the nanostructural surfaces and, by including charge redistribution on the surface of conducting materials held at constant potential, is applicable to mixed boundary conditions. The method is validated by comparison to analytical solutions for an infinite plane (Gouy-Chapman), an infinite cylinder (Bessel functions), and an infinite plane which contains a hole and which is held at constant potential. Excellent agreement between the potentials obtained by our numerical method and the closed form solutions is found for these conditions. The method is applied to the calculation of the electric field enhancement in the vicinity of a nanomembrane whose pore wall is held at constant charge and whose membrane surfaces are held at constant potential. The electric field is found to be enhanced by the charge buildup in the rim of the hole of the nanomembrane; the buildup results from the potential being held constant in the conducting region. Ion concentrations are also calculated. Positive ion rejection is found to be enhanced by this charge buildup in the region of the rim when a constant positive potential is applied.

Characterization of hydrated Na+(phenol) and K+(phenol) complexes using infrared spectroscopy

Hydrated alkali metal ion-phenol complexes were studied to model these species in aqueous solution for M=Na and K. IR predissociation spectroscopy in the O-H stretch region was used to analyze the structures of M+(Phenol)(H2O)n cluster ions, for n = 1-4. The onset of hydrogen bonding was observed to occur at n=4. Ab initio calculations were used to qualitatively explore the types of hydrogen-bonded structures of the M+(Phenol)(H2O)4 isomers. By combining the ab initio calculations and IR spectra, several different structures were identified for each metal ion. In contrast to benzene, detailed in a previous study of Na+(Benzene)n(H2O)m [J. Chem. Phys. 110, 8429 (1999)], phenol is able to bind directly to Na+ even in the presence of four waters. This is likely the result of the sigma-type interaction between the phenol oxygen and the ion. With K+, the dominant isomers are those in which the phenol O-H group is involved in a hydrogen bond with the water molecules, while with Na+, the dominant isomers are those in which the phenol O-H group is free and the water molecules are hydrogen-bonded to each other. Spectra and ab initio calculations for the M+(Phenol)Ar cluster ions for M=Na and K are reported to characterize the free phenol O-H stretch in the M+(Phenol) complex. While pi-type configurations were observed for binary M+(Phenol) complexes, sigma-type configurations appear to dominate the hydrated cluster ions.