Charged Biological Membranes Repel Large Neutral Molecules by Surface Dielectrophoresis and Counterion Pressure

Macromolecular crowding is the usual condition of cells. The implications of the crowded cellular environment for protein stability and folding, protein-protein interactions, and intracellular transport drive a growing interest in quantifying the effects of crowding. While the properties of crowded solutions have been extensively studied, less attention has been paid to the interaction of crowders with the cellular boundaries, i.e., membranes. However, membranes are key components of cells and most subcellular organelles, playing a central role in regulating protein channel and receptor functions by recruiting and binding charged and neutral solutes. While membrane interactions with charged solutes are dominated by electrostatic forces, here we show that significant charge-induced forces also exist between membranes and neutral solutes. Using neutron reflectometry measurements and molecular dynamics simulations of poly(ethylene glycol) (PEG) polymers of different molecular weights near charged and neutral membranes, we demonstrate the roles of surface dielectrophoresis and counterion pressure in repelling PEG from charged membrane surfaces. The resulting depletion zone is expected to have consequences for drug design and delivery, the activity of proteins near membrane surfaces, and the transport of small molecules along the membrane surface.

A three-dimensional model to describe complete human corneal oxygenation during contact lens wear

We perform a novel 3D study to quantify the corneal oxygen consumption and diffusion in each part of the cornea with different contact lens materials. The oxygen profile is calculated as a function of oxygen tension at the cornea-tear interface and the oxygen transmissibility of the lens, with values used in previous studies. We aim to determine the influence of a detailed geometry of the cornea in their modeling compared to previous low dimensional models used in the literature. To this end, a 3-D study based on an axisymmetric volume element analysis model was applied to different contact lenses currently on the market. We have obtained that the model provides a valuable tool for understanding the flux and cornea oxygen profiles through the epithelium, stroma, and endothelium. The most important results are related to the dependence of the oxygen flux through the cornea-lens system on the contact lens thickness and geometry. Both parameters play an important role in the corneal flux and oxygen tension distribution. The decline in oxygen consumption experienced by the cornea takes place just inside the epithelium, where the oxygen tension falls to between 95 and 16 mmHg under open eye conditions, and 30 to 0.3 mmHg under closed eye conditions, depending on the contact lens worn. This helps to understand the physiological response of the corneal tissue under conditions of daily and overnight contact lens wear, and the importance of detailed geometry of the cornea in the modeling of diffusion for oxygen and other species.

Big dynorphin is a neuroprotector scaffold against amyloid β-peptide aggregation and cell toxicity

Amyloid β-peptide (Aβ) misfolding into β-sheet structures triggers neurotoxicity inducing Alzheimer’s disease (AD). Molecules able to reduce or to impair Aβ aggregation are highly relevant as possible AD treatments since they should protect against Aβ neurotoxicity. We have studied the effects of the interaction of dynorphins, a family of opioid neuropeptides, with Aβ₄₀ the most abundant species of Aβ. Biophysical measurements indicate that Aβ₄₀ interacts with Big Dynorphin (BigDyn), lowering the amount of hydrophobic aggregates, and slowing down the aggregation kinetics. As expected, we found that BigDyn protects against Aβ₄₀ aggregates when studied in human neuroblastoma cells by cell survival assays. The cross-interaction between BigDyn and Aβ₄₀ provides insight into the mechanism of amyloid pathophysiology and may open up new therapy possibilities.

A refined model on flow and oxygen consumption in the human cornea depending on the oxygen tension at the interface cornea/post lens tear film during contact lens wear

The study of oxygen consumption rate under" in vivo" human cornea during contact lens wear has been technically a challenge and several attempts have been made in the last 20 years to model the physiology of the human cornea during contact lens wear. Unfortunately, some of these models, based on a constant corneal oxygen consumption rate, produce areas on the cornea where the oxygen tension is negative, which has no physical sense. In order to avoid such inconsistency, different researchers have developed alternative models of oxygen consumption, which predict the likely oxygen metrics available at the interface cornea/post lens tear film by determination of oxygen flux, oxygen consumption, and oxygen tension through the different layers (endothelium, stroma, and epithelium). Although oxygen deficiency produces corneal edema, corneal swelling, hypoxia, acidosis, and other abnormalities, the estimation of the oxygen distribution below the impact of a contact lens wear is interesting to know which lens transmissibility was adequate to maintain the cornea and avoid epithelial and stromal anoxia. The estimation of minimum transmissibility for a lens for extended wear applications will be very useful for both clinicians and manufacturers. The aim of this work is to present a complete discussion based on Monod kinetics model that permits give an estimation of oxygen partial pressure distribution, the profile distribution of corneal flux and oxygen consumption rate, and finally the estimation of the relaxation mechanism of the cornea depending on the oxygen tension at the interface cornea/post lens tear film. Relaxation time in this context can quantify the capability of the corneal tissue to adapt to increasing concentrations of oxygen. It is proposed this parameter as a biological meaningful indicator of the interaction between contact lens polymers and living tissues such as the corneal cellular layer.

Dynorphin A induces membrane permeabilization by formation of proteolipidic pores. Insights from electrophysiology and computational simulations

Dynorphins are endogenous neuropeptides that function as ligands for the κ-opioid receptor. In addition to opioid activity, dynorphins can induce several pathological effects such as neurological dysfunctions and cell death. Previous studies have suggested that Dynorphin A (DynA) mediates some pathogenic actions through formation of transient pores in lipid domains of the plasma membrane. Here, we use planar bilayer electrophysiology to show that DynA induces pore formation in negatively charged membranes. We find a large variability in pore conformations showing equilibrium conductance fluctuations, what disregards electroporation as the dominant mechanism of pore formation. Ion selectivity measurements showing cationic selectivity indicate that positive protein charges of DynA are stabilized by phosphatidyl serine negative charges in the formation of combined structures. We complement our study with computational simulations that assess the stability of diverse peptide arrangements in the hydrophobic core of the bilayer. We show that DynA is capable of assembling in charged membranes to form water-filled pores that conduct ions.

PEG Equilibrium Partitioning in the α-Hemolysin Channel: Neutral Polymer Interaction with Channel Charges

We study the interaction of neutral polyethylene glycol (PEG) molecules of different molecular weights (MWs) with the charged residues of the α-hemolysin channel secreted by Staphylococcus aureus. Previously reported experiments of PEG equilibrium partitioning into this nanopore show that the charge state of the channel changes the ability of PEG entry in an MW-dependent manner. We explain such an effect by parameter-free calculations of the PEG self-energy from the channel 3D atomic structure that include repulsive dielectrophoretic and hydrostatic forces on the polymer. We found that the pH-induced shift in the measured free energy of partitioning ΔΔG_exp from single-channel conductance measurements agrees with calculated energy changes ΔΔE_calc. Our results show that the PEG-sizing technique may need corrections in the case of charged biological pores.

Corneal relaxation time estimation as a function of tear oxygen tension in human cornea during contact lens wear

The purpose is to estimate the oxygen diffusion coefficient and the relaxation time of the cornea with respect to the oxygen tension at the cornea-tears interface. Both findings are discussed. From the experimental data provided by Bonanno et al., the oxygen tension measurements in vivo for human cornea-tears-contact lens (CL), the relaxation time of the cornea, and their oxygen diffusion coefficient were obtained by numerical calculation using the Monod-kinetic model. Our results, considering the relaxation time of the cornea, observe a different behavior. At the time less than 8 s, the oxygen diffusivity process is upper-diffusive, and for the relaxation time greater than 8 s, the oxygen diffusivity process is lower-diffusive. Both cases depend on the partial pressure of oxygen at the entrance of the cornea. The oxygen tension distribution in the cornea-tears interface is separated into two different zones: one for conventional hydrogels, which is located between 6 and 75 mmHg, with a relaxation time included between 8 and 19 s, and the other zone for silicone hydrogel CLs, which is located at high oxygen tension, between 95 and 140 mmHg, with a relaxation time in the interval of 1.5-8 s. It is found that in each zone, the diffusion coefficient varies linearly with the oxygen concentration, presenting a discontinuity in the transition of 8 s. This could be interpreted as an aerobic-to-anaerobic transition. We attribute this behavior to the coupling formalism between oxygen diffusion and biochemical reactions to produce adenosine triphosphate. © 2019 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 108B:14-21, 2020.

Scaling Behavior of Ionic Transport in Membrane Nanochannels

Ionic conductance in membrane channels exhibits a power-law dependence on electrolyte concentration ( G ∼ c^α). The many scaling exponents, α, reported in the literature usually require detailed interpretations concerning each particular system under study. Here, we critically evaluate the predictive power of scaling exponents by analyzing conductance measurements in four biological channels with contrasting architectures. We show that scaling behavior depends on several interconnected effects whose contributions change with concentration so that the use of oversimplified models missing critical factors could be misleading. In fact, the presence of interfacial effects could give rise to an apparent universal scaling that hides the channel distinctive features. We complement our study with 3D structure-based Poisson-Nernst-Planck (PNP) calculations, giving results in line with experiments and validating scaling arguments. Our findings not only provide a unified framework for the study of ion transport in confined geometries but also highlight that scaling arguments are powerful and simple tools with which to offer a comprehensive perspective of complex systems, especially those in which the actual structure is unknown.

Analysis of the application of the generalized monod kinetics model to describe the human corneal oxygen-consumption rate during soft contact lens wear

This work is an analysis of the application of the generalized Monod kinetics model describing human corneal oxygen consumption during soft contact lens wear to models previously used by Chhabra et al. (J Biomed Mater Res B Appl Biomater, 2009a;90:202-209, Optom Vis Sci 2009b;86:454-466) and Larrea and Büchler (Invest Ophthalmol Vis Sci 2009;50:1076-1080). We use oxygen tension from in vivo estimations provided by Bonanno [Bonanno et al., Invest Ophthalmol Vis Sci 2002;43:371-376, and Bonanno et al 2009]. We consider four hydrogel and six silicone hydrogel lenses. The cornea is considered a single homogeneous layer, with constant oxygen permeability regardless of the type of lens worn. Our calculations yield different values for the maximum oxygen consumption rate Q_c,max , whith differents oxygen tensions (high and low p_c ) at the cornea-tears interface. Surprisingly, for both models, we observe an increase in oxygen consumption near an oxygen tension of 105 mmHg until a maximum is reached, then decreasing for higher levels of oxygen pressure. That is, when lowering the pressure of oxygen, the parameter Q_c,max initially increases depending on the intensity of the change in pressure. Which, it could be related with the variation of the pH. Furthermore, it is also noted that to greater reductions in pressure, this parameter decreases, possibly due to changes in the concentration of glucose related to the anaerobic respiration. The averaged in vivo human corneal oxygen consumption rate of 1.47 × 10^-4 cm³ of O₂ /cm³ tissue s, with Monod kinetics model, considering all the lenses studied, is smaller than the average oxygen consumption rate value obtained using the Larrea and Büchler model. The impact that these calculations have on the oxygen partial pressure available at different depths in the corneal tissue is presented and discussed, taking into consideration previous models used in this study. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 2269-2281, 2017.

Effects of extreme pH on ionic transport through protein nanopores: the role of ion diffusion and charge exclusion

We combine electrophysiological experiments with the structure-based Poisson–Nernst–Planck 3D calculations to investigate the transport properties of the bacterial porin OmpF under large pH gradients and particularly low salt concentrations.

Selectivity of Protein Ion Channels and the Role of Buried Charges. Analytical Solutions, Numerical Calculations, and MD Simulations

The preference of large protein ion channels for cations or anions is mainly determined by the electrostatic interactions of mobile ions with charged residues of the protein. Here we discuss the widely spread paradigm that the charges determining the channel selectivity are only those that can be considered solvent-accessible because of their location near the permeation pathways of ions and water molecules. Theoretical predictions for the electric potential and average ion densities inside the pore are presented using several approaches of increasing resolution: from analytical and numerical solutions of electrostatic equations in a model channel up to all-atom molecular dynamics simulations and continuum electrostatic calculations performed in a particular biological channel, the bacterial porin OmpF. The results highlight the role of protein dieletric properties and the importance of the initial choice of the residue ionization states in the understanding of the molecular basis of large channel selectivity irrespective of the level of resolution of the computational approach used.

Quatsomes: vesicles formed by self-assembly of sterols and quaternary ammonium surfactants

Thermodynamically stable nanovesicle structures are of high interest for academia and industry in a wide variety of application fields, ranging from preparation of nanomaterials to nanomedicine. Here, we show the ability of quaternary ammonium surfactants and sterols to self-assemble, forming stable amphiphilic bimolecular building-blocks with the appropriate structural characteristics to form in aqueous phases, closed bilayers, named quatsomes, with outstanding stability, with time and temperature. The molecular self-assembling of cholesterol and surfactant cetyltrimethylammonium bromide (CTAB) was studied by quasi-elastic light scattering, cryogenic transmission electron microscopy, turbidity (optical density) measurements, and molecular dynamic simulations with atomistic detail, upon varying the cholesterol-to-surfactant molar ratio. As pure species, CTAB forms micelles and insoluble cholesterol forms crystals in water. However, our molecular dynamic simulations reveal that the synergy between CTAB and cholesterol molecules makes them self-assemble into bimolecular amphiphiles and then into bilayers in the presence of water. These bilayers have the same structure of those formed by double-tailed unimolecular amphiphiles.

First-passage-time analysis of atomic-resolution simulations of the ionic transport in a bacterial porin

We have studied the dynamics of chloride and potassium ions in the interior of the Outer membrane porin F (OmpF) under the influence of an external electric field. From the results of extensive all-atom molecular dynamics (MD) simulations of the system, we computed several first-passage-time (FPT) quantities to characterize the dynamics of the ions in the interior of the channel. Such FPT quantities obtained from MD simulations demonstrate that it is not possible to describe the dynamics of chloride and potassium ions inside the whole channel with a single constant diffusion coefficient. However, we showed that a valid, statistically rigorous description in terms of a constant diffusion coefficient D and an effective deterministic force F(eff) can be obtained after appropriate subdivision of the channel in different regions suggested by the x-ray structure. These results have important implications for popular simplified descriptions of channels based on the one-dimensional Poisson-Nernst-Planck equations. Also, the effect of entropic barriers on the diffusion of the ions is identified and briefly discussed.

Insights on the permeability of wide protein channels: measurement and interpretation of ion selectivity

Ion channels are hollow proteins that have evolved to exhibit discrimination between charged solutes. This property, known as ion selectivity is critical for several biological functions. By using the bacterial porin OmpF as a model system of wide protein channels, we demonstrate that significant insights can be gained when selectivity measurements are combined with electrodiffusion continuum models and simulations based on the atomic structure. A correct interpretation of the mechanisms ruling the many sources of channel discrimination is a first, indispensable step for the understanding of the controlled movement of ions into or out of cells characteristic of many physiological processes. We conclude that the scattered information gathered from several independent approaches should be appropriately merged to provide a unified and coherent picture of the channel selectivity.

Ionic partition and transport in multi-ionic channels: a molecular dynamics simulation study of the OmpF bacterial porin

We performed all-atom molecular dynamics simulations studying the partition of ions and the ionic current through the bacterial porin OmpF and two selected mutants. The study is motivated by new, interesting experimental findings concerning their selectivity and conductance behavior at neutral pH. The mutations considered here are designed to study the effect of removal of negative charges present in the constriction zone of the wild-type OmpF channel (which contains, on one side, a cluster with three positive residues, and on the other side, two negatively charged residues). Our results show that these mutations induce an exclusion of cations from the constriction zone of the channel, substantially reducing the flow of cations. In fact, the partition of ions inside the mutant channels is strongly inhomogeneous, with regions containing an excess of cations and regions containing an excess of anions. Interestingly, the overall number of cations inside the channel is larger than the number of anions, this excess being different for each protein channel. We found that the differences in ionic charge inside these channels are justified by the differences in electric charge between the wild-type OmpF and the mutants, following an electroneutral balance.

Continuum electrostatic calculations of the pKa of ionizable residues in an ion channel: dynamic vs. static input structure

We have computed the pK(a)'s of the ionizable residues of a protein ion channel, the Staphylococcus aureus toxin alpha-hemolysin, by using two types of input structures, namely the crystal structure of the heptameric alpha-hemolysin and a set of over four hundred snapshots from a 4.38 ns Molecular Dynamics simulation of the protein inserted in a phospholipid planar bilayer. The comparison of the dynamic picture provided by the Molecular Simulation with the static one based on the X-ray crystal structure of the protein embedded in a lipid membrane allows analyzing the influence of the fluctuations in the protein structure on its ionization properties. We find that the use of the dynamic structure provides interesting information about the sensitivity of the computed pK(a) of a given residue to small changes in the local structure. The calculated pK(a) are consistent with previous indirect estimations obtained from single-channel conductance and selectivity measurements.

Electrostatic properties and macroscopic electrodiffusion in OmpF porin and mutants

The bacterial porin OmpF found in the outer membrane of E. coli is a wide channel, characterized by its poor selectivity and almost no ion specificity. It has an asymmetric structure, with relatively large entrances and a narrow constriction. By applying continuum electrostatic methods we determine the ionization states of titratable amino acid residues in the protein and calculate self-consistently the electric potential 3-D distribution within the channel. The average electrostatic properties are then represented by an effective fixed charge distribution along the pore which is the input for a macroscopic electrodiffusion model. The theoretical predictions agree with measurements performed under different salt gradients and pH. The sensitivity of reversal potential and conductance to the direction of the salt gradient and the solution pH is captured by the model. The theory is also able to explain the influence of the lipid membrane charge. The same methodology is satisfactorily applied to some OmpF mutants involving slight structural changes but a large number of net charges. The correlation found between atomic structure and ionic selectivity shows that the transport characteristics of wide channels like OmpF and its mutants are mainly regulated by the collective action of a large number of residues, rather than by the specific interactions of residues at particular locations.

Blocking of an ion channel by a highly charged drug: modeling the effects of applied voltage, electrolyte concentration, and drug concentration

We present a simple physical model to estimate the blocked pore probability of an ion channel that can be blocked by a highly charged drug in solution. The model is inspired by recent experimental work on the blocking of the PA(63) channel, involved in the anthrax toxin infection, by a highly charged drug [Karginov PNAS 102, 15075 (2005)]. The drug binding to the pore is highly specific but the strong dependence of blocking on the applied voltage and electrolyte concentration suggests that long range electrostatic interactions are important. Since basic electrostatic concepts rather than detailed molecular models are considered, the microscopic details of the channel blocking are ignored, although the model captures most of the qualitative characteristics of the problem.

Theoretical Description of the Ion Transport Across Nanopores With Titratable Fixed Charges: Analogies Between Ion Channels and Synthetic Pores

Recently developed nanometer-sized synthetic pores display several properties so far believed to be distinctive features of a large variety of biological wide ion channels. Thus conductance in the pS-nS range, pH-dependent ion selectivity, fluctuations of current between open and closed states, flux inhibition caused by protons or divalent cations, current rectification, and the ability to perform selective macromolecule sizing and counting are found in synthetic and biological channels alike. Despite other differences such as pore size and geometry, the similarities open a new field for exploring specific technological applications via the chemical modification of synthetic pores with biological molecules. This article reviews some of the basic concepts and theories relevant to ion transport in nanopores with titratable charges stressing the analogies between synthetic pores and biological ion channels. The ultimate goal is to show that continuum theories may account for the essential features of these systems. A simple electrodiffusion model and its comparison with experimental results are chosen as a case study.

Computing numerically the access resistance of a pore

The access resistance (AR) of a channel is an important component of the conductance of ion channels, particularly in wide and short channels, where it accounts for a substantial fraction of the total resistance to the movement of ions. The AR is usually calculated by using a classical and simple expression derived by Hall from electrostatics (J.E. Hall 1975 J. Gen. Phys. 66:531-532), though other expressions, both analytical and numerical, have been proposed. Here we report some numerical results for the AR of a channel obtained by solving the Poisson-Nernst-Planck equations at the entrance of a circular pore. Agreement is found between numerical calculations and analytical results from Hall's equation for uncharged pores in neutral membranes. However, for channels embedded in charged membranes, Hall's expression overestimates the AR, which is much lower and can even be neglected in some cases. The weak dependence of AR on the pore radius for charged membranes at low salt concentration can be exploited to separate the channel and the access contributions to the measured conductance.

Salting out the ionic selectivity of a wide channel: the asymmetry of OmpF

Although the crystallographic structure of the bacterial porin OmpF has been known for a decade, the physical mechanisms of its ionic selectivity are still under investigation. We address this issue in a series of experiments with varied pH, salt concentrations, inverted salt gradient, and charged and uncharged lipids. Measuring reversal potential, we show that OmpF selectivity (traditionally regarded as slightly cationic) depends strongly on pH and salt concentration and is conditionally asymmetric, that is, the calculated selectivity is sensitive to the direction of salt concentration gradient. At neutral pH and subdecimolar salt concentrations the channel exhibits nearly ideal cation selectivity (t(G)(+)=0.98+/-0.01). Substituting neutral DPhPC with DPhPS, we demonstrate that the fixed charge of the host lipid has a small but measurable effect on the channel reversal potential. The available structural information allows for a qualitative explanation of our experimental findings. These findings now lead us to re-examine the ionization state of 102 titratable sites of the OmpF channel. Using standard methods of continuum electrostatics tailored to our particular purpose, we find the charge distribution in the channel as a function of solution acidity and relate the pH-dependent asymmetry in channel selectivity to the pH-dependent asymmetry in charge distribution. In an attempt to find a simple phenomenological description of our results, we also discuss different macroscopic models of electrodiffusion through large channels.

Interaction of a polar molecule with an ion channel

The binding of a polar macromolecule to a large ion channel is studied theoretically, paying special attention to the influence of external conditions (applied voltage and ion strength of solution). The molecule behavior in bound state is considered as random thermal fluctuations within a limited fraction of its phase space. The mean duration of molecule binding (residence time tau r) is represented as the mean first passage time to reach the boundary of that restricted domain. By invoking the adiabatic approximation we reduce the problem to one dimension with the angle between macromolecule dipole and channel axes being the key variable of the problem. The model accounts for experimental measurements of tau r for the antibiotic Ampicillin within the bacterial porin OmpF of Escherichia coli. By assuming that the electrical interaction between Ampicillin dipole and OmpF ionizable groups affects the fluctuations, we find that the biased residence time-voltage dependence observed in experiments is the result of the strong transversal electric field in OmpF constriction with a tilt approximately 30 degrees aside the cis side.