Viroporins: A new target for fighting viral infections

Over the last years an increasing number of viruses have jumped into the mass media and several names or acronyms (Ebola, zika, SARS, MERS,…) have become familiar to the general public because of the high mortality rates associated with their infection in humans. The threat they pose to human life has to do mainly with the risk of infection spreading from the initial outbreak location to other countries and population sectors. Along with these pathogens, there are other viruses that remain a serious health problem, despite considerable therapeutic advances: The human immunodeficiency virus (HIV), responsible for the immunodeficiency syndrome (AIDS); the Hepatitis C virus (HCV), causing hepatitis C and some cancers; the influenza A virus (IAV); the Human respiratory syncytial virus (HRSV) a major cause of lower respiratory tract infections during infancy and childhood. This list is far from complete

Access resistance in protein nanopores. A structure-based computational approach

Single-channel conductance measurements in biological pores have demonstrated the importance of interfacial effects in nanopores, particularly in protein channels with low aspect ratio (length over aperture radius). Access resistance (AR), the contribution to the total measured resistance arising from the electrodiffusive limitation that ions experience in passing from bulk solution to confinement within the pore, becomes essential in the description of ionic transport across these biological channels. Common analytical estimates of AR are based on idealized nanopore models, cylindrical in shape, electrically neutral and embedded in a neutral substrate. Here we calculate the AR of five protein channels by using their atomic structure and a mean-field approach based on solving 3D Poisson and Nernst-Planck equations. Our approach accounts for the influence of the protein charged ionizable residues, the geometry of the pore mouth and the ion concentration gradients near the pore. We compare numerical calculations with the few available AR measurements and show for several protein channels that analytical predictions tend to overestimate AR for physiological concentrations and below. We also discuss the relationship between AR and the size of the channel aperture in single-pore channels and three-pore channels and demonstrate that in the latter case, there is an enhancement of AR

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 ΔΔGexp from single-channel conductance measurements agrees with calculated energy changes ΔΔEcalc. Our results show that the PEG-sizing technique may need corrections in the case of charged biological pores

Dielectric saturation of water in a membrane protein channel

Water molecules in confined geometries like nanopores and biological ion channels exhibit structural and dynamical properties very different from those found in free solution. Protein channels that open aqueous pores through biological membranes provide a complex spatial and electrostatic environment that decreases the translational and rotational mobility of water molecules, thus altering the effective dielectric constant of the pore water. By using the Booth equation, we study the effect of the large electric field created by ionizable residues of an hour-glass shaped channel, the bacterial porin OmpF, on the pore water dielectric constant, ew. We find a space-dependent significant reduction (down to 20) of ew that may explain some ad hoc assumptions about the dielectric constant of the protein and the water pore made to reconcile model calculations with measurements of permeation properties and pKa’s of protein residues. The electric potential calculations based on the OmpF protein atomic structure and the Booth field-dependent dielectric constant show that protein dielectric constants ca. 10 yield good agreement with molecular dynamics simulations as well as permeation experiment

The Ionic selectivity of large protein ion channels

Els canals iònics de gran amplada i de conductància alta exerceixen una funció molt important en el cicle de vida de les cèl· lules. Permeten l'intercanvi de soluts neutres i carregats a través de la membrana cel·lular i regulen l'aportació de nutrients i la sortida de deixalles. Per a realitzar aquesta funció, els canals han de discriminar entre diferents espècies iòniques. Els canals mesoscòpics permeten el transport multiiònic passiu i generalment presenten una selectivitat moderada respecte a ions positius i negatius. Aquí revisem les metodologies més usades per a estimar quantitativament la selectivitat iònica. Entre elles, la mesura del potencial elèctric necessari per a anul·lar el corrent elèctric a través del canal en presència d'un gradient de concentració, cosa que es coneix com a potencial de corrent zero. Assenyalem els factors clau que cal tenir en compte per a una interpretació física correcta d'aquests experiments d'electrofisiologia.Large, highly conductive ion channels have a major functional role in the cell life cycle. They allow the exchange of charged and neutral solutes across the cell membrane envelope and regulate the influx of nutrients and the extrusion of waste products. To perform this function, channels must discriminate between different ionic species. Mesoscopic channels allow multiionic, passive transport and are usually moderately selective toward positive or negative ions. Here we review one of the most common approaches used for the quantitative estimation of channel selectivity: the measurement of the potential needed to get zero current across a channel in the presence of an electrolyte concentration gradient, also known as Reversal Potential. We highlight several key points that need to be addressed for a correct physical interpretation of these experiments in electrophysiology

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

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

[EN] 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.This research was funded by the Universitat Jaume I (UJI) under the project UJI-B2018-53. We thanks to Robert Jones for the English language revision.Aguilella-Arzo, M.; Compañ Moreno, V. (2023). A three-dimensional model to describe complete human corneal oxygenation during contact lens wear. Journal of Biomedical Materials Research Part B Applied Biomaterials. 111(3):610-621. https://doi.org/10.1002/jbm.b.35180610621111

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

α-Synuclein emerges as a potent regulator of VDAC-facilitated calcium transport

Voltage-dependent anion channel (VDAC) is the most ubiquitous channel at the mitochondrial outer membrane, and is believed to be the pathway for calcium entering or leaving the mitochondria. Therefore, understanding the molecular mechanisms of how VDAC regulates calcium influx and efflux from the mitochondria is of particular interest for mitochondrial physiology. When the Parkinson’s disease (PD) related neuronal protein, alpha-synuclein (αSyn), is added to the reconstituted VDAC, it reversibly and partially blocks VDAC conductance by its acidic C-terminal tail. Using single-molecule VDAC electrophysiology of reconstituted VDAC we now demonstrate that, at CaCl2 concentrations below 150 mM, αSyn reverses the channel’s selectivity from anionic to cationic. Importantly, we find that the decrease in channel conductance upon its blockage by αSyn is hugely overcompensated by a favorable change in the electrostatic environment for calcium, making the blocked state orders-of-magnitude more selective for calcium and thus increasing its net flux. -Our findings with higher calcium concentrations also demonstrate that the phenomenon of “charge inversion” is taking place at the level of a single polypeptide chain. Measurements of ion selectivity of three VDAC isoforms in CaCl2 gradient show that VDAC3 exhibits the highest calcium permeability among them, followed by VDAC2 and VDAC1, thus pointing to isoform-dependent physiological function. Mutation of the E73 residue – VDAC1 purported calcium binding site – shows that there is no measurable effect of the mutation in either open or αSyn-blocked VDAC1 states. Our results confirm VDACs involvement in calcium signaling and reveal a new regulatory role of αSyn, with clear implications for both normal calcium signaling and PD-associated mitochondrial dysfunction