Computational Insights into Membrane Disruption by Cell-Penetrating Peptides.

Cell-penetrating peptides (CPPs) can translocate into cells without inducing cytotoxicity. The internalization process implies several steps at different time scales ranging from microseconds to minutes. We combine adaptive Steered Molecular Dynamics (aSMD) with conventional Molecular Dynamics (cMD) to observe nonequilibrium and equilibrium states to study the early mechanisms of peptide-bilayer interaction leading to CPPs internalization.

Supralinear scaling behavior of ionic transport in membrane nanochannels regulated by outer-surface charges.

The peculiarity of ion transport at the nanoscale is revealed through electrophysiological studies of two biological ion channels: the cation-selective bacterial porin-OmpF and the mitochondrial voltage-dependent anion channel (VDAC). We provide evidence of an unprecedented scaling behavior in the power-law relationship between conductivity and concentration ∼ with > 1 when functional groups attached to the pore inner wall have opposite charges to those located in the nanochannel's outer surface. Indeed, we find ∼ 1.

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.

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 Aβ the most abundant species of Aβ.

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.

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.

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).

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 . 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.

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.

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.

Scaling Behavior of Ionic Transport in Membrane Nanochannels.

Ionic conductance in membrane channels exhibits a power-law dependence on electrolyte concentration ( G ∼ c). 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.

Corneal Equilibrium Flux as a Function of Corneal Surface Oxygen Tension.

Purpose: Oxygen is essential for aerobic mammalian cell physiology. Oxygen tension (PO2) should reach a minimum at some position within the corneal stroma, and oxygen flux should be zero, by definition, at this point as well. We found the locations and magnitudes of this "corneal equilibrium flux" (xmin) and explored its physiological implications.

Modeling Corneal Oxygen with Scleral Gas Permeable Lens Wear.

Purpose: The main goal of this current work is to use an updated calculation paradigm, and updated boundary conditions, to provide theoretical guidelines to assist the clinician whose goal is to improve his or her scleral gas permeable (GP) contact lens wearing patients' anterior corneal oxygen supply.

Methods: Our model uses a variable value of corneal oxygen consumption developed through Monod equations that disallows negative oxygen tensions within the stroma to predict oxygen tension at the anterior corneal surface of scleral GP contact lens wearing eyes, and to describe oxygen tension and flux profiles, for various boundary conditions, through the lens, tears, and cornea. We use several updated tissue and boundary parameters in our model.

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. We show that under extreme pH conditions protons and hydroxyls contribute decisively to the overall measured current, challenging the traditional interpretation of some electrokinetic parameters such as channel selectivity and rectification properties. We analyze with unprecedented detail the two intertwined factors ruling the ionic permeation through the channel, namely the differences between cation and anion mobilities and the electrostatic exclusion due to the interaction between permeating ions and channel ionizable residues.

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.

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.

Oxygen diffusion and edema with modern scleral rigid gas permeable contact lenses.

Purpose: We defined the theoretical oxygen tension behind modern scleral contact lenses (CLs) made of different rigid gas permeable (RGP) materials, assuming different thickness of the tear layer behind the lens. A second goal was to show clinically the effect of the postlens tear film on corneal swelling.

Methods: We simulated the partial pressure of oxygen across the cornea behind scleral CLs made of different lens materials (oxygen permeability Dk, 75-200 barrer) and different thickness (Tav, 100-300 μm).

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.

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.

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.

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).

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.

Ion selectivity of a biological channel at high concentration ratio: insights on small ion diffusion and binding.

The ionic selectivity of the bacterial porin OmpF has been investigated in several chloride salts of alkali metal cations under a wide range of concentration ratios. We report a novel way of studying the several factors contributing to ionic selectivity of large channels: measuring reversal potential beyond the gradients commonly used in channel selectivity experiments, i.e.