Ion transport across transmembrane pores

Synthesis Method and High Salt Concentration Can Affect Electrodeformation of GUVs under Strong Pulsed DC Fields

The study focuses on two important issues in the electrodeformation of giant unilamellar vesicles (GUVs) as biomimic objects, with regard to their electroporation. The results are presented with respect to the ratio of the conductivities of the inner and outer fluids of the GUV, (β = Λen/Λsus), and the concentration of salt in the enclosed medium (C en). In this work, low and high salt concentration regimes are referred to as C en ≤ 0.3 mM and C en ≥ 25 mM respectively. First, responses of GUVs under strong pulsed DC fields are observed to be sensitive to the synthesis methods (electroporation or gel-assisted method) for both β = 1 and β < 1 in the low salt concentration regime. This might be caused by a higher initial membrane tension (in the case of electroformed GUVs) or possibly a greater membrane edge tension (in the case of GUVs prepared by the gel-assisted method). Second, the effect of salt concentration on the electrohydrodynamic behavior of GUVs under strong pulsed DC fields indicates that the extent of poration and pore growth and, correspondingly, the shape deformation can be qualitatively different at different salt concentrations. This suggests the possibility of higher edge tension in GUVs as well as faster "electrical shorting" of the membrane due to the abundance of ions and thereby lower pore growth in high-salt GUVs. The study shows that the extrapolation of results obtained in GUV electroporation to biological cells should be done with caution.

Recent advances of droplet-based microfluidics for engineering artificial cells

Artificial cells, synthetic cells, or minimal cells are microengineered cell-like structures that mimic the biological functions of cells. Artificial cells are typically biological or polymeric membranes where biologically active components, including proteins, genes, and enzymes, are encapsulated. The goal of engineering artificial cells is to build a living cell with the least amount of parts and complexity. Artificial cells hold great potential for several applications, including membrane protein interactions, gene expression, biomaterials, and drug development. It is critical to generate robust, stable artificial cells using high throughput, easy-to-control, and flexible techniques. Recently, droplet-based microfluidic techniques have shown great potential for the synthesis of vesicles and artificial cells. Here, we summarized the recent advances in droplet-based microfluidic techniques for the fabrication of vesicles and artificial cells. We first reviewed the different types of droplet-based microfluidic devices, including flow-focusing, T-junction, and coflowing. Next, we discussed the formation of multi-compartmental vesicles and artificial cells based on droplet-based microfluidics. The applications of artificial cells for studying gene expression dynamics, artificial cell-cell communications, and mechanobiology are highlighted and discussed. Finally, the current challenges and future outlook of droplet-based microfluidic methods for engineering artificial cells are discussed. This review will provide insights into scientific research in synthetic biology, microfluidic devices, membrane interactions, and mechanobiology.

Thermodynamics of Metal-Acetate Interactions

Metal ions play crucial roles in protein- and ligand-mediated interactions. They not only act as catalysts to facilitate biological processes but are also important as protein structural elements. Accurately predicting metal ion interactions in computational studies has always been a challenge, and various methods have been suggested to improve these interactions. One such method is the 12-6-4 Lennard-Jones (LJ)-type nonbonded model. Using this model, it has been possible to successfully reproduce the experimental properties of metal ions in aqueous solution. The model includes induced dipole interactions typically ignored in the standard 12-6 LJ nonbonded model. In this we expand the applicability of this model to metal ion-carboxylate interactions. Using 12-6-4 parameters that reproduce the solvation free energies of the metal ions leads to an overestimation of metal ion-acetate interactions, thus, prompting us to fine-tune the model to specifically handle the latter. We also show that the standard 12-6 LJ model significantly falls short in reproducing the experimental binding free energy between acetate and 11 metal ions (Ni(II), Mg(II), Cu(II), Zn(II), Co(II), Cu(I), Fe(II), Mn(II), Cd(II), Ca(II), and Ag(I)). In this study, we describe optimized C4 parameters for the 12-6-4 LJ nonbonded model to be used with three widely employed water models (Transferable Intermolecular Potential with 3 Points (TIP3P), Simple Point Charge Extended (SPC/E), and Optimal Point Charge (OPC) water models). These parameters can accurately match the experimental binding free energy between 11 metal ions and acetate. These parameters can be applied to the study of metalloproteins and transition metal ion channels and transporters, as acetate serves as a representative of the negatively charged amino acid side chains from aspartate and glutamate.

Experimental and Theoretical Brownian Dynamics Analysis of Ion Transport During Cellular Electroporation of E. coli Bacteria

Escherichia coli bacterium is a rod-shaped organism composed of a complex double membrane structure. Knowledge of electric field driven ion transport through both membranes and the evolution of their induced permeabilization has important applications in biomedical engineering, delivery of genes and antibacterial agents. However, few studies have been conducted on Gram-negative bacteria in this regard considering the contribution of all ion types. To address this gap in knowledge, we have developed a deterministic and stochastic Brownian dynamics model to simulate in 3D space the motion of ions through pores formed in the plasma membranes of E. coli cells during electroporation. The diffusion coefficient, mobility, and translation time of Ca2+, Mg2+, Na+, K+, and Cl- ions within the pore region are estimated from the numerical model. Calculations of pore's conductance have been validated with experiments conducted at Gustave Roussy. From the simulations, it was found that the main driving force of ionic uptake during the pulse is the one due to the externally applied electric field. The results from this work provide a better understanding of ion transport during electroporation, aiding in the design of electrical pulses for maximizing ion throughput, primarily for application in cancer treatment.

Designing Reaction Coordinate for Ion-Induced Pore-Assisted Mechanism of Halide Ions Permeation through Lipid Bilayer by Umbrella Sampling

Ion permeation mechanism through lipid membranes helps to understand cellular processes. We propose new reaction coordinates that allow ions to permeate according to their water affinity and interaction with the hydrophilic layer. Simulations were done for three different halides (F-, Cl-, and I-) in two different lipid bilayers, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dinervonoyl-sn-glycero-3-phosphocholine (DNPC). It is found that the involvement of the water molecules decreases the free energy barrier. The ions were found to follow different pathways for permeation. Formation of proper pores required a collaboration effort of the hydration shell water molecules and the hydrophilic lipid layer, which was favored in the case of Cl- ions. The optimum charge density and good water affinity of Cl- with respect to F- and I- ions helped to form the pore. The effect was prominently seen in the case of DNPC membrane because of its higher hydrophobic thickness. The umbrella sampling results were compared with other methods such as the Markov state model (MSM) and well-tempered metadynamics (WT-metaD).

Studying the roles of salt ions in the pore initiation and closure stages in the biomembrane electroporation

Electroporation shows great potential in biology and biomedical applications. However, there is still a lack of reliable protocol for cell electroporation to achieve a high perforation efficiency due to the unclear influence mechanism of various factors, especially the salt ions in buffer solution. The tiny membrane structure of a cell and the electroporation scale make it difficult to monitor the electroporation process. In this study, we used both molecular dynamics (MD) simulation and experimental methods to explore the influence of salt ions on the electroporation process. Giant unilamellar vesicles (GUVs) were constructed as the model, and sodium chloride (NaCl) was selected as the representative salt ion in this study. The results show that the electroporation process follows lag-burst kinetics, where the lag period first appears after applying the electric field, followed by a rapid pore expansion. For the first time, we find that the salt ion plays opposite roles in different stages of the electroporation process. The accumulation of salt ions near the membrane surface provides an extra potential to promote the pore initiation, while the charge screening effect of the ions within the pore increases the line tension of the pore to induce the instability of the pore and lead to the closure. The GUV electroporation experiments obtain qualitatively consistent results with MD simulations. This work can provide guidance for the selection of parameters for cell electroporation process.

Ligand-modified nanocarriers for oral drug delivery: Challenges, rational design, and applications

Ligand-modified nanocarriers (LMNCs) specific to their targets have attracted increasing interest for enhanced oral drug delivery in recent decades. Although the design of LMNCs for enhanced endocytosis and improved exposure of the loaded drugs through the oral route has received abundant attention, it remains unclear how the design influences their transcellular process, especially the key factors affecting their functions. This review discusses the extracellular and cellular barriers to orally administered LMNCs in the gastrointestinal (GI) tract and new discoveries regarding the GI protein corona and the sequential transport barriers that impede the preplanned movements of LMNCs after oral administration. Furthermore, innovative progress in considering key factors (including target selection, ligand properties, and other important factors) in the rational design of LMNCs for oral drug delivery is presented. In particular, some factors that endow LMNCs with efficient transcytosis rather than only endocytosis are highlighted. Finally, the prospects of orally administered LMNCs in disease therapy for the enhanced oral/local bioavailability of active pharmaceutical ingredients, as well as emerging delivery routes, such as lymphatic drug delivery and systemic location-specific drug release based on oral transcellular LMNCs, are discussed.

Effects of Osmolarity on Ultrasound-Induced Membrane Depolarization in Isolated Crayfish Motor Axon

We have previously identified a novel non-selective membrane conductance (g_US) opened by focused ultrasound (FUS) in crayfish motor axons. In the work described here, we studied g_US properties further by comparing FUS-evoked depolarization (FUSD) in control and hypotonic saline with 75% of control osmolarity. The FUS was a train of 20 FUS bursts (2.1 MHz and 50 µs per burst) delivered at 1 kHz. The amplitude, onset latency, frequency of occurrence and duration of FUSD were compared in a 15-min time window before and after switching to hypotonic saline. Significant increases were observed for amplitude (p < 0.001) and frequency of occurrence (p < 0.01) while the onset latency exhibited a significant decrease (p < 0.001). FUSD duration did not significantly differ. These results support predictions based on our hypothesis that g_US is mediated by opening of nanopores in the lipid bilayer and that stretching of axonal membrane caused by swelling at low osmolarity should increase the probability of nanopore formation under FUS. The FUSD parameters, in addition, exhibited time-dependent trends when the window of observation was expanded to 45 min in each saline. The statistical significance of amplitude and duration differed between 15- and 45-min time windows, indicating the presence of adaptive responses of axonal membrane to osmotic manipulation.

Ion Selectivity in the ENaC/DEG Family: A Systematic Review with Supporting Analysis

The Epithelial Sodium Channel/Degenerin (ENaC/DEG) family is a superfamily of sodium-selective channels that play diverse and important physiological roles in a wide variety of animal species. Despite their differences, they share a high homology in the pore region in which the ion discrimination takes place. Although ion selectivity has been studied for decades, the mechanisms underlying this selectivity for trimeric channels, and particularly for the ENaC/DEG family, are still poorly understood. This systematic review follows PRISMA guidelines and aims to determine the main components that govern ion selectivity in the ENaC/DEG family. In total, 27 papers from three online databases were included according to specific exclusion and inclusion criteria. It was found that the G/SxS selectivity filter (glycine/serine, non-conserved residue, serine) and other well conserved residues play a crucial role in ion selectivity. Depending on the ion type, residues with different properties are involved in ion permeability. For lithium against sodium, aromatic residues upstream of the selectivity filter seem to be important, whereas for sodium against potassium, negatively charged residues downstream of the selectivity filter seem to be important. This review provides new perspectives for further studies to unravel the mechanisms of ion selectivity.

The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes

Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport "phospholipid bilayer transport is negligible".

A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation

Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.

Effects of different temperatures on seawater acclimation in rainbow trout Oncorhynchus mykiss: osmoregulation and branchial phospholipid fatty acid composition

This study aimed to investigate the effects of different temperatures on seawater acclimation in rainbow trout (Oncorhynchus mykiss), in terms of growth performance, osmoregulatory capacity, and branchial phospholipid fatty acid (PLFA) composition. The fish (initial weight, 94.73 g) were reared at 9, 12.5, and 16 °C for 28 days, then acclimated to seawater, and subsequently reared for 14 days. Sampling points were on the last day in freshwater, and the 1st, 4th, 7th, and 14th days after the salinity reached 30. The results showed the final weight, percent weight gain, and specific growth rate of rainbow trout at 12.5 °C were significantly higher than those at 9 °C, while the thermal growth coefficient at 16 °C was significantly lower than that in other treatments. The branchial PLFA composition in rainbow trout changed more rapidly at 9 and 12.5 °C than at 16 °C. The branchial PLFA composition was significantly affected by temperature and salinity and their interaction. The polyunsaturated fatty acid content of phospholipids in the gill at 9 and 12.5 °C was significantly higher than those at 16 °C. Low temperature (9 °C) and seawater acclimation significantly increased the degree of unsaturation of membrane, enhancing membrane fluidity, which is related to Na⁺-K⁺ ATPase activity. Responses of plasma ion, Na⁺-K⁺ ATPase activity, and plasma glucose followed a similar pattern at different temperatures. Overall, the study suggests that 12.5 °C is the ideal temperature for seawater acclimation in rainbow trout.

Elucidating the anomalous membrane permeability of Ag(I), Cu(II), Zn(II) and Au(III) towards new nanoreactor strategies for synthesizing metal nanoparticles

The main structural element defining the cell is the lipid membrane, which is an integral part of regulating the fluxes of ion and nutrition molecules in and out of the cell. Surprisingly, copper ions were found to have anomalous membrane permeability. This led us to consider a broader spectrum of cations and further a new approach for using liposomes as nanoreactors for synthesis of metal and metal alloy nanoparticles. In the present study, the high membrane permeability of Cu2+ and its neighbouring transition elements in the periodic table was investigated. The permeability of Ni2+, Cu2+, Zn2+, Ag+, Au3+, Mg2+, Ca2+ and Lu3+ was assessed, and we report that Zn2+, Cu2+, Ag+ and Au3+ surprisingly are able to cross lipid bilayers. This knowledge is highly relevant for understanding trafficking of cations in biological systems, as well as for design of novel nanoparticle and nanoreactor systems. An example of its use is presented as a platform for synthesizing single highly uniform gold nanoparticles inside liposomal nanoreactors. We envision that this approach could provide a new nanoreactor methodology for forming highly structurally constrained uniform metal and metal alloy nanoparticles, as well as new methods for in vivo tracking of liposomes.

Molecular dynamics simulations of mechanical stress on oxidized membranes

Biomembranes are under constant attack of free radicals that may lead to lipid oxidation in conditions of oxidative stress. The products generated during lipid oxidation are responsible for structural and dynamical changes which may jeopardize the membrane function. For instance, the local rearrangements of oxidized lipid molecules may induce membrane rupture. In this study, we investigated the effects of mechanical stress on oxidized phospholipid bilayers (PLBs). Model bilayers were stretched until pore formation (or poration) using non-equilibrium molecular dynamics simulations. We studied single-component homogeneous membranes composed of lipid oxidation products, as well as two-component heterogeneous membranes with coexisting native and oxidized domains. In homogeneous membranes, the oxidation products with -OH and -OOH groups reduced the areal strain required for pore formation, whereas the oxidation product with O group behaved similarly to the native membrane. In heterogeneous membranes composed of oxidized and non-oxidized domains, we tested the hypothesis according to which poration may be facilitated at the domain interface region. However, results were inconclusive due to their large statistical variance and sensitivity to simulation setup parameters. We pointed out important technical issues that need to be considered in future simulations of mechanically-induced poration of heterogeneous membranes. This research is of interest for photodynamic therapy and plasma medicine, because ruptured and intact plasma membranes are experimentally considered hallmarks of necrotic and apoptotic cell death.

Lipid Head Group Parameterization for GROMOS 54A8: A Consistent Approach with Protein Force Field Description

Membranes are a crucial component of both bacterial and mammalian cells, being involved in signaling, transport, and compartmentalization. This versatility requires a variety of lipid species to tailor the membrane’s behavior as needed, increasing the complexity of the system. Molecular dynamics simulations have been successfully applied to study model membranes and their interactions with proteins, elucidating some crucial mechanisms at the atomistic detail and thus complementing experimental techniques. An accurate description of the functional interplay of the diverse membrane components crucially depends on the selected parameters that define the adopted force field. A coherent parameterization for lipids and proteins is therefore needed. In this work, we propose and validate new lipid head group parameters for the GROMOS 54A8 force field, making use of recently published parametrizations for key chemical moieties present in lipids. We make use additionally of a new canonical set of partial charges for lipids, chosen to be consistent with the parameterization of soluble molecules such as proteins. We test the derived parameters on five phosphocholine model bilayers, composed of lipid patches four times larger than the ones used in previous studies, and run 500 ns long simulations of each system. Reproduction of experimental data like area per lipid and deuterium order parameters is good and comparable with previous parameterizations, as well as the description of liquid crystal to gel-phase transition. On the other hand, the orientational behavior of the head groups is more realistic for this new parameter set, and this can be crucial in the description of interactions with other polar molecules. For that reason, we tested the interaction of the antimicrobial peptide lactoferricin with two model membranes showing that the new parameters lead to a weaker peptide–membrane binding and give a more realistic outcome in comparing binding to antimicrobial versus mammal membranes.

Modulation of Antimicrobial Peptide Potency in Stressed Lipid Bilayers

It is shown that the tendency of an archetypal antimicrobial peptide to insert into and perforate a simple lipid bilayer is strongly modulated by tensile stress in the membrane. The results, obtained through molecular dynamics simulations, have been demonstrated with several lipid compositions and appear to be general, although quantitative details differ. The findings imply that the potency of antimicrobial peptides may not be a purely intrinsic chemical property and, instead, depends on the mechanical state of the target membrane.

Membrane Electroporation and Electropermeabilization: Mechanisms and Models

Exposure of biological cells to high-voltage, short-duration electric pulses causes a transient increase in their plasma membrane permeability, allowing transmembrane transport of otherwise impermeant molecules. In recent years, large steps were made in the understanding of underlying events. Formation of aqueous pores in the lipid bilayer is now a widely recognized mechanism, but evidence is growing that changes to individual membrane lipids and proteins also contribute, substantiating the need for terminological distinction between electroporation and electropermeabilization. We first revisit experimental evidence for electrically induced membrane permeability, its correlation with transmembrane voltage, and continuum models of electropermeabilization that disregard the molecular-level structure and events. We then present insights from molecular-level modeling, particularly atomistic simulations that enhance understanding of pore formation, and evidence of chemical modifications of membrane lipids and functional modulation of membrane proteins affecting membrane permeability. Finally, we discuss the remaining challenges to our full understanding of electroporation and electropermeabilization.

Ion Permeation through a Phospholipid Membrane: Transition State, Path Splitting, and Calculation of Permeability

We investigate the thermodynamics and kinetics of the permeation of a potassium ion through a phospholipid membrane. We illustrate that the conventional reaction coordinate (the position of the ion along the normal to the membrane plane) is insufficient to capture essential elements of the process. It is necessary to add coarse variables that measure membrane distortion. New coarse variables are suggested, and a two-dimensional coarse-space is proposed to describe the permeation. We illustrate path splitting and two transition states of comparable barrier heights. The alternative pathways differ by the extent of water solvation of the ion-phosphate pairs. The permeation process cannot be described by a local one-dimensional reaction coordinate, and a network formulation is more appropriate. We use Milestoning with Voronoi tessellation in two dimensions to quantify the equilibrium and rate of the permeation of the positively charged ion. The permeation coefficient is computed and compared favorably to experiment.

Molecular-Level "Observations" of the Behavior of Gold Nanoparticles in Aqueous Solution and Interacting with a Lipid Bilayer Membrane

We use coarse-grained molecular dynamics simulations to "observe" details of interactions between ligand-covered gold nanoparticles and a lipid bilayer model membrane. In molecular dynamics simulations, one puts the individual atoms and groups of atoms of the physical system to be "observed" into a simulation box, specifies the forms of the potential energies of interactions between them (ultimately quantum based), and lets them individually move classically according to Newton's equations of motion, based on the forces arising from the assumed potential energy forms. The atoms that are chemically bonded to each other stay chemically bonded, following known potentials (force fields) that permit internal degrees of freedom (internal rotation, torsion, vibrations), and the interactions between nonbonded atoms are simplified to Lennard-Jones forms (in our case) and coulombic (where electrical charges are present) in which the parameters are previously optimized to reproduce thermodynamic properties or are based on quantum electronic calculations. The system is started out at a reasonable set of coordinates for all atoms or groups of atoms, and then permitted to develop according to the equations of motion, one small step (usually 10 fs time step) at a time, for millions of steps until the system is at a quasi-equilibrium (usually reached after hundreds of nanoseconds). We then let the system play out its motions further for many nanoseconds to observe the behavior, periodically taking snapshots (saving all positions and energies), and post-processing the snapshots to obtain various average descriptions of the system. Alkanethiols of various lengths serve as examples of hydrophobic ligands and methyl-terminated PEG with various numbers of monomer units serve as examples of hydrophilic ligands. Spherical gold particles of various diameters as well as gold nanorods form the core to which ligands are attached. The nanoparticles are characterized at the molecular level, especially the distributions of ligand configurations and their dependence on ligand length, and surface coverage. Self-assembly of the bilayer from an isotropic solution and observation of membrane properties that correspond well to experimental values validate the simulations. The mechanism of permeation of a gold NP coated with either a hydrophobic or a hydrophilic ligand, and its dependence on surface coverage, ligand length, core diameter, and core shape, is investigated. Lipid response such as lipid flip-flops, lipid extraction, and changes in order parameter of the lipid tails are examined in detail. The mechanism of permeation of a PEGylated nanorod is shown to occur by tilting, lying down, rotating, and straightening up. The nature of the information provided by molecular dynamics simulations permits understanding of the detailed behavior of gold nanoparticles interacting with lipid membranes which in turn helps to understand why some known systems work better than others and aids the design of new particles and improvement of methods for preparing existing ones.

Cholesterol suppresses membrane leakage by decreasing water penetrability

Membrane fusion is a fundamental biological process that lies at the heart of enveloped virus infection, synaptic signaling, intracellular vesicle trafficking, gamete fertilization, and cell-cell fusion. Membrane fusion is initiated as two apposed membranes merge to a single bilayer called a hemifusion diaphragm. It is believed that the contents of the two fusing membranes are released through a fusion pore formed at the hemifusion diaphragm, and yet another possible pathway has been proposed in which an undefined pore may form outside the hemifusion diaphragm at the apposed membranes, leading to the so-called leaky fusion. Here, we performed all-atom molecular dynamics simulations to study the evolution of the hemifusion diaphragm structure with various lipid compositions. We found that the lipid cholesterol decreased water penetrability to inhibit leakage pore formation. Biochemical leakage experiments support these simulation results. This study may shed light on the underlying mechanism of the evolution pathways of the hemifusion structure, especially the understanding of content leakage during membrane fusion.

Atomistic Simulations of Electroporation of Model Cell Membranes

Electroporation is a phenomenon that modifies the fundamental function of the cell since it perturbs transiently or permanently the integrity of its membrane. Today, this technique is applied in fields ranging from biology and biotechnology to medicine, e.g., for drug and gene delivery into cells, tumor therapy, etc., in which it made it to preclinical and clinical treatments. Experimentally, due to the complexity and heterogeneity of cell membranes, it is difficult to provide a description of the electroporation phenomenon in terms of atomically resolved structural and dynamical processes, a prerequisite to optimize its use. Atomistic modeling in general and molecular dynamics (MD) simulations in particular have proven to be an effective approach for providing such a level of detail. This chapter provides the reader with a comprehensive account of recent advances in using such a technique to complement conventional experimental approaches in characterizing several aspects of cell membranes electroporation.

Gold nanoparticle-mediated laser stimulation induces a complex stress response in neuronal cells

Stimulation of neuronal cells generally resorts to electric signals. Recent advances in laser-based stimulation methods could present an alternative with superior spatiotemporal resolution. The avoidance of electronic crosstalk makes these methods attractive for in vivo therapeutic application. In particular, nano-mediators, such as gold nanoparticles, can be used to transfer the energy from a laser pulse to the cell membrane and subsequently activate excitable cells. Although the underlying mechanisms of neuronal activation have been widely unraveled, the overall effect on the targeted cell is not understood. Little is known about the physiological and pathophysiological impact of a laser pulse targeted onto nanoabsorbers on the cell membrane. Here, we analyzed the reaction of the neuronal murine cell line Neuro-2A and murine primary cortical neurons to gold nanoparticle mediated laser stimulation. Our study reveals a severe, complex and cell-type independent stress response after laser irradiation, emphasizing the need for a thorough assessment of this approach’s efficacy and safety.

ChannelsDB: database of biomacromolecular tunnels and pores

ChannelsDB (http://ncbr.muni.cz/ChannelsDB) is a database providing information about the positions, geometry and physicochemical properties of channels (pores and tunnels) found within biomacromolecular structures deposited in the Protein Data Bank. Channels were deposited from two sources; from literature using manual deposition and from a software tool automatically detecting tunnels leading to the enzymatic active sites and selected cofactors, and transmembrane pores. The database stores information about geometrical features (e.g. length and radius profile along a channel) and physicochemical properties involving polarity, hydrophobicity, hydropathy, charge and mutability. The stored data are interlinked with available UniProt annotation data mapping known mutation effects to channel-lining residues. All structures with channels are displayed in a clear interactive manner, further facilitating data manipulation and interpretation. As such, ChannelsDB provides an invaluable resource for research related to deciphering the biological function of biomacromolecular channels.

Molecular thermodynamic modeling of a bilayer perforation in mixed catanionic surfactant systems

An interplay between electrostatics and deformation of surfactant tails is responsible for the spontaneous formation of pores in self-assembled bilayers.

Driving Force for Spontaneous Perforation of Bilayers Formed by Ionic Amphiphiles in Aqueous Salt

Spontaneous perforation of amphiphilic membranes is important in both living matter and technology because of an impact on functions of biological membranes and shape transitions of self-assembling structures. Nevertheless, no definite molecular mechanism has been established so far even for simple ionic surfactant systems. We show that spontaneous perforation of a bilayer formed by an ionic amphiphile is driven by electrostatics. Creation of large pores with a concave-convex geometry of the rim is promoted by lower electrostatic free energy than that for a flat nonperforated bilayer. The opposite effect comes from the elasticity of the hydrocarbon tails of the amphiphile that prefer flat geometry of a nonperforated bilayer. The balance between electrostatics and tail deformation controls the appearance of pores; this balance is modulated by added salt that screens the electrostatic interactions. We illustrate the proposed mechanism with the aid of classical aggregation model that has been extended by including an analytical description of the electrostatic contribution for the toroidal rim of a pore. Numerical solution of the linearized Poisson-Boltzmann equation confirms the role of electrostatic forces in formation of pores. For the ionic surfactants of C_nTAB family, we predict shape transitions including bilayer perforations and formation of branched micellar networks induced by changing salinity or temperature and demonstrate the effect of surfactant's molecular parameters on these transitions.

Assessment of Passive Intestinal Permeability Using an Artificial Membrane Insert System

Despite reasonable predictive power of current cell-based and cell-free absorption models for the assessment of intestinal drug permeability, high costs and lengthy preparation steps hamper their use. The use of a simple artificial membrane (without any lipids present) as intestinal barrier substitute would overcome these hurdles. In the present study, a set of 14 poorly water-soluble drugs, dissolved in 2 different media (fasted state simulated/human intestinal fluids [FaSSIF/FaHIF]), were applied to the donor compartment of an artificial membrane insert system (AMI-system) containing a regenerated cellulose membrane. Furthermore, to investigate the predictive capacity of the AMI-system as substitute for the well-established Caco-2 system to assess intestinal permeability, the same set of 14 drugs dissolved in FaHIF were applied to the donor compartment of a Caco-2 system. For 14 drugs, covering a broad range of physicochemical parameters, a reasonable correlation between both absorption systems was observed, characterized by a Pearson correlation coefficient r of 0.95 (FaHIF). Using the AMI-system, an excellent predictive capacity of FaSSIF as surrogate medium for FaHIF was demonstrated (r = 0.96). Based on the acquired data, the AMI-system appears to be a time- and cost-effective tool for the early-stage estimation of passive intestinal permeability for poorly water-soluble drugs.

How does ytterbium chloride interact with DMPC bilayers? A computational and experimental study

Lanthanide salts have been studied for many years, primarily in Nuclear Magnetic Resonance (NMR) experiments of mixed lipid–protein systems and more recently to study lipid flip-flop in model membrane systems.

Line Tension Assists Membrane Permeation at the Transition Temperature in Mixed-Phase Lipid Bilayers

The umbrella sampling method has been used to evaluate the free energy profile for a large permeant moving through a lipid bilayer, represented using a coarse-grained simulation model, at and below its gel-fluid transition temperature. At the lipid transition temperature, determined to be 302 K for the MARTINI 2.0 model of DPPC, the permeation barrier for passage through an enclosed fluid domain embedded in a patch of gel was significantly lower than that for passage through a fluid stripe domain. In contrast, permeation through a fluid domain in a stripe geometry produced a free energy profile nearly identical to that of a gel-free fluid bilayer. In both cases, insertion of the permeant into a fluid domain coexisting with the gel phase led to a shift in phase composition, as lipids transitioned from fluid to gel to accommodate the area occupied by the permeant. In the case of the enclosed fluid domain, this transition produced a decrease in the length of the fluid-gel interface as the approximately circular fluid domain shrank. The observed decrease in the apparent permeation barrier, combined with an approximation for the change in interfacial length, enabled estimation of the interfacial line tension to be between 10 and 13 pN for this model. The permeation barrier was shown to drop even further in simulations performed at temperatures below the transition temperature. The results suggest a mechanism to explain the experimentally observed anomalous peak in the temperature-dependent permeability of lipid bilayers near their transition temperatures. The contribution of this mechanism toward the permeability of a gel phase containing a thermal distribution of fluid-phase domains is estimated using a simple statistical thermodynamic model.

Passive Transmembrane Permeation Mechanisms of Monovalent Ions Explored by Molecular Dynamics Simulations

Passive or unassisted ion permeation through lipid bilayers involves a type of rare events by which cells regulate their salt concentrations and pH. It is important to understand its mechanism in order to develop technologies of, for example, delivering or maintaining small drug-like molecules inside cells. In earlier simulations of passive ion permeations, the commonly used sampling methods usually define the positions of ions relative to the membrane as a measure of permeation, i.e., the collective variable, ignoring the active participations of other particles. Newly defined collective variables involving the movements of ions, lipids, and water molecules allow us to identify the transition paths on the free energy landscape using the 2D umbrella sampling techniques. In this work, this technique was used to study the permeation processes of some well-known ions, sodium, potassium, and chloride. It is found permeations of sodium and potassium are assisted by important lipid bilayer deformations and massive water solvation, while chloride may not. Chloride may have two different possible pathways, in which the energetic favorable one is similar to the solubility-diffusion model. The free energy barriers for the permeation of these ions are in semiquantitative agreement with experiments. Further analyses on the distributions of oxygens and interaction energies suggest the electrostatic interactions between ions and polar headgroups of lipids may greatly influence membrane deformation as well as the water wire and furthermore the free energy barriers of waterwire mediated pathways. For chloride, the nonwaterwire pathway may be energetically favorable.

Geometrical Characterization of an Electropore from Water Positional Fluctuations

We present here a new method for calculating the radius of a transmembrane pore in a phospholipid bilayer. To compare size-related properties of pores in bilayers of various compositions, generated and maintained under different physical and chemical conditions, reference metrics are needed. Operational metrics can be associated with some observed behavior. For example, pore size can be defined by the largest object that will pass through the length of the pore. The novelty of the present approach resides in the characterization of electropore geometry via a statistical approach, based on essential dynamics rules. We define the pore size geometrically with an algorithm for determining the pore radius. In particular, we extract the radius from the tri-dimensional surface of a defined pore region. The method is applied to a pore formed in a phospholipid bilayer by application of an external electric field. Although the details described here are specific for lipid pores in molecular dynamics simulations, the method can be generalized for any kind of pores for which appropriate structural information is available.

A molecular insight into the electro-transfer of small molecules through electropores driven by electric fields

The transport of chemical compounds across the plasma membrane into the cell is relevant for several biological and medical applications. One of the most efficient techniques to enhance this uptake is reversible electroporation. Nevertheless, the detailed molecular mechanism of transport of chemical species (dyes, drugs, genetic materials, …) following the application of electric pulses is not yet fully elucidated. In the past decade, molecular dynamics (MD) simulations have been conducted to model the effect of pulsed electric fields on membranes, describing several aspects of this phenomenon. Here, we first present a comprehensive review of the results obtained so far modeling the electroporation of lipid membranes, then we extend these findings to study the electrotransfer across lipid bilayers subject to microsecond pulsed electric fields of Tat11, a small hydrophilic charged peptide, and of siRNA. We use in particular a MD simulation protocol that allows to characterize the transport of charged species through stable pores. Unexpectedly, our results show that for an electroporated bilayer subject to transmembrane voltages in the order of 500mV, i.e. consistent with experimental conditions, both Tat11 and siRNA can translocate through nanoelectropores within tens of ns. We discuss these results in comparison to experiments in order to rationalize the mechanism of drug uptake by cells. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Computational Methods for Structural and Functional Studies of Alzheimer's Amyloid Ion Channels

Aggregation can be studied by a range of methods, experimental and computational. Aggregates form in solution, across solid surfaces, and on and in the membrane, where they may assemble into unregulated leaking ion channels. Experimental probes of ion channel conformations and dynamics are challenging. Atomistic molecular dynamics (MD) simulations are capable of providing insight into structural details of amyloid ion channels in the membrane at a resolution not achievable experimentally. Since data suggest that late stage Alzheimer's disease involves formation of toxic ion channels, MD simulations have been used aiming to gain insight into the channel shapes, morphologies, pore dimensions, conformational heterogeneity, and activity. These can be exploited for drug discovery. Here we describe computational methods to model amyloid ion channels containing the β-sheet motif at atomic scale and to calculate toxic pore activity in the membrane.

Membrane pore formation in atomistic and coarse-grained simulations

Biological cells and their organelles are protected by ultra thin membranes. These membranes accomplish a broad variety of important tasks like separating the cell content from the outer environment, they are the site for cell-cell interactions and many enzymatic reactions, and control the in- and efflux of metabolites. For certain physiological functions e.g. in the fusion of membranes and also in a number of biotechnological applications like gene transfection the membrane integrity needs to be compromised to allow for instance for the exchange of polar molecules across the membrane barrier. Mechanisms enabling the transport of molecules across the membrane involve membrane proteins that form specific pores or act as transporters, but also so-called lipid pores induced by external fields, stress, or peptides. Recent progress in the simulation field enabled to closely mimic pore formation as supposed to occur in vivo or in vitro. Here, we review different simulation-based approaches in the study of membrane pores with a focus on lipid pore properties such as their size and energetics, poration mechanisms based on the application of external fields, charge imbalances, or surface tension, and on pores that are induced by small molecules, peptides, and lipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

How drugs get into cells: tested and testable predictions to help discriminate between transporter-mediated uptake and lipoidal bilayer diffusion

One approach to experimental science involves creating hypotheses, then testing them by varying one or more independent variables, and assessing the effects of this variation on the processes of interest. We use this strategy to compare the intellectual status and available evidence for two models or views of mechanisms of transmembrane drug transport into intact biological cells. One (BDII) asserts that lipoidal phospholipid Bilayer Diffusion Is Important, while a second (PBIN) proposes that in normal intact cells Phospholipid Bilayer diffusion Is Negligible (i.e., may be neglected quantitatively), because evolution selected against it, and with transmembrane drug transport being effected by genetically encoded proteinaceous carriers or pores, whose “natural” biological roles, and substrates are based in intermediary metabolism. Despite a recent review elsewhere, we can find no evidence able to support BDII as we can find no experiments in intact cells in which phospholipid bilayer diffusion was either varied independently or measured directly (although there are many papers where it was inferred by seeing a covariation of other dependent variables). By contrast, we find an abundance of evidence showing cases in which changes in the activities of named and genetically identified transporters led to measurable changes in the rate or extent of drug uptake. PBIN also has considerable predictive power, and accounts readily for the large differences in drug uptake between tissues, cells and species, in accounting for the metabolite-likeness of marketed drugs, in pharmacogenomics, and in providing a straightforward explanation for the late-stage appearance of toxicity and of lack of efficacy during drug discovery programmes despite macroscopically adequate pharmacokinetics. Consequently, the view that Phospholipid Bilayer diffusion Is Negligible (PBIN) provides a starting hypothesis for assessing cellular drug uptake that is much better supported by the available evidence, and is both more productive and more predictive.

Nanoplasmonically-induced defects in lipid membrane monitored by ion current: transient nanopores versus membrane rupture

We have developed a nanoplasmonic-based approach to induce nanometer-sized local defects in the phospholipid membranes. Here, gold nanorods and nanoparticles having plasmon resonances in the near-infrared (NIR) spectral range are used as optical absorption centers in the lipid membrane. Defects optically induced by NIR-laser irradiation of gold nanoparticles are continuously monitored by high-precision ion conductance measurement. Localized laser-mediated heating of nanorods and nanoparticle aggregates cause either (a) transient nanopores in lipid membranes or (b) irreversible rupture of the membrane. To monitor transient opening and closing, an electrophysiological setup is assembled wherein a giant liposome is spread over a micrometer hole in a glass slide forming a single bilayer of high Ohmic resistance (so-called gigaseal), while laser light is coupled in and focused on the membrane. The energy associated with the localized heating is discussed and compared with typical elastic parameters in the lipid membranes. The method presented here provides a novel methodology for better understanding of transport across artificial or natural biological membranes.

In situ precipitation: a novel approach for preparation of iron-oxide magnetoliposomes

Background

Conventional methods of preparing magnetoliposomes are complicated and inefficient. A novel approach for magnetoliposomes preparation was investigated in the study reported here.

Methods

FeCl₃/FeCl₂ solutions were hydrated with lipid films to obtain liposome-encapsulated iron ions by ultrasonic dispersion. Non-encapsulated iron ions were removed by dialysis. NH₃ · H₂O was added to the system to adjust the pH to a critical value. Four different systems were prepared. Each was incubated at a different temperature for a different length of time to facilitate the permeation of NH₃ · H₂O into the inner phase of the liposomes and the in situ formation of magnetic iron-oxide cores in the liposomes. Single-factor analysis and orthogonal-design experiments were applied to determinate the effects of alkalization pH, temperature, duration, and initial Fe concentration on encapsulation efficiency and drug loading.

Results

The magnetoliposomes prepared by in situ precipitation had an average particle size of 168±14 nm, zeta potential of −26.2±1.9 mV and polydispersity index of 0.23±0.06. The iron-oxide cores were confirmed as Fe₃O₄ by X-ray diffraction and demonstrated a superparamagnetic response. Encapsulation efficiency ranged from 3% to 22%, while drug loading ranged from 0.2 to 1.58 mol Fe/mol lipid. The optimal conditions for in situ precipitation were found to be an alkalization pH of 12, temperature of 60°C, time of 60 minutes, and initial Fe concentration of 100 mM Fe³⁺ + 50 mM Fe²⁺.

Conclusion

In situ precipitation could be a simple and efficient approach for the preparation of iron-oxide magnetoliposomes.

Continuum approaches to understanding ion and peptide interactions with the membrane

Experimental and computational studies have shown that cellular membranes deform to stabilize the inclusion of transmembrane (TM) proteins harboring charge. Recent analysis suggests that membrane bending helps to expose charged and polar residues to the aqueous environment and polar head groups. We previously used elasticity theory to identify membrane distortions that minimize the insertion of charged TM peptides into the membrane. Here, we extend our work by showing that it also provides a novel, computationally efficient method for exploring the energetics of ion and small peptide penetration into membranes. First, we show that the continuum method accurately reproduces energy profiles and membrane shapes generated from molecular simulations of bare ion permeation at a fraction of the computational cost. Next, we demonstrate that the dependence of the ion insertion energy on the membrane thickness arises primarily from the elastic properties of the membrane. Moreover, the continuum model readily provides a free energy decomposition into components not easily determined from molecular dynamics. Finally, we show that the energetics of membrane deformation strongly depend on membrane patch size both for ions and peptides. This dependence is particularly strong for peptides based on simulations of a known amphipathic, membrane binding peptide from the human pathogen Toxoplasma gondii. In total, we address shortcomings and advantages that arise from using a variety of computational methods in distinct biological contexts.

The free energy of nanopores in tense membranes

Membrane nanopores are central players for a range of important cellular membrane remodeling processes as well as membrane rupture. Understanding pore formation in tense membranes requires comprehension of the molecular mechanism of pore formation and the associated free energy change as a function of the membrane tension. Here we propose a scheme to calculate the free energy change associated with the formation of a nanometer sized pore in molecular dynamics simulations as a function of membrane tension, which requires the calculation of only one computationally expensive potential of mean force. We show that membrane elastic theory can be used to estimate the pore formation free energy at different tension values from the free energy change in a relaxed membrane and the area expansion curves of the membranes. We have computed the pore formation free energy for a dipalmitoyl-phosphatidylcholine (DPPC) membrane at two different lateral pressure values, 1 bar and -40 bar, by calculating the potential of mean force acting on the head group of a single lipid molecule. Unrestrained simulations of the closing process confirm that the intermediate states along this reaction coordinate are reasonable and show that hydrophilic indentations spanning half the bilayer connected by a hydrophobic pore segment represent the corresponding high energy transition state. A comparison of the stability of simulated membranes to experiment at high loading rates show that, contrary to expectation, pores form too easily in small simulated membrane patches. This discrepancy originates from a combination of the absence of ions in the simulations and the small membrane size.

Free energy of lipid bilayer defects affected by Alzheimer's disease-associated amyloid-β42 monomers

Experimental evidence suggests that the amyloid β-peptide (Aβ) associated with Alzheimer's disease strongly disturbs the integrity of lipid bilayers and cell membranes, as a possible origin of the toxicity of this peptide. Here, we have used molecular dynamics simulations to compute the free energy of membrane pores in the presence and absence of Aβ. The validation of our approach included the calculation of lipid flip-flop waiting times, which were found to agree well with recent experiments, in contrast with an earlier simulation study that apparently overestimated these waiting times. We find that, compared with peptide-free lipid bilayers, attached Aβ42 peptides (i) increase the order parameters of the lipid tails but (ii) decrease the effective width of the hydrophobic region, (iii) reduce the free energy and thus enlarge the density of membrane pores, and (iv) increase the lifetime of pores. A detailed understanding of the interaction of Aβ42 with lipid bilayer membranes may assist in the design of therapeutical strategies against Alzheimer's disease.

Functional truncated membrane pores

Membrane proteins are generally divided into two classes. Integral proteins span the lipid bilayer, and peripheral proteins are located at the membrane surface. Here, we provide evidence for membrane proteins of a third class that stabilize lipid pores, most probably as toroidal structures. We examined mutants of the staphylococcal α-hemolysin pore so severely truncated that the protein cannot span a bilayer. Nonetheless, the doughnut-like structures elicited well-defined transmembrane ionic currents by inducing pore formation in the underlying lipids. The formation of lipid pores, produced here by a structurally defined protein, is supported by the lipid and voltage dependences of pore formation, and by molecular dynamics simulations. We discuss the role of stabilized lipid pores in amyloid disease, the action of antimicrobial peptides, and the assembly of the membrane-attack complexes of the immune system.

Molecular dynamics simulations of ion conductance in field-stabilized nanoscale lipid electropores

Molecular dynamics (MD) simulations of electrophoretic transport of monovalent ions through field-stabilized electropores in POPC lipid bilayers permit systematic characterization of the conductive properties of lipid nanopores. The radius of the electropore can be controlled by the magnitude of the applied sustaining external electric field, which also drives the transport of ions through the pore. We examined pore conductances for two monovalent salts, NaCl and KCl, at physiological concentrations. Na(+) conductance is significantly less than K(+) and Cl(-) conductance and is a nonlinear function of pore radius over the range of pore radii investigated. The single pore electrical conductance of KCl obtained from MD simulation is comparable to experimental values measured by chronopotentiometry.