Structural and Kinetic Molecular Dynamics Study of Electroporation in Cholesterol-Containing Bilayers

Effect of cholesterol on nanoparticle translocation across a lipid bilayer

Nanoparticles (NPs) have attracted significant attention as carriers for the delivery of drugs, genes, and macromolecules for biomedical and therapeutic applications. These technologies require NPs to be delivered to the interior of the cell. However, this translocation is unlikely because of the presence of a cell membrane composed of phospholipids, cholesterol, proteins, and glycans. The cell membrane composition can influence its rigidity; thus, membrane composition is a crucial factor in determining the translocation of NPs across the cell membrane. Here, we focus on cholesterol, which is an essential component of biological cell membranes, and investigate NP translocation across membranes containing cholesterol under an applied electric field using a coarse-grained molecular dynamics simulation. We found that NPs could translocate directly across cholesterol-containing membranes without irreversible membrane disruption. This unique translocation was induced by two key phenomena. Before NP translocation, a phospholipid-rich/cholesterol-poor domain was formed at the NP-membrane contact interface. Second, a smaller transmembrane pore was formed in the cholesterol-containing membrane during membrane crossing of the NP. Our findings imply that the delivery of NPs to the cell interior across the cholesterol-containing membrane can be achieved by appropriately controlling the strength of the applied electric field, depending on the cholesterol content in the membrane.

Structure and Dynamics of Aqueous 2-Aminothiazole/NaCl Electrolytes at Electrified Interfaces

A computational study was performed to investigate the dynamics of aqueous electrolytes containing organic corrosion inhibitors near electrified interfaces by using the constant-charge model in classical molecular dynamics simulations. The results showed that when inhibitors form films at the interface, the surface charge of the electrode causes displacement of the molecules, referred to as electroporation. The hydrophobicity of the inhibitor molecules affects both the stability of the films and their recovery time. This study highlights the value of computational investigations of the dynamics within inhibitor films as a complementary approach to the traditional focus on inhibitor-substrate interactions, leading to deeper insights into the mechanisms of corrosion inhibition mechanisms.

Equivalence of Charge Imbalance and External Electric Fields during Free Energy Calculations of Membrane Electroporation

Electric fields across lipid membranes play important roles in physiology, medicine, and biotechnology, rationalizing the wide interest in modeling transmembrane potentials in molecular dynamics simulations. Transmembrane potentials have been implemented with external electric fields or by imposing charge imbalance between the two water compartments of a stacked double-membrane system. We compare the two methods in the context of membrane electroporation, which involves a large change of membrane structure and capacitance. We show that, given that Ewald electrostatics are defined with tinfoil boundary conditions, the two methods lead to (i) identical potentials of mean force (PMFs) of pore formation and expansion at various potentials, demonstrating that the two methods impose equivalent driving forces for large-scale transitions at membranes, and (ii) to identical polarization of water within thin water wires or open pores, suggesting that the two methods furthermore impose equivalent local electric fields. Without tinfoil boundary conditions, effects from external fields on pore formation are spuriously suppressed or even removed. Together, our study shows that both methods, external fields and charge imbalance, are well suitable for studying large-scale transitions of lipid membranes that involve changes of membrane capacitance. However, using charge imbalance is technically more challenging for maintaining a constant transmembrane potential since it requires updating of the charge imbalance as the membrane capacitance changes.

Effect of the cholesterol on electroporation of planar lipid bilayer

Electroporation threshold depends on the membrane composition, with cholesterol being one of its key components already studied in the past, but the results were inconclusive. The aim of our study was to determine behaviour of planar lipid bilayers with varying cholesterol concentrations under electric field. This would give us a better insight into cholesterol effect on membrane properties during electroporation process, since cholesterol is one of the major components of biological membranes and plays a crucial role in membrane organisation, dynamics, and function. Planar lipid bilayers were prepared from phosphatidylcholine lipids with 0, 20, 30, 50 and 80 mol% cholesterol. Capacitance was measured using the discharge method. Results show no statistical difference of cBLM between the cholesterol concentrations. Breakdown voltage Ubr of planar lipid bilayers was measured by means of linear rising voltage with seven different slopes. Obtained results were fitted to a strength-duration curve, where parameter Ubrmin represents minimal breakdown voltage, and parameter τRC represents the inclination of the strength-duration curve. Adding cholesterol to planar lipid bilayer gradually increased its Ubrmin until 50 mol% cholesterol concentration. Afterwards at 80 mol% Ubrmin does not further increase, in fact it reduces by 20% of the Ubrmin at 50 mol% cholesterol concentration.

Identification of electroporation sites in the complex lipid organization of the plasma membrane

The plasma membrane of a biological cell is a complex assembly of lipids and membrane proteins, which tightly regulate transmembrane transport. When a cell is exposed to strong electric field, the membrane integrity becomes transiently disrupted by formation of transmembrane pores. This phenomenon termed electroporation is already utilized in many rapidly developing applications in medicine including gene therapy, cancer treatment, and treatment of cardiac arrhythmias. However, the molecular mechanisms of electroporation are not yet sufficiently well understood; in particular, it is unclear where exactly pores form in the complex organization of the plasma membrane. In this study, we combine coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis to identify how formation of pores depends on the local lipid organization. We show that pores do not form homogeneously across the membrane, but colocalize with domains that have specific features, the most important being high density of polyunsaturated lipids. We further show that knowing the lipid organization is sufficient to reliably predict poration sites with machine learning. Additionally, by analysing poration kinetics with Bayesian survival analysis we show that poration does not depend solely on local lipid arrangement, but also on membrane mechanical properties and the polarity of the electric field. Finally, we discuss how the combination of atomistic and coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis can guide the design of future experiments and help us to develop an accurate description of plasma membrane electroporation on the whole-cell level. Achieving this will allow us to shift the optimization of electroporation applications from blind trial-and-error approaches to mechanistic-driven design.

Electric-driven membrane poration: A rationale for water role in the kinetics of pore formation

Electroporation is a well-established technique used to stimulate cells, enhancing membrane permeability by inducing reversible membrane pores. In the absence of experimental observation of the dynamics of pore creation, molecular dynamics studies provide the molecular-level evidence that the electric field promotes pore formation. Although single steps in the pore formation process are well assessed, a kinetic model representing the mathematical description of the electroporation process, is lacking. In the present work we studied the basis of the pore formation process, providing a rationale for the definition of a first-order kinetic scheme. Here, authors propose a three-state kinetic model for the process based on the assessed mechanism of water defects intruding at the water/lipid interface, when applying electric field intensities at the edge of the linear regime. The methodology proposed is based on the use of two robust biophysical quantities analyzed for the water molecules intruding at the water/lipid interface: (i) number of hydrogen bonds; (ii) number of contacts. The final model, sustained by a robust statistical sampling, provides kinetic constants for the transitions from the intact bilayer state to the hydrophobic pore state.

Genetic, cellular, and structural characterization of the membrane potential-dependent cell-penetrating peptide translocation pore

Cell-penetrating peptides (CPPs) allow intracellular delivery of bioactive cargo molecules. The mechanisms allowing CPPs to enter cells are ill-defined. Using a CRISPR/Cas9-based screening, we discovered that KCNQ5, KCNN4, and KCNK5 potassium channels positively modulate cationic CPP direct translocation into cells by decreasing the transmembrane potential (V_m). These findings provide the first unbiased genetic validation of the role of V_m in CPP translocation in cells. In silico modeling and live cell experiments indicate that CPPs, by bringing positive charges on the outer surface of the plasma membrane, decrease the V_m to very low values (–150 mV or less), a situation we have coined megapolarization that then triggers formation of water pores used by CPPs to enter cells. Megapolarization lowers the free energy barrier associated with CPP membrane translocation. Using dyes of varying dimensions in CPP co-entry experiments, the diameter of the water pores in living cells was estimated to be 2 (–5) nm, in accordance with the structural characteristics of the pores predicted by in silico modeling. Pharmacological manipulation to lower transmembrane potential boosted CPP cellular internalization in zebrafish and mouse models. Besides identifying the first proteins that regulate CPP translocation, this work characterized key mechanistic steps used by CPPs to cross cellular membranes. This opens the ground for strategies aimed at improving the ability of cells to capture CPP-linked cargos in vitro and in vivo.

Before a drug can have its desired effect, it must reach its target tissue or organ, and enter its cells. This is not easy because cells are surrounded by the plasma membrane, a fat-based barrier that separates the cell from its external environment. The plasma membrane contains proteins that act as channels, shuttling specific molecules in and out of the cell, and it also holds charge, with its inside surface being more negatively charged than its outside surface.

Cell-penetrating peptides are short sequences of amino acids (the building blocks that form proteins) that carry positive charges. These positive charges allow them to cross the membrane easily, but it is not well understood how.

To find out how cell-penetrating peptides cross the membrane, Trofimenko et al. attached them to dyes of different sizes. This revealed that the cell-penetrating peptides enter the cell through temporary holes called water pores, which measure about two nanometres across. The water pores form when the membrane becomes ‘megapolarized’, this is, when the difference in charge between the inside and the outside of the membrane becomes greater than normal. This can happen when the negative charge on the inside surface or the positive charge on the outer surface of the membrane increase. Megapolarization depends on potassium channels, which transport positive potassium ions outside the cell, making the outside of the membrane positive. When cell-penetrating peptides arrive at the outer surface of the cell near potassium channels, they make it even more positive. This increases the charge difference between the inside and the outside of the cell, allowing water pores to form. Once the peptides pass through the pores, the charge difference between the inside and the outside of the cell membrane dissipates, and the pores collapse.

Drug developers are experimenting with attaching cell-penetrating peptides to drugs to help them get inside their target cells. Currently there are several experimental medications of this kind in clinical trials. Understanding how these peptides gain entry, and what size of molecule they could carry with them, provides solid ground for further drug development.

The Effect of the Osmotically Active Compound Concentration Difference on the Passive Water and Proton Fluxes across a Lipid Bilayer

The molecular details of the passive water flux across the hydrophobic membrane interior are still a matter of debate. One of the postulated mechanisms is the spontaneous, water-filled pore opening, which facilitates the hydrophilic connection between aqueous phases separated by the membrane. In the paper, we provide experimental evidence showing that the spontaneous lipid pore formation correlates with the membrane mechanics; hence, it depends on the composition of the lipid bilayer and the concentration of the osmotically active compound. Using liposomes as an experimental membrane model, osmotically induced water efflux was measured with the stopped-flow technique. Shapes of kinetic curves obtained at low osmotic pressure differences are interpreted in terms of two events: the lipid pore opening and water flow across the aqueous channel. The biological significance of the dependence of the lipid pore formation on the concentration difference of an osmotically active compound was illustrated by the demonstration that osmotically driven water flow can be accompanied by the dissipation of the pH gradient. The application of the Helfrich model to describe the probability of lipid pore opening was validated by demonstrating that the probability of pore opening correlates with the membrane bending rigidity. The correlation was determined by experimentally derived bending rigidity coefficients and probabilities of lipid pores opening.

Recent developments in the kinetics of ruptures of giant vesicles under constant tension

External tension in membranes plays a vital role in numerous physiological and physicochemical phenomena. In this review, recent developments in the constant electric- and mechanical-tension-induced rupture of giant unilamellar vesicles (GUVs) are considered. We summarize the results relating to the kinetics of GUV rupture as a function of membrane surface charge, ions in the bathing solution, lipid composition, cholesterol content in the membrane, and osmotic pressure. The mechanical stability and line tension of the membrane under these conditions are discussed. The membrane tension due to osmotic pressure and the critical tension of rupture for various membrane compositions are also discussed. The results and their analysis provide a biophysical description of the kinetics of rupture, along with insight into biological processes. Future directions and possible developments in this research area are included.

Effects of osmotic pressure on the irreversible electroporation in giant lipid vesicles

Irreversible electroporation (IRE) is a nonthermal tumor/cell ablation technique in which a series of high-voltage short pulses are used. As a new approach, we aimed to investigate the rupture of giant unilamellar vesicles (GUVs) using the IRE technique under different osmotic pressures (Π), and estimated the membrane tension due to Π. Two categories of GUVs were used in this study. One was prepared with a mixture of dioleoylphosphatidylglycerol (DOPG), dioleoylphosphatidylcholine (DOPC) and cholesterol (chol) for obtaining more biological relevance while other with a mixture of DOPG and DOPC, with specific molar ratios. We determined the rate constant (kp) of rupture of DOPG/DOPC/chol (46/39/15)-GUVs and DOPG/DOPC (40/60)-GUVs induced by constant electric tension (σc) under different Π. The σc dependent kp values were fitted with a theoretical equation, and the corresponding membrane tension (σoseq) at swelling equilibrium under Π was estimated. The estimated membrane tension agreed well with the theoretical calculation within the experimental error. Interestingly, the values of σoseq were almost same for both types of synthesized GUVs under same osmotic pressure. We also examined the sucrose leakage, due to large osmotic pressure-induced pore formation, from the inside of DOPG/DOPC/chol(46/39/15)-GUVs. The estimated membrane tension due to large Π at which sucrose leaked out was very similar to the electric tension at which GUVs were ruptured without Π. We explained the σc and Π induced pore formation in the lipid membranes of GUVs.

5 ns electric pulses induce Ca2+-dependent exocytotic release of catecholamine from adrenal chromaffin cells

Previously we reported that adrenal chromaffin cells exposed to a 5 ns, 5 MV/m pulse release the catecholamines norepinephrine (NE) and epinephrine (EPI) in a Ca²⁺-dependent manner. Here we determined that NE and EPI release increased with pulse number (one versus five and ten pulses at 1 Hz), established that release occurs by exocytosis, and characterized the exocytotic response in real-time. Evidence of an exocytotic mechanism was the appearance of dopamine-β-hydroxylase on the plasma membrane, and the demonstration by total internal reflection fluorescence microscopy studies that a train of five or ten pulses at 1 Hz triggered the release of the fluorescent dye acridine orange from secretory granules. Release events were Ca²⁺-dependent, longer-lived relative to those evoked by nicotinic receptor stimulation, and occurred with a delay of several seconds despite an immediate rise in Ca²⁺. In complementary studies, cells labeled with the plasma membrane fluorescent dye FM 1-43 and exposed to a train of ten pulses at 1 Hz underwent Ca²⁺-dependent increases in FM 1-43 fluorescence indicative of granule fusion with the plasma membrane due to exocytosis. These results demonstrate the effectiveness of ultrashort electric pulses for stimulating catecholamine release, signifying their promise as a novel electrostimulation modality for neurosecretion.

Tuning the transdermal transport by application of external continuous electric field: a coarse-grained molecular dynamics study

The control of skin permeability to specific substances (e.g., medications, vitamins, and nutrients) through stratum corneum is a challenge. Iontophoresis is an option in spite of the lack of a detailed understanding of the underlying molecular mechanism. In the present work, the simulations concerning application of an external continuous electric field to stratum corneum, in a range of low intensity (0-24 mV nm^-1), were carried out using the coarse-grained molecular dynamics approach. Using a set of random seed replicas of the starting configuration, we observed that in the range of electric field intensity of 22-23 mV nm^-1, water-rich lipid vesicles were formed in 20% of cases. Pores appeared in the remaining 80%. We argue that lipids undergo fast re-orientations under electric field inducing mechanical instability, which originates the pores. We presented a simple electrostatic model to interpret the results where the mismatch between electrical permittivities of the membrane and external media and the gradient of the local electric field in the membrane surface, govern the time scales and electric fields for vesicle formation. Our results indicate that just 10% difference between electrical permittivities of the membrane and external media decreases 1/6 the minimal time required for vesicle formation. The minimal electric field required decreases 10 times. The control and tunning of formation of biologically compatible vesicles, capable of transporting substances under low-intensity electric fields, has a promising application in fields such as drug therapy and dermo-cosmetics allowing the use of hydrophilic substances in dermal applications.

Cationic Antiseptics Facilitate Pore Formation in Model Bacterial Membranes

Antiseptics are an essential line of defense against bacterial and viral infections in modern medical practice. Many of them are supposed to act on microbial membranes. However, the detailed mechanisms of their action are still elusive. Here, we utilized coarse-grained molecular dynamics simulations to investigate interactions of different types of cationic antiseptics (CAs) with a model bacterial membrane. The simulations revealed qualitatively distinct patterns of dynamic and structural alterations of membrane induced by different types of antiseptics although none of them caused disintegration or solubilization of the bilayer even at the highest explored concentration. At the same time, the adsorption of antiseptics rendered membranes more vulnerable to poration under exposure to the external electric field. We further discuss the possible relation of the enhanced pore formation induced by CAs to their cytotoxic action.

Influence of cholesterol on electroporation in lipid membranes of giant vesicles

Irreversible electroporation (IRE) is primarily a nonthermal ablative technology that uses a series of high-voltage and ultra-short pulses with high-frequency electrical energy to induce cell death. This paper presents the influence of cholesterol on the IRE-induced probability of pore formation and the rate constant of pore formation in giant unilamellar vesicles (GUVs). The GUVs are prepared by a mixture of dioleoylphosphatidylglycerol (DOPG), dioleoylphosphatidylcholine (DOPC) and cholesterol using the natural swelling method. An IRE signal of frequency 1.1 kHz is applied to the membranes of GUVs. The probability of pore formation and the rate constant of pore formation events are obtained using statistical analysis from several single GUVs. The time-dependent fraction of intact GUVs among all those examined is fitted to a single exponential decay function from where the rate constant of pore formation is calculated. The probability of pore formation and the rate constant of pore formation decreases with an increase in cholesterol content in the membranes of GUVs. Theoretical equations are fitted to the tension-dependent rate constant of pore formation and to the probability of pore formation, which allows us to obtain the line tension of membranes. The obtained line tension increases with an increase in cholesterol in the membranes. The increase in the energy barrier of the prepore state, due to the increase of cholesterol in membranes, is the main factor explaining the decrease in the rate constant of pore formation.

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.

Transprotein-Electropore Characterization: A Molecular Dynamics Investigation on Human AQP4

Electroporation characterization is a topic of intensive interest probed by extensive ongoing research efforts. Usually, these studies are carried out on lipid-bilayer electroporation. Surprisingly, the possibility of water-channel electropore formation across transmembrane proteins themselves, particularly in view of such a promising application, has not yet been elucidated. The present work examines the geometrical and kinetic aspects of electropores and their stability in such a protein milieux (as opposed through the phospholipid membranes) in depth, by means of scrutiny of such a process in human-AQP4 as a well-representative prototype. The residues forming the electropore's walls, organized in loops, reveal the formation mechanism by their dipole alignment and translational response in response to applied axial electric fields in nonequilibrium molecular dynamics simulation. The magnitude of sustaining electric fields (keeping a stable electropore open) were determined. This suggests that transmembrane proteins could play a central role in electroporation applications, e.g., in medicine and biotechnology.

Electroporation of Skin Stratum Corneum Lipid Bilayer and Molecular Mechanism of Drug Transport: A Molecular Dynamics Study

The electroporation technique has been used significantly to increase drug permeation through the skin. This technique relies on the application of short-timed (microseconds to millisecond) electric fields (generally, order of 50--300 V) on the skin to create microscopic pores. However, the molecular mechanism of pore formation, resulting in an enhanced flux of active molecules through the skin, remains poorly understood. In this study, extensive atomistic molecular dynamics simulation of skin lipids [made up of ceramide (CER), cholesterol (CHOL), and free fatty acid (FFA)] has been performed at various external electric fields. We show for the first time the pore formation in the skin lipid bilayer during electroporation. We show the effect of the applied external electrical field (0.6-1.0 V/nm) on the pore formation dynamics in the lipid bilayer of different sizes (154, 616, and 2464 lipids) and compositions (CER/CHOL/FFA, 1:0:0, 1:0:1, 1:1:0, 1:1:1). The pore formation and resealing kinetics were different and were found to be highly dependent on the composition of the skin lipid bilayer. The pore formation time decreased with increase in the bilayer size. The pore sustaining electric field was found to be in the range of 0.20-0.25 V/nm for equimolar CER, CHOL, and FFA lipid bilayers. The skin lipid bilayer (1:1:1) sealed itself within 20 ns after the removal of the external electric field. We also present the molecular mechanism of enhancement of drug permeation in the presence of external field as compared to the passive diffusion. The molecular-level understanding obtained here could help in optimizing/designing the electroporation experiments for effective drug delivery. For a given skin composition and size of the drug molecule, the combination of pore formation time and pore growth model can be used to know a priori the desired electric field and time for the application of the electric field.

Lipid vesicles in pulsed electric fields: Fundamental principles of the membrane response and its biomedical applications

The present review focuses on the effects of pulsed electric fields on lipid vesicles ranging from giant unilamellar vesicles (GUVs) to small unilamellar vesicles (SUVs), from both fundamental and applicative perspectives. Lipid vesicles are the most popular model membrane systems for studying biophysical and biological processes in living cells. Furthermore, as vesicles are made from biocompatible and biodegradable materials, they provide a strategy to create safe and functionalized drug delivery systems in health-care applications. Exposure of lipid vesicles to pulsed electric fields is a common physical method to transiently increase the permeability of the lipid membrane. This method, termed electroporation, has shown many advantages for delivering exogenous molecules including drugs and genetic material into vesicles and living cells. In addition, electroporation can be applied to induce fusion between vesicles and/or cells. First, we discuss in detail how research on cell-size GUVs as model cell systems has provided novel insight into the basic mechanisms of cell electroporation and associated phenomena. Afterwards, we continue with a thorough overview how electroporation and electrofusion have been used as versatile methods to manipulate vesicles of all sizes in different biomedical applications. We conclude by summarizing the open questions in the field of electroporation and possible future directions for vesicles in the biomedical field.

Molecular dynamics simulations of heterogeneous cell membranes in response to uniaxial membrane stretches at high loading rates

The chemobiomechanical signatures of diseased cells are often distinctively different from that of healthy cells. This mainly arises from cellular structural/compositional alterations induced by disease development or therapeutic molecules. Therapeutic shock waves have the potential to mechanically destroy diseased cells and/or increase cell membrane permeability for drug delivery. However, the biomolecular mechanisms by which shock waves interact with diseased and healthy cellular components remain largely unknown. By integrating atomistic simulations with a novel multiscale numerical framework, this work provides new biomolecular mechanistic perspectives through which many mechanosensitive cellular processes could be quantitatively characterised. Here we examine the biomechanical responses of the chosen representative membrane complexes under rapid mechanical loadings pertinent to therapeutic shock wave conditions. We find that their rupture characteristics do not exhibit significant sensitivity to the applied strain rates. Furthermore, we show that the embedded rigid inclusions markedly facilitate stretch-induced membrane disruptions while mechanically stiffening the associated complexes under the applied membrane stretches. Our results suggest that the presence of rigid molecules in cellular membranes could serve as “mechanical catalysts” to promote the mechanical destructions of the associated complexes, which, in concert with other biochemical/medical considerations, should provide beneficial information for future biomechanical-mediated therapeutics.

Investigation of the morphological transition of a phospholipid bilayer membrane in an external electric field via molecular dynamics simulation

Elucidating the mechanisms for morphological transitions of the phospholipid bilayer membrane during cellular activity should lead to greater understanding of these membrane transitions and allow us to optimize biotechnologies such as drug delivery systems in organisms. To investigate the mechanism for and the dynamics of morphological changes in the phospholipid membrane, we performed molecular dynamics simulation of a phospholipid membrane with and without membrane protein under the influence of electric fields with different strengths. In the absence of membrane protein, it was possible to control the transition from one lamellar membrane morphology to another by applying a strong electric field. The strong electric field initially disordered the lipid molecules in the membrane, leading to the formation of a hydrophilic pore. The lipid molecules then spontaneously fused into a new lamellar membrane morphology. In the presence of membrane protein, a morphological transition from lamellar membrane to vesicle under the influence of a strong electric field was observed. Studying the complex transition dynamics associated with these changes in membrane morphology allowed us to gain deep insight into the electrofusion and electroporation that occur in the presence or absence of membrane protein, and the results obtained here should prove useful in work aimed at controlling membrane morphology. Graphical Abstract Memebrane morphological transition under the electric field of 0.6 V/nm with the membrane protein (down) and without membrane protein (up).

A statistical analytical model for hydrophilic electropore characterization: a comparison study

A new procedure for lipid pore characterization, which extracts the pore geometry from a statistical analysis of the tridimensional surface of the pore, is compared with other methods in the literature.

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.

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.

Electric Destabilization of Supramolecular Lipid Vesicles Subjected to Fast Electric Pulses

Biological membranes are weakly permeable to hydrophilic molecules and ions and electric pulses can induce their transient permeabilization, but this process is not well characterized. We directly assay the electropermeabilization process, on the minimum model of lipid vesicles, by using a highly sensitive fluorescence method based on manganese ion transport. The approach gives access, at the single-lipid self-assembly level, to the transmembrane potential needed to detect divalent ion permeabilization on supramolecular giant unilamellar lipid vesicles. The critical values are strongly dependent on the lipid composition and are observed to vary from 10 to 150 mV. These values appear to be much lower than those previously reported in the literature for cells and vesicles. The detection method appears to be a decisive parameter as it is controlled by the transport of the reporter dye. We also provide evidence that the electropermeabilization process is a transient transition of the lipid self-organization due to the loss of assembly cohesion induced by bioelectrochemical perturbations of the zwitterionic interface with the solution.

Effects of Stretching Speed on Mechanical Rupture of Phospholipid/Cholesterol Bilayers: Molecular Dynamics Simulation

Rupture of biological cell membrane under mechanical stresses is critical for cell viability. It is triggered by local rearrangements of membrane molecules. We investigated the effects of stretching speed on mechanical rupture of phospholipid/cholesterol bilayers using unsteady molecular dynamics simulations. We focused on pore formation, the trigger of rupture, in a 40 mol% cholesterol-including bilayer. The unsteady stretching was modeled by proportional and temporal scaling of atom positions at stretching speeds from 0.025 to 30 m/s. The effects of the stretching speed on the critical areal strain, where the pore forms, is composed of two regimes. At low speeds (<1.0 m/s), the critical areal strain is insensitive to speed, whereas it significantly increases at higher speeds. Also, the strain is larger than that of a pure bilayer, regardless of the stretching speeds, which qualitatively agrees with available experimental data. Transient recovery of the cholesterol and phospholipid molecular orientations was evident at lower speeds, suggesting the formation of a stretch-induced interdigitated gel-like phase. However, this recovery was not confirmed at higher speeds or for the pure bilayer. The different responses of the molecular orientations may help explain the two regimes for the effect of stretching speed on pore formation.

Electroporation threshold of POPC lipid bilayers with incorporated polyoxyethylene glycol (C12E8)

Electroporation relates to a phenomenon in which cell membranes are permeabilized after being exposed to high electric fields. On the molecular level, the mechanism is not yet fully elucidated, although a considerable body of experiments and molecular dynamic (MD) simulations were performed on model membranes. Here we present the results of a combined theoretical and experimental investigation of electroporation of palmitoy-oleoyl-phosphatidylcholine (POPC) bilayers with incorporated polyoxyethylene glycol (C12E8) surfactants. The experimental results show a slight increase of the capacitance and a 22% decrease of the voltage breakdown upon addition of C12E8 to pure POPC bilayers. These results were qualitatively confirmed by the MD simulations. They later revealed that the polyoxyethylene glycol molecules play a major role in the formation of hydrophilic pores in the bilayers above the electroporation threshold. The headgroup moieties of the latter are indeed embedded in the interior of the bilayer, which favors formation of water wires that protrude into its hydrophobic core. When the water wires extend across the whole bilayer, they form channels stabilized by the C12E8 head groups. These hydrophilic channels can transport ions across the membrane without the need of major lipid head-group rearrangements.

Cholesterol, sphingolipids, and glycolipids: what do we know about their role in raft-like membranes?

Lipids rafts are considered to be functional nanoscale membrane domains enriched in cholesterol and sphingolipids, characteristic in particular of the external leaflet of cell membranes. Lipids, together with membrane-associated proteins, are therefore considered to form nanoscale units with potential specific functions. Although the understanding of the structure of rafts in living cells is quite limited, the possible functions of rafts are widely discussed in the literature, highlighting their importance in cellular functions. In this review, we discuss the understanding of rafts that has emerged based on recent atomistic and coarse-grained molecular dynamics simulation studies on the key lipid raft components, which include cholesterol, sphingolipids, glycolipids, and the proteins interacting with these classes of lipids. The simulation results are compared to experiments when possible.

Effects of dimethyl sulfoxide on lipid membrane electroporation

Pores can be generated in lipid membranes by the application of an external electric field or by the addition of particular chemicals such as dimethyl sulfoxide (DMSO). Molecular dynamics (MD) has been shown to be a useful tool for unveiling many aspects of pore formation in lipid membranes in both situations. By means of MD simulations, we address the formation of electropores in cholesterol-containing lipid bilayers under the influence of DMSO. We show how a combination of physical and chemical mechanisms leads to more favorable conditions for generating membrane pores and, in particular, how the addition of DMSO to the medium significantly reduces the minimum electric field required to electroporate a lipid membrane. The strong alteration of membrane transversal properties and the energetic stabilization of the hydrophobic pore stage by DMSO provide the physicochemical mechanisms that explain this effect.

Electropermeabilization of the cell membrane

Membrane electropermeabilization is the observation that the permeability of a cell membrane can be transiently increased when a micro-millisecond external electric field pulse is applied on a cell suspension or on a tissue. Applicative aspects for the transfer of foreign molecules (macromolecules) into the cytoplasm are routinely used. But only a limited knowledge about what is really occurring in the cell and its membranes at the molecular levels is available. This chapter is a critical attempt to report the present state of the art and to point out some of the still open problems. The experimental facts associated to membrane electropermeabilization are firstly reported. They are valid on biological and model systems. Secondly, soft matter approaches give access to the bioelectrochemical description of the thermodynamical constraints supporting the destabilization of simplified models of the biological membrane. It is indeed described as a thin dielectric leaflet, where a molecular transport takes place by electrophoresis and then diffusion. This naïve approach is due to the lack of details on the structural aspects affecting the living systems as shown in a third part. Membranes are part of the cell machinery. The critical property of cells as being an open system from the thermodynamical point of view is almost never present. Computer simulations are now contributing to our knowledge on electropermeabilization. The last part of this chapter is a (very) critical report of all the efforts that have been performed. The final conclusion remains that we still do not know all the details on the reversible structural and dynamical alterations of the cell membrane (and cytoplasm) supporting its electropermeabilization. We have a long way in basic and translational researches to reach a pertinent description.

The alteration of lipid bilayer dynamics by phloretin and 6-ketocholestanol

Lipid bilayer properties are quantified with a variety of arbitrary selected parameters such as molecular packing and dynamics, electrostatic potentials or permeability. In the paper we determined the effect of phloretin and 6-ketocholestanol (dipole potential modifying agents) on the membrane hydration and efficiency of the trans-membrane water flow. The dynamics of water molecules within the lipid bilayer interface was evaluated using solvent relaxation method, whereas the osmotically induced trans-membrane water flux was estimated with the stopped-flow method using the liposome shrinkage kinetics. The presence of phloretin or 6-ketocholestanol resulted in a change of both, the interfacial hydration level and osmotically driven water fluxes. Specifically, the presence of 6-ketocholestanol reduced the amount and mobility of water in the membrane interface. It also slows the osmotically induced water flow. The interfacial hydration change caused by phloretin was much smaller and the effect on osmotically induced water flow was opposite to that of 6-ketocholestanol.

On the electroporation thresholds of lipid bilayers: molecular dynamics simulation investigations

Electroporation relates to the cascade of events that follows the application of high electric fields and that leads to cell membrane permeabilization. Despite a wide range of applications, little is known about the electroporation threshold, which varies with membrane lipid composition. Here, using molecular dynamics simulations, we studied the response of dipalmitoyl-phosphatidylcholine, diphytanoyl-phosphocholine-ester and diphytanoyl-phosphocholine-ether lipid bilayers to an applied electric field. Comparing between lipids with acyl chains and methyl branched chains and between lipids with ether and ester linkages, which change drastically the membrane dipole potential, we found that in both cases the electroporation threshold differed substantially. We show, for the first time, that the electroporation threshold of a lipid bilayer depends not only on the "electrical" properties of the membrane, i.e., its dipole potential, but also on the properties of its component hydrophobic tails.

Nanoscale, electric field-driven water bridges in vacuum gaps and lipid bilayers

Formation of a water bridge across the lipid bilayer is the first stage of pore formation in molecular dynamic (MD) simulations of electroporation, suggesting that the intrusion of individual water molecules into the membrane interior is the initiation event in a sequence that leads to the formation of a conductive membrane pore. To delineate more clearly the role of water in membrane permeabilization, we conducted extensive MD simulations of water bridge formation, stabilization, and collapse in palmitoyloleoylphosphatidylcholine bilayers and in water-vacuum-water systems, in which two groups of water molecules are separated by a 2.8 nm vacuum gap, a simple analog of a phospholipid bilayer. Certain features, such as the exponential decrease in water bridge initiation time with increased external electric field, are similar in both systems. Other features, such as the relationship between water bridge lifetime and the diameter of the water bridge, are quite different between the two systems. Data such as these contribute to a better and more quantitative understanding of the relative roles of water and lipid in membrane electropore creation and annihilation, facilitating a mechanism-driven development of electroporation protocols. These methods can be extended to more complex, heterogeneous systems that include membrane proteins and intracellular and extracellular membrane attachments, leading to more accurate models of living cells in electric fields.

Effects of dimethyl sulfoxide in cholesterol-containing lipid membranes: a comparative study of experiments in silico and with cells

Dimethyl sulfoxide (DMSO) has been known to enhance cell membrane permeability of drugs or DNA. Molecular dynamics (MD) simulations with single-component lipid bilayers predicted the existence of three regimes of action of DMSO: membrane loosening, pore formation and bilayer collapse. We show here that these modes of action are also reproduced in the presence of cholesterol in the bilayer, and we provide a description at the atomic detail of the DMSO-mediated process of pore formation in cholesterol-containing lipid membranes. We also successfully explore the applicability of DMSO to promote plasma membrane permeability to water, calcium ions (Ca(2+)) and Yo-Pro-1 iodide (Yo-Pro-1) in living cell membranes. The experimental results on cells in culture can be easily explained according to the three expected regimes: in the presence of low doses of DMSO, the membrane of the cells exhibits undulations but no permeability increase can be detected, while at intermediate DMSO concentrations cells are permeabilized to water and calcium but not to larger molecules as Yo-Pro-1. These two behaviors can be associated to the MD-predicted consequences of the effects of the DMSO at low and intermediate DMSO concentrations. At larger DMSO concentrations, permeabilization is larger, as even Yo-Pro-1 can enter the cells as predicted by the DMSO-induced membrane-destructuring effects described in the MD simulations.

Size-controlled nanopores in lipid membranes with stabilizing electric fields

Molecular dynamics (MD) has been shown to be a useful tool for unveiling many aspects of pore formation in lipid membranes under the influence of an applied electric field. However, the study of the structure and transport properties of electropores by means of MD has been hampered by difficulties in the maintenance of a stable electropore in the typically small simulated membrane patches. We describe a new simulation scheme in which an initially larger porating field is systematically reduced after pore formation to lower stabilizing values to produce stable, size-controlled electropores, which can then be characterized at the molecular level. A new method allows the three-dimensional modeling of the irregular shape of the pores obtained as well as the quantification of its volume. The size of the pore is a function of the value of the stabilizing field. At lower fields the pore disappears and the membrane recovers its normal shape, although in some cases long-lived, fragmented pores containing unusual lipid orientations in the bilayer are observed.