Electroporation of archaeal lipid membranes using MD simulations

Enrichment of cinnamaldehyde from Cinnamomum cassia by electroosmotic coupled particle-assisted solvent flotation

Cinnamaldehyde has been widely applied in various fields due to its special flavor and various pharmacological activities, such as antioxidant, anti-inflammatory and antibacterial properties. The strategy of quick and efficient enrichment for cinnamaldehyde is imperative. In this study, an electroosmotic coupled particle-assisted solvent flotation (ECPASF) system was designed for the cinnamaldehyde enrichment from cinnamon. The response surface method was used to optimize extraction parameters. Under optimal operating conditions, its yield was 9.33 ± 0.11 mg/g. Such high yield of cinnamaldehyde using the ECPASF might be because electroosmosis effectively alters the permeability of plant cells, which facilitates the release of cinnamaldehyde. In addition, both the crude extract of cinnamon and pure cinnamaldehyde showed good antioxidant activity. The results demonstrated that the ECPASF system is a sustainable and effective method for the extraction of cinnamaldehyde from cinnamon. It also has the prospect of being extended to the extraction of other natural products.

Advances in Physicochemical and Biochemical Characterization of Archaeosomes from Polar Lipids of Aeropyrum pernix K1 and Stability in Biological Systems

Archaeosomes are vesicles made from archaeal lipids. They are characterized by remarkable thermostability, resistance to enzymatic degradation, long-term stability, and immunomodulatory properties. In this review the current status of physicochemical properties of archaeal lipids and their stability in biological systems is presented, focusing on total polar lipids from Aeropyrum pernix K1. The isolated total polar lipids from Aeropyrum pernix K1 consist exclusively of glycerol ether lipids with isoprenoid groups attached to glycerol via ether linkages. More specifically, the two major polar lipids extracted from the membranes are C_25,25-achaetidyl(glucosyl)inositol and C_25,25-achaetidylinositol. An overview of the results of the effects of temperature and pH on the stability, structural organization, fluidity, and permeability of archaeosomes composed of pure C_25,25 was examined by a combination of techniques, including fluorescence emission spectroscopy, electron paramagnetic resonance, differential scanning calorimetry, and confocal microscopy. We also compared the physicochemical properties of pure vesicles composed of either archaeal lipids or conventional lipids (e.g., 1,2-dipalmitoyl-sn-glycero-3-phosphocholine) with mixed vesicles composed of both lipid types. Archaeal lipids are discussed in terms of their potential use as a targeted drug delivery system based on the results of in vivo and cytotoxicity studies.

Effect of Cobalt Ferrite Nanoparticles in a Hydrophilic Shell on the Conductance of Bilayer Lipid Membrane

We measured the conductance of bilayer lipid membranes of diphytanoylphosphatidylcholine induced by interaction with cubic magnetic nanoparticles (MNPs) of cobalt ferrite 12 and 27 nm in size and coated with a hydrophilic shell. The MNP coating is human serum albumin (HSA) or polyethylene glycol (PEG). The interaction of nanoparticles added to the bulk solution with the lipid bilayer causes the formation of metastable conductive pores, which, in turn, increases the integral conductance of the membranes. The increase in conductance with increasing MNP concentration was practically independent of the particle size. The dependence of the bilayer conductance on the concentration of PEG-coated MNPs was much weaker than that on the concentration with a shell of HSA. Analyzing the current traces, we believe that the conductive pores formed as a result of the interaction of nanoparticles with the membrane can change their size, remaining metastable. The form of multilevel current traces allows us to assume that there are several metastable pore states close in energy. The average radius of the putative cylindrical pores is in the range of 0.4-1.3 nm.

A lateral electric field inhibits gel-to-fluid transition in lipid bilayers

We report evidence of lateral electric field-induced changes in the phase transition temperatures of lipid bilayers. Our atomic scale molecular dynamics simulations show that a lateral electric field increases the melting temperatures of DPPC, POPC and POPE bilayers. Remarkably, these shifts in the melting temperatures are only induced by lateral electric fields, and not normal electric fields. This mechanism could provide new mechanistic insights into lipid-lipid and lipid-protein interactions in the presence of endogenous and exogenous electric fields.

All-atom molecular dynamics simulations of the combined effects of different phospholipids and cholesterol content on electroporation

The electroporation mechanism could be related to the composition of the plasma membrane, and the combined effect of different phospholipid molecules and cholesterol content on electroporation has rarely been studied nor conclusions drawn. In this paper, we applied all-atom molecular dynamics (MD) simulations to study the effects of phospholipids and cholesterol content on bilayer membrane electroporation. The palmitoyloleoylphosphatidylcholine (POPC) model, palmitoyloleoylphosphatidylethanolamine (POPE) model, and a 1 : 1 mixed model of POPC and POPE called PEPC, were the three basic models used. An electric field of 0.45 V nm-1 was applied to nine models, which were the three basic models, each with three different cholesterol content values of 0%, 24%, and 40%. The interfacial water molecules moved under the electric field and, once the first water bridge formed, the rest of the water molecules would dramatically flood into the membrane. The simulation showed that a rapid rise in the Z-component of the average dipole moment of the interfacial water molecules (Z-DM) indicated the occurrence of electroporation, and the same increment of Z-DM represented a similar change in the size of the water bridge. With the same cholesterol content, the formation of the first water bridge was the most rapid in the POPC model, regarding the average electroporation time (t ep), and the average t ep of the PEPC model was close to that of the POPE model. We speculate that the differences in membrane thickness and initial number of hydrogen bonds of the interfacial water molecules affect the average t ep for different membrane compositions. Our results reveal the influence of membrane composition on the electroporation mechanism at the molecular level.

The Exploration of the Thermococcus barophilus Lipidome Reveals the Widest Variety of Phosphoglycolipids in Thermococcales

One of the most distinctive characteristics of archaea is their unique lipids. While the general nature of archaeal lipids has been linked to their tolerance to extreme conditions, little is known about the diversity of lipidic structures archaea are able to synthesize, which hinders the elucidation of the physicochemical properties of their cell membrane. In an effort to widen the known lipid repertoire of the piezophilic and hyperthermophilic model archaeon Thermococcus barophilus, we comprehensively characterized its intact polar lipid (IPL), core lipid (CL), and polar head group compositions using a combination of cutting-edge liquid chromatography and mass spectrometric ionization systems. We tentatively identified 82 different IPLs based on five distinct CLs and 10 polar head group derivatives of phosphatidylhexoses, including compounds reported here for the first time, e.g., di-N-acetylhexosamine phosphatidylhexose-bearing lipids. Despite having extended the knowledge on the lipidome, our results also indicate that the majority of T. barophilus lipids remain inaccessible to current analytical procedures and that improvements in lipid extraction and analysis are still required. This expanded yet incomplete lipidome nonetheless opens new avenues for understanding the physiology, physicochemical properties, and organization of the membrane in this archaeon as well as other archaea.

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.

On the molecular mechanisms implicated in the bipolar cancellation of membrane electroporation

Bipolar cancellation is the phenomenon in which the permeability of cell membranes subjected to high intensity short pulsed electric field (ns-μs range) is reduced or eliminated when the system is subjected to bipolar instead of monopolar pulses. Although several studies have tried to explain bipolar cancellation, the underlying mechanisms remain unclear. Very few articles study bipolar cancellation by means of molecular dynamics (MD) simulation. In this paper, we investigated the molecular mechanisms underlying the difference in electroporation induced by bipolar and monopolar picosecond electric pulses (EPs) using MD simulation. The electric field gradients and electric forces on water molecules of the two pulses were analyzed in detail for the first time. For a certain pulse width, when the field intensity is relatively small, the direction of bipolar electric force on the interfacial water molecule reverses as the bipolar EPs reverse, while the electric force on interfacial water molecules of the cathode side remains in the same direction as that of applied monopolar EPs. The bipolar electric force reversal delays the water protrusion and increases the pore formation time. Therefore, this phenomenon could correspond to bipolar cancellation. When the field intensity is relatively large, although the bipolar electric force direction still reverses, half of the total time of the monopolar EPs has no electric fields. The electric forces of monopolar no-field half-cycles are much smaller than those of the bipolar EPs. Therefore, the pore formation time of bipolar EPs reduces, and this phenomenon is called bipolar enhancement. The occurrence of bipolar cancellation or bipolar enhancement depends on conditions such as the width and intensity of the pulse.

Atorvastatin Modulates the Efficacy of Electroporation and Calcium Electrochemotherapy

Electroporation is influenced by the features of the targeted cell membranes, e.g., the cholesterol content and the surface tension of the membrane. The latter is eventually affected by the organization of actin fibers. Atorvastatin is a statin known to influence both the cholesterol content and the organization of actin. This work analyzes the effects of the latter on the efficacy of electroporation of cancer cells. In addition, herein, electroporation was combined with calcium chloride (CaEP) to assess as well the effects of the statin on the efficacy of electrochemotherapy. Cholesterol-rich cell lines MDA-MB231, DU 145, and A375 underwent (1) 48 h preincubation or (2) direct treatment with 50 nM atorvastatin. We studied the impact of the statin on cholesterol and actin fiber organization and analyzed the cells’ membrane permeability. The viability of cells subjected to PEF (pulsed electric field) treatments and CaEP with 5 mM CaCl₂ was examined. Finally, to assess the safety of the therapy, we analyzed the N-and E-cadherin localization using confocal laser microscopy. The results of our investigation revealed that depending on the cell line, atorvastatin preincubation decreases the total cholesterol in the steroidogenic cells and induces reorganization of actin nearby the cell membrane. Under low voltage PEFs, actin reorganization is responsible for the increase in the electroporation threshold. However, when subject to high voltage PEF, the lipid composition of the cell membrane becomes the regulatory factor. Namely, preincubation with atorvastatin reduces the cytotoxic effect of low voltage pulses and enhances the cytotoxicity and cellular changes induced by high voltage pulses. The study confirms that the surface tension regulates of membrane permeability under low voltage PEF treatment. Accordingly, to reduce the unfavorable effects of preincubation with atorvastatin, electroporation of steroidogenic cells should be performed at high voltage and combined with a calcium supply.

Cell transmembrane potential in contactless permeabilization by time-varying magnetic fields

BACKGROUND

Although experimental results proved the feasibility of using time-varying magnetic field as a contactless cells permeabilization method, the underlying mechanism is still poorly understood. In this study a numerical analysis of the time-dependent transmembrane potential (TMP) at cell membranes during permeabilization by time-varying magnetic fields was proposed, and a first quantification of mechanical stress induced by the magnetic and electric fields, hypothesized to play an important role in the permeabilization mechanism, was carried out.

METHODS

Starting from the simulation of real in vitro experimental conditions, the analysis was widened quantifying the influence of pulse frequency, cell dimension and distance of the cell from the magnetic field source. The mechanical pressure on cell membrane due to the interaction between free charges and induced electric field and due to the gradient of the magnetic field was quantified in all those conditions in which the TMP values were not high enough to cause membrane permeabilization.

RESULTS

TMP values induced by typical in-vitro experimental conditions were far below the values needed for membrane permeabilization, with a strong dependence on pulse frequency and distance of the cell from the coil.

CONCLUSION

The preliminary assessment of the mechanical pressure on cell membrane showed that stress values evaluated in conditions in which TMP values were too low to cause membrane permeabilization were comparable to those known to influence the pores opening mechanisms. Results represent a significant step towards a better comprehension of the mechanism underlying cell membrane permeabilization by time-varying magnetic fields.

Triggered Drug Release From Liposomes: Exploiting the Outer and Inner Tumor Environment

Since more than 40 years liposomes have being extensively studied for their potential as carriers of anticancer drugs. The basic principle behind their use for cancer treatment consists on the idea that they can take advantage of the leaky vasculature and poor lymphatic drainage present at the tumor tissue, passively accumulating in this region. Aiming to further improve their efficacy, different strategies have been employed such as PEGlation, which enables longer circulation times, or the attachment of ligands to liposomal surface for active targeting of cancer cells. A great challenge for drug delivery to cancer treatment now, is the possibility to trigger release from nanosystems at the tumor site, providing efficacious levels of drug in the tumor. Different strategies have been proposed to exploit the outer and inner tumor environment for triggering drug release from liposomes and are the focus of this review.

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.

Gene transfer to plants by electroporation: methods and applications

Developing gene transfer technologies enables the genetic manipulation of the living organisms more efficiently. The methods used for gene transfer fall into two main categories; natural and artificial transformation. The natural methods include the conjugation, transposition, bacterial transformation as well as phage and retroviral transductions, contain the physical methods whereas the artificial methods can physically alter and transfer genes from one to another organisms' cell using, for instance, biolistic transformation, micro- and macroinjection, and protoplast fusion etc. The artificial gene transformation can also be conducted through chemical methods which include calcium phosphate-mediated, polyethylene glycol-mediated, DEAE-Dextran, and liposome-mediated transfers. Electrical methods are also artificial ways to transfer genes that can be done by electroporation and electrofusion. Comparatively, among all the above-mentioned methods, electroporation is being widely used owing to its high efficiency and broader applicability. Electroporation is an electrical transformation method by which transient electropores are produced in the cell membranes. Based on the applications, process can be either reversible where electropores in membrane are resealable and cells preserve the vitality or irreversible where membrane is not able to reseal, and cell eventually dies. This problem can be minimized by developing numerical models to iteratively optimize the field homogeneity considering the cell size, shape, number, and electrode positions supplemented by real-time measurements. In modern biotechnology, numerical methods have been used in electrotransformation, electroporation-based inactivation, electroextraction, and electroporative biomass drying. Moreover, current applications of electroporation also point to some other uncovered potentials for various exploitations in future.

Establishing an Electrostatics Paradigm for Membrane Electroporation in the Framework of Dissipative Particle Dynamics

With an exclusive aim to looking into a mechanism of membrane electroporation on mesoscopic length and time scales, we report the dissipative particle dynamics (DPD) simulation results for systems with and without electrolytes. A polarizable DPD model of water is employed for accurate modeling of long-range electrostatics near the water-lipid interfaces. A great deal of discussion on field induced change in dipole moments of water and lipids together with the special variation of electric field is made in order to understand the dielectrophoretic movement of water, initiating a pore formation via an intrusion through the bilayer core. The presence of salt alters the dipolar arrangement of lipids and water, and thereby it reduces the external field required to create a pore in the membrane. The species fluxes through the pore, distributions for bead density, electrostatic potential, stresses across the membrane, etc. are used to answer some of the key questions pertaining to mechanism of electroporation. The findings are compared with the molecular dynamics simulation results found in the literature, and the comparison successfully establishes an electrostatics paradigm for biomembrane studies using DPD simulations.

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.

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.

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.

Single exponential decay waveform; a synergistic combination of electroporation and electrolysis (E2) for tissue ablation

Background

Electrolytic ablation and electroporation based ablation are minimally invasive, non-thermal surgical technologies that employ electrical currents and electric fields to ablate undesirable cells in a volume of tissue. In this study, we explore the attributes of a new tissue ablation technology that simultaneously delivers a synergistic combination of electroporation and electrolysis (E2).

Method

A new device that delivers a controlled dose of electroporation field and electrolysis currents in the form of a single exponential decay waveform (EDW) was applied to the pig liver, and the effect of various parameters on the extent of tissue ablation was examined with histology.

Results

Histological analysis shows that E2 delivered as EDW can produce tissue ablation in volumes of clinical significance, using electrical and temporal parameters which, if used in electroporation or electrolysis separately, cannot ablate the tissue.

Discussion

The E2 combination has advantages over the three basic technologies of non-thermal ablation: electrolytic ablation, electrochemical ablation (reversible electroporation with injection of drugs) and irreversible electroporation. E2 ablates clinically relevant volumes of tissue in a shorter period of time than electrolysis and electroporation, without the need to inject drugs as in reversible electroporation or use paralyzing anesthesia as in irreversible electroporation.

Nanowire-Modified Three-Dimensional Electrode Enabling Low-Voltage Electroporation for Water Disinfection

More than 10% of the people in the world still suffer from inadequate access to clean water. Traditional water disinfection methods (e.g., chlorination and ultraviolet radiation) include concerns about the formation of carcinogenic disinfection byproducts (DBPs), pathogen reactivation, and/or excessive energy consumption. Recently, a nanowire-assisted electroporation-disinfection method was introduced as an alternative. Here, we develop a new copper oxide nanowire (CuONW)-modified three-dimensional copper foam electrode using a facile thermal oxidation approach. An electroporation-disinfection cell (EDC) equipped with two such electrodes has achieved superior disinfection performance (>7 log removal and no detectable bacteria in the effluent). The disinfection mechanism of electroporation guarantees an exceedingly low operation voltage (1 V) and level of energy consumption (25 J L(-1)) with a short contact time (7 s). The low operation voltage avoids chlorine generation and thus reduces the potential of DBP formation. Because of irreversible electroporation damage on cell membranes, no regrowth and/or reactivation of bacteria occurs during storage after EDC treatment. Water disinfection using EDCs has great potential for practical applications.

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.

Specific electrical capacitance and voltage breakdown as a function of temperature for different planar lipid bilayers

The breakdown voltage and specific electrical capacitance of planar lipid bilayers formed from lipids isolated from the membrane of archaeon Aeropyrum pernix K1 as a function of temperature were studied and compared with data obtained previously in MD simulation studies. Temperature dependence of breakdown voltage and specific electrical capacitance was measured also for dipalmitoylphosphatidylcholine (DPPC) bilayers and bilayers formed from mixture of diphytanoylphosphocholine (DPhPC) and DPPC in ratio 80:20. The breakdown voltage of archaeal lipids planar lipid bilayers is more or less constant until 50°C, while at higher temperatures a considerable drop is observed, which is in line with the results from MD simulations. The breakdown voltage of DPPC planar lipid bilayer at melting temperature is considerably higher than in the gel phase. Specific electrical capacitance of planar lipid bilayers formed from archaeal lipids is approximately constant for temperatures up to 40°C and then gradually decreases. The difference with MD simulation predictions is discussed. Specific electrical capacitance of DPPC planar lipid bilayers in fluid phase is 1.75 times larger than that of the gel phase and it follows intermediated phases before phase transition. Increase in specific electrical capacitance while approaching melting point of DPPC is visible also for DPhPC:DPPC mixture.

Properties of lipid electropores I: Molecular dynamics simulations of stabilized pores by constant charge imbalance

Molecular dynamics (MD) simulations have become a powerful tool to study electroporation (EP) in atomic detail. In the last decade, numerous MD studies have been conducted to model the effect of pulsed electric fields on membranes, providing molecular models of the EP process of lipid bilayers. Here we extend these investigations by modeling for the first time conditions comparable to experiments using long (μs-ms) low intensity (~kV/cm) pulses, by studying the characteristics of pores formed in lipid bilayers maintained at a constant surface tension and subject to constant charge imbalance. This enables the evaluation of structural (size) and electrical (conductance) properties of the pores formed, providing information hardly accessible directly by experiments. Extensive simulations of EP of simple phosphatidylcholine bilayers in 1M NaCl show that hydrophilic pores with stable radii (1-2.5 nm) form under transmembrane voltages between 420 and 630 mV, allowing for ionic conductance in the range of 6.4-29.5 nS. We discuss in particular these findings and characterize both convergence and size effects in the MD simulations. We further extend these studies in a follow-up paper (Rems et al., Bioelectrochemistry, Submitted), by proposing an improved continuum model of pore conductance consistent with the results from the MD simulations.

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.

Electroporation-based applications in biotechnology

Electroporation is already an established technique in several areas of medicine, but many of its biotechnological applications have only started to emerge; we review here some of the most promising. We outline electroporation as a phenomenon and then proceed to applications, first outlining the best established - the use of reversible electroporation for heritable genetic modification of microorganisms (electrotransformation), and then explore recent advances in applying electroporation for inactivation of microorganisms, extraction of biomolecules, and fast drying of biomass. Although these applications often aim to upscale to the industrial and/or clinical level, we also outline some important chip-scale applications of electroporation. We conclude our review with a discussion of the main challenges and future perspectives.

Modelling the Bioelectronic Interface in Engineered Tethered Membranes: From Biosensing to Electroporation

This paper studies the construction and predictive models of three novel measurement platforms: (i) a Pore Formation Measurement Platform (PFMP) for detecting the presence of pore forming proteins and peptides, (ii) the Ion Channel Switch (ICS) biosensor for detecting the presence of analyte molecules in a fluid chamber, and (iii) an Electroporation Measurement Platform (EMP) that provides reliable measurements of the electroporation phenomenon. Common to all three measurement platforms is that they are comprised of an engineered tethered membrane that is formed via a rapid solvent exchange technique allowing the platform to have a lifetime of several months. The membrane is tethered to a gold electrode bioelectronic interface that includes an ionic reservoir separating the membrane and gold surface, allowing the membrane to mimic the physiological response of natural cell membranes. The electrical response of the PFMP, ICS, and EMP are predicted using continuum theories for electrodiffusive flow coupled with boundary conditions for modelling chemical reactions and electrical double layers present at the bioelectronic interface. Experimental measurements are used to validate the predictive accuracy of the dynamic models. These include using the PFMP for measuring the pore formation dynamics of the antimicrobial peptide PGLa and the protein toxin Staphylococcal α-Hemolysin; the ICS biosensor for measuring nano-molar concentrations of streptavidin, ferritin, thyroid stimulating hormone (TSH), and human chorionic gonadotropin (pregnancy hormone hCG); and the EMP for measuring electroporation of membranes with different tethering densities, and membrane compositions.

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics' equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

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.

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.

Structural properties of archaeal lipid bilayers: small-angle X-ray scattering and molecular dynamics simulation study

Aeropyrum pernix is an aerobic hyperthermophilic archaeon that grows in harsh environmental conditions and as such possesses unique structural and metabolic features. Its membrane interfaces with the extreme environment and is the first line of defense from external factors. Therefore, lipids composing this membrane have special moieties that increase its stability. The membrane of A. pernix is composed predominantly of two polar lipids 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-1'(2'-O-α-D-glucosyl)-myo-inositol (AGI) and 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-myo-inositol (AI). Both have methyl branches in their lipid tails and ether linkages and carbohydrates in their headgroup. These moieties significantly affect the structure and dynamics of the bilayer. To provide a molecular level insight into these characteristics, we used here Molecular Dynamics (MD) simulations of lipid bilayers of composition similar to those of the archaeal membranes. First, we show that the electron density profiles along the normal to the bilayers derived from the simulations are in good agreement with the profiles obtained by the small-angle X-ray scattering (SAXS) technique, which provides confidence in the force fields used. Analyses of the simulation data show that the archaeal lipid bilayers are less hydrated than conventional phosphatidylcholine (PC) lipids and that their structure is not affected by the salt present in the surrounding solution. Furthermore, the lateral pressure in their hydrophobic core, due to the presence of the branched tails, is much higher than that at PC-based lipid bilayers. Both the methyl branched tails and the special headgroup moieties contribute to slow drastically the lateral diffusion of the lipids. Furthermore, we found that the lipid head groups associate via hydrogen bonding, which affects their reorientational dynamics. All together, our data provide links between the microscopic properties of these membranes and their overall stability in harsh environments.