Cholesterol-induced modifications in lipid bilayers: a simulation study

Oleic Acid Could Act as a Channel Blocker in the Inhibition of nAChR: Insights from Molecular Dynamics Simulations

The activation of the muscular nicotinic acetylcholine receptor (nAChR) produces the opening of the channel, with the consequent increase in the permeability of cations, triggering an excitatory signal. Free fatty acids (FFA) are known to modulate the activity of the receptor as noncompetitive antagonists, acting at the membrane-AChR interface. We present molecular dynamics simulations of a model of nAChR in a desensitized closed state embedded in a lipid bilayer in which distinct membrane phospholipids were replaced by two different monounsaturated FFA that differ in the position of a double bond. This allowed us to detect and describe that the cis-18:1ω-9 FFA were located at the interface between the transmembrane segments of α2 and γ subunits diffused into the channel lumen with the consequent potential ability to block the channel to the passage of ions.

Effects of grafted polymers on the lipid membrane fluidity

Since the membrane fluidity controls the cellular functions, it is important to identify the factors that determine the cell membrane viscosity. Cell membranes are composed of not only lipids and proteins but also polysaccharide chain-anchored molecules, such as glycolipids. To reveal the effects of grafted polymers on the membrane fluidity, in this study, we measured the membrane viscosity of polymer-grafted giant unilamellar vesicles (GUVs), which were prepared by introducing the poly (ethylene glycol) (PEG)-anchored lipids to the ternary GUVs composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and cholesterol. The membrane viscosity was obtained from the velocity field on the GUV generated by applying a point force, based on the hydrodynamic model proposed by Henle and Levine. The velocity field was visualized by a motion of the circular liquid ordered (Lo) domains formed by a phase separation. With increasing PEG density, the membrane viscosity of PEG-grafted GUVs increased gradually in the mushroom region and significantly in the brush region. We propose a hydrodynamic model that includes the excluded volume effect of PEG chains to explain the increase in membrane viscosity in the mushroom region. This work provides a basic understanding of how grafted polymers affect the membrane fluidity.

Graph-Based Analyses of Dynamic Water-Mediated Hydrogen-Bond Networks in Phosphatidylserine: Cholesterol Membranes

Phosphatidylserine lipids are anionic molecules present in eukaryotic plasma membranes, where they have essential physiological roles. The altered distribution of phosphatidylserine in cells such as apoptotic cancer cells, which, unlike healthy cells, expose phosphatidylserine, is of direct interest for the development of biomarkers. We present here applications of a recently implemented Depth-First-Search graph algorithm to dissect the dynamics of transient water-mediated lipid clusters at the interface of a model bilayer composed of 1-palmytoyl-2-oleoyl-sn-glycero-2-phosphatidylserine (POPS) and cholesterol. Relative to a reference POPS bilayer without cholesterol, in the POPS:cholesterol bilayer there is a somewhat less frequent sampling of relatively complex and extended water-mediated hydrogen-bond networks of POPS headgroups. The analysis protocol used here is more generally applicable to other lipid:cholesterol bilayers.

Unveiling growth and dynamics of liposomes by graphene liquid cell-transmission electron microscopy

Liposome is a model system for biotechnological and biomedical purposes spanning from targeted drug delivery to modern vaccine research. Yet, the growth mechanism of liposomes is largely unknown. In this work, the formation and evolution of phosphatidylcholine-based liposomes are studied in real-time by graphene liquid cell-transmission electron microscopy (GLC-TEM). We reveal important steps in the growth, fusion and denaturation of phosphatidylcholine (PC) liposomes. We show that initially complex lipid aggregates resembling micelles start to form. These aggregates randomly merge while capturing water and forming small proto-liposomes. The nanoscopic containers continue sucking water until their membrane becomes convex and free of redundant phospholipids, giving stabilized PC liposomes of different sizes. In the initial stage, proto-liposomes grow at a rate of 10-15 nm s^-1, which is followed by their growth rate of 2-5 nm s^-1, limited by the lipid availability in the solution. Molecular dynamics (MD) simulations are used to understand the structure of micellar clusters, their evolution, and merging. The liposomes are also found to fuse through lipid bilayers docking followed by the formation of a hemifusion diaphragm and fusion pore opening. The liposomes denaturation can be described by initial structural destabilization and deformation of the membrane followed by the leakage of the encapsulated liquid. This study offers new insights on the formation and growth of lipid-based molecular assemblies which is applicable to a wide range of amphiphilic molecules.

Computational study of DMPC liposomes loaded with the N-(2-Hydroxyphenyl)-2-propylpentanamide (HO-AAVPA) and determination of its antiproliferative activity in vitro in NIH-3T3 cells

N-(2-Hydroxyphenyl)-2-propylpentanamide (HO-AAVPA) is a valproic acid (VPA) derivative that has shown promising antiproliferative effects in different cancer cell lines, such as A204, HeLa, and MDA-MB-231. However, its low water solubility could reduce its therapeutic effectiveness. To solve this problem, in this work, we incorporated HO-AAVPA into dimyristoyl-phosphatidylcholine (DMPC) liposomes in the presence or absence of cholesterol (CHOL). Using differential scanning calorimetry (DSC), we found that the transition enthalpy (ΔH_tr) of DMPC liposomes is reduced in the presence of CHOL and/or HO-AAVPA, indicating the favorable interactions between CHOL and/or HO-AAVPA and DMPC. Further, by molecular dynamics simulations it was possible to observed that HO-AAVPA migrates from the center of the bilayer toward the water and lipid interface of the DPMC bilayer systems exposing the amine group to water and the aliphatic chain toward the interior of the bilayer. As a consequence, we observed an ordering of the lipid bilayer. Moreover, CHOL harbors into the inner bilayer membrane, increasing the order parameter of the system. The liposomal solutions loaded with HO-AAVPA were tested in the NIH3T3 cell line, showing a reduction in cell proliferation compared to those cells presented without liposomes.Communicated by Ramaswamy H. Sarma.

Therapeutic Effects of Cold Atmospheric Plasma on Solid Tumor

Cancer is a devastating disease, and there is no particularly effective treatment at present. Recently, a new treatment, cold atmospheric plasma (CAP), has been proposed. At present, CAP is confirmed to have selective killing effect on tumor by many studies in vitro and in vivo. A targeted literature search was carried out on the study of cold atmospheric plasma. Through analysis and screening, a narrative review approach was selected to describe therapeutic effects of cold atmospheric plasma on solid tumor. According to the recent studies on plasma, some hypothetical therapeutic schemes of CAP are proposed in this paper. The killing mechanism of CAP on solid tumor is expounded in terms of the selectivity of CAP to tumor, the effects of CAP on cells, tumor microenvironment (TME) and immune system. CAP has many effects on solid tumors, and these effects are dose-dependent. The effects of optimal doses of CAP on solid tumors include killing tumor cells, inhibiting non-malignant cells and ECM in TME, affecting the communication between tumor cells, and inducing immunogenic death of tumor cells. In addition, several promising research directions of CAP are proposed in this review, which provide guidance for future research.

Dynamic response on a nanometer scale of binary phospholipid-cholesterol vesicles: Low-frequency Raman scattering insight

Low-frequency Raman spectroscopy was used to study the dynamic response on a nanometer scale of aqueous suspensions of two-component lipid vesicles. Binary mixtures of saturated phospholipid (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, DPPC) and cholesterol are interesting for possible coexistence of solidlike and liquid-ordered phases, while the phase coexistence was not reported for unsaturated phospholipid (1,2-dioleoyl-sn-glycero-3-phosphocholine, DOPC) and cholesterol mixtures. The DOPC-DPPC mixtures represent the well-documented case of coexisting domains of solidlike and liquid-disordered phases. These three series of lipid mixtures are studied here. A broad peak with the maximum in the range of 30-50cm^{-1} and a narrow peak near 10cm^{-1} are observed in the Raman susceptibility of the binary mixtures and attributed to the acousticlike vibrational density of states and layer modes, respectively. Parameters of the broad and narrow peaks are sensitive to lateral and conformational hydrocarbon chain ordering. It was also demonstrated that the low-frequency Raman susceptibility of multicomponent lipid bilayers allows one to determine the phase state of lipid bilayers and distinguish the homogeneous distribution of molecular complexes from coexisting domains with sizes above several nanometers. Thus, the low-frequency Raman spectroscopy provides unique information in studying phase coexistence in lipid bilayers.

Artificial stabilization of the fusion pore by intra-organelle styrene-maleic acid copolymers

Styrene-maleic acid copolymers have become an advantageous detergent-free alternative for membrane protein isolation. Since their discovery, experimental membrane protein extraction and purification by keeping intact their lipid environment has become significantly easier. With the aim of identifying new applications of these interesting copolymers, their molecular binding and functioning mechanisms have recently become intense objects of study. In this work, we describe the use of styrene-maleic acid copolymers as an artificial tool to stabilize the fusion pore. We show that when these copolymers circumscribe the water channel that defines the fusion pore, they keep it from shrinking and closing. We describe how only intra-organelle copolymers have stabilizing capabilities while extra-organelle ones have negligible or even contrary effects on the fusion pore life-time.

Unravelling the Effects of Cholesterol on the Second-Order Nonlinear Optical Responses of Di-8-ANEPPS Dye Embedded in Phosphatidylcholine Lipid Bilayers

Cholesterol is known for its role in maintaining the correct fluidity and rigidity of the animals cell membranes and thus their functions. Assessing the content and the role of cholesterol in lipid bilayers is therefore of crucial importance for a deeper understanding and control of membrane functioning. In this computational work, we investigate bilayers built from three types of glycerophospholipid phosphatidylcholine (PC) lipids, namely dipalmitoylphosphatidylcholine (DPPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and dioleoylphosphatidylcholine (DOPC), and containing different amounts of cholesterol by analyzing the second-harmonic generation (SHG) nonlinear optical (NLO) response of a probe molecule, di-8-ANEPPS, inserted into the membranes. This molecular property presents the advantage to be specific to interfacial regions such as lipid bilayers. To unravel these effects, Molecular Dynamics (MD) simulations have been performed on both DPPC and DOPC lipids by varying the cholesterol mole fraction (from 0 to 0.66), while POPC was only considered as a pure bilayer. In the case of the structural properties of the bilayers, all the analyses converge toward the same conclusion: as the mole fraction of cholesterol increases, the systems become more rigid, confirming the condensing effect of cholesterol. In addition, the chromophore is progressively more aligned with respect to the normal to the bilayer. On the contrary, addition of unsaturation disorders the lipid bilayers, with barely no impact on the alignment of the chromophore. Then, using the frames obtained from the MD simulations, the first hyperpolarizability β of the dye in its environment has been computed at the TDDFT level. On the one hand, the addition of cholesterol induces a progressive increase of the diagonal component the β tensor parallel to the bilayer normal. On the other hand, larger β values have been calculated for the unsaturated than for the saturated lipid systems. In summary, this study illustrates the relationship between the composition and structure of the bilayers and the NLO responses of the embedded dye.

A quantitative determination of lipid bilayer deposition efficiency using AFM

The efficacy of a number of different methods for depositing a dimyristoylphosphatidylcholine (DMPC) lipid bilayer or DMPC–cholesterol (3 : 1) mixed bilayer onto a silicon substrate has been investigated in a quantitative manner using atomic force microscopy (AFM) image analysis to extract surface coverage. Complementary AFM-IR measurements were used to confirm the presence of the lipids. For the Langmuir–Blodgett/Schaefer deposition method at temperatures below the chain-melting transition temperature (T_m), a large number of bilayer defects resulted when DMPC was deposited from a water subphase. Addition of calcium ions to the trough led to smaller, more frequent defects, whereas addition of cholesterol to the lipid mixture led to a vast improvement in bilayer coverage. Poor coverage was achieved for deposition at temperatures above T_m. Formation of the deposited bilayer from vesicle fusion proved a more reliable method for all systems, with formation of near-complete bilayers within 60 seconds at temperatures above T_m, although this method led to a higher probability of multilayer formation and rougher bilayer surfaces.

The efficacy of different methods for depositing a DMPC or mixed DMPC–cholesterol (3 : 1) lipid bilayer onto a silicon substrate has been investigated in a quantitative manner using atomic force microscopy image analysis to extract surface coverage.

Microscopic Interactions of Melatonin, Serotonin and Tryptophan with Zwitterionic Phospholipid Membranes

The interactions at the atomic level between small molecules and the main components of cellular plasma membranes are crucial for elucidating the mechanisms allowing for the entrance of such small species inside the cell. We have performed molecular dynamics and metadynamics simulations of tryptophan, serotonin, and melatonin at the interface of zwitterionic phospholipid bilayers. In this work, we will review recent computer simulation developments and report microscopic properties, such as the area per lipid and thickness of the membranes, atomic radial distribution functions, angular orientations, and free energy landscapes of small molecule binding to the membrane. Cholesterol affects the behaviour of the small molecules, which are mainly buried in the interfacial regions. We have observed a competition between the binding of small molecules to phospholipids and cholesterol through lipidic hydrogen-bonds. Free energy barriers that are associated to translational and orientational changes of melatonin have been found to be between 10-20 kJ/mol for distances of 1 nm between melatonin and the center of the membrane. Corresponding barriers for tryptophan and serotonin that are obtained from reversible work methods are of the order of 10 kJ/mol and reveal strong hydrogen bonding between such species and specific phospholipid sites. The diffusion of tryptophan and melatonin is of the order of 10-7 cm2/s for the cholesterol-free and cholesterol-rich setups.

Structure and Dynamics of Dioleoyl-Phosphatidylcholine Bilayers under the Influence of Quercetin and Rutin

Quercetin and rutin, two widely studied flavonoids with applications foreseen in the sectors of pharmaceutical and cosmetic industries, have been chosen as model compounds for a detailed structural and dynamical investigation onto their influence on fluid lipid bilayers. Combining global small angle X-ray scattering analysis with molecular dynamics, various changes in the properties of dioleoyl-phosphatidylcholine (DOPC) bilayers have been determined. The solubility of quercetin in DOPC membranes is assured up to 12 mol %, whereas rutin, with additional glucose and rhamnose groups, are fully soluble only up to 6 mol %. Both flavonoids induce an increase in membrane undulations and thin the bilayers slightly (<1 Å) in a concentration dependent manner, wherein quercetin shows a stronger effect. Concomitantly, in the order of 2-4%, the adjacent bilayer distance increases with the flavonoid's concentration. Partial molecular areas of quercetin and rutin are determined to be 26 and 51 Ų, respectively. Simulated averaged areas per molecule confirm these estimates. A 60° tilted orientation of quercetin is observed with respect to the bilayer normal, whereas the flavonoid moiety of rutin is oriented more perpendicular (α-angle 30°) to the membrane surface. Both flavonoid moieties are located at a depth of 12 and 16 Å for quercetin and rutin, respectively, while their anionic forms display a location closer to the polar interface. Finally, at both simulated concentrations (1.5 and 12 mol %), DOPC-rutin systems induce a stronger packing of the pure DOPC lipid bilayer, mainly due to stronger attractive electrostatic interactions in the polar lipid head region.

Cholesterol-like Condensing Effect of Perfluoroalkyl Substances on a Phospholipid Bilayer

To understand the potential cytotoxicity of perfluoroalkyl substances (PFAS), we study their interactions with a model phospholipid bilayer membrane using molecular dynamics (MD) simulations. Four typical PFAS molecules are investigated, including perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), perfluorooctanesulfonic acid (PFOS), and perfluorohexane sulfonate (PFHxS). All of these PFAS molecules are found to spontaneously penetrate the lipid bilayer within a short simulation time (a few nanoseconds). During the penetration process, further free-energy analysis reveals that a PFAS molecule encounters an energy barrier at the bilayer/water interface. To overcome this free-energy barrier, the PFAS molecule flips itself at the interface. We further investigate the influence of embedded PFAS molecules on the membrane properties. All of the embedded PFAS molecules are found to produce a cholesterol-like condensing effect on the lipid bilayer, which includes increases of the order parameters of lipid tails and the thickness of the lipid bilayer and a decrease of area per lipid. Moreover, the PFAS molecules are found to form hydrogen bonds with oxygen atoms at three different positions of a lipid molecule. Our work reveals the penetration pathway of PFAS molecules entering into a lipid bilayer. In addition, the cholesterol-like condensing effect induced by embedded PFAS molecules on model membranes is systematically investigated and discussed. Our simulations can help understand the physical mechanisms of PFAS cytotoxicity.

Cellular absorption of small molecules: free energy landscapes of melatonin binding at phospholipid membranes

Free energy calculations are essential to unveil mechanisms at the atomic scale such as binding of small solutes and their translocation across cell membranes, eventually producing cellular absorption. Melatonin regulates biological rhythms and is directly related to carcinogenesis and neurodegenerative disorders. Free energy landscapes obtained from well-tempered metadynamics simulations precisely describe the characteristics of melatonin binding to specific sites in the membrane and reveal the role of cholesterol in free energy barrier crossing. A specific molecular torsional angle and the distance between melatonin and the center of the membrane along the normal to the membrane Z-axis have been considered as suitable reaction coordinates. Free energy barriers between two particular orientations of the molecular structure (folded and extended) have been found to be of about 18 kJ/mol for z-distances of about 1–2 nm. The ability of cholesterol to expel melatonin out of the internal regions of the membrane towards the interface and the external solvent is explained from a free energy perspective. The calculations reported here offer detailed free energy landscapes of melatonin embedded in model cell membranes and reveal microscopic information on its transition between free energy minima, including the location of relevant transition states, and provide clues on the role of cholesterol in the cellular absorption of small molecules.

Dipolar Janus liposomes: formation, electrokinetic motion and self-assembly

Presented herein is the first report on dipolar Janus liposomes-liposomes that contain opposite surface charges decorating the two hemispheres of the same colloidal body. Such heterogeneous organization of surface charge is achieved through cholesterol-modulated lipid phase separation, which sorts anionic/cationic lipids into coexisting liquid-ordered/liquid-disordered domains. We present optimized experimental conditions to produce these liposomes in high yields, based on the gel-assisted hydration of ternary lipid systems consisting of cholesterol, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine, and 1,2-dioleoyl-sn-glycero-3-phosphocholine. The size/charge distribution and domain configuration of these liposomes are characterized in detail by confocal fluorescence microscopy, nanosphere binding and zeta potential measurements. Using confocal fluorescence microscopy, we also follow the electrokinetic motion as well as the electrostatic self-assembly of these new dipolar Janus particles.

Atomic-scale modeling of the effect of lipid peroxidation on the permeability of reactive species

Biomembranes and lipid systems are rich in unsaturated lipid components and are subject to photo-induced lipid peroxidation. The peroxidized lipid products in cellular systems are known to affect the structural organization and function of the biomembrane. We employed molecular dynamics simulations to study the effects of phospholipid peroxidation on membrane properties and the permeability of different reactive species. The results suggest that when the lipids are peroxidized, the peroxide group moves toward the membrane surface, which causes the membrane system to expand laterally and increase in area. The permeability profile revealed that nitrogen species can easily permeate through the native and peroxidized system in comparison to oxygen species, suggesting its importance in plasma-based treatment. Thus, by breaching the energy barrier with lower energy, they can traverse the cell membrane and induce oxidative stress, which leads to apoptosis.Communicated by Ramaswamy H. Sarma.

Molecular Mechanisms of the Efficacy of Cold Atmospheric Pressure Plasma (CAP) in Cancer Treatment

Recently, the potential use of cold atmospheric pressure plasma (CAP) in cancer treatment has gained increasing interest. Especially the enhanced selective killing of tumor cells compared to normal cells has prompted researchers to elucidate the molecular mechanisms for the efficacy of CAP in cancer treatment. This review summarizes the current understanding of how CAP triggers intracellular pathways that induce growth inhibition or cell death. We discuss what factors may contribute to the potential selectivity of CAP towards cancer cells compared to their non-malignant counterparts. Furthermore, the potential of CAP to trigger an immune response is briefly discussed. Finally, this overview demonstrates how these concepts bear first fruits in clinical applications applying CAP treatment in head and neck squamous cell cancer as well as actinic keratosis. Although significant progress towards understanding the underlying mechanisms regarding the efficacy of CAP in cancer treatment has been made, much still needs to be done with respect to different treatment conditions and comparison of malignant and non-malignant cells of the same cell type and same donor. Furthermore, clinical pilot studies and the assessment of systemic effects will be of tremendous importance towards bringing this innovative technology into clinical practice.

Interleaflet coupling of n-alkane incorporated bilayers

The relationship between the membrane bending modulus (κ) and compressibility modulus (K_A) depends on the extent of coupling between the two monolayers (leaflets). Using neutron spin echo (NSE) spectroscopy, we investigate the effects of n-alkanes on the interleaflet coupling of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers. Structural studies with small-angle X-ray and neutron scattering (SAXS and SANS) showed that the bilayer thickness increased with increasing n-alkane length, while NSE suggested that the bilayers became softer. Additional measurements of the membrane thickness fluctuations with NSE suggested that the changes in elastic moduli were due to a decrease in coupling between the leaflets upon addition of the longer n-alkanes. The decreased coupling with elongating n-alkane length was explained based on the n-alkane distribution within the bilayers characterized by SANS measurement of bilayers composed of protiated DPPC and deuterated n-alkanes. A higher fraction of the incorporated long n-alkanes were concentrated at the central plane of the bilayers and decreased the physical interaction between the leaflets. Using NSE and SANS, we successfully correlated changes in the mesoscopic collective dynamics and microscopic membrane structure upon incorporation of n-alkanes.

Concurrent Compression of Phospholipid Membranes by Calcium and Cholesterol

Regulation of cell metabolism, membrane fusion, association of proteins with cellular membranes, and cellular signaling altogether would not be possible without Ca²⁺ ions. The distribution of calcium within the cell is uneven with the negatively charged inner leaflet of the plasma membrane being one of the primary targets of its accumulation. Therefore, we decided to map the influence of Ca²⁺ on the properties of lipid bilayers closely resembling natural lipid membranes. We combined fluorescence spectroscopy (analysis of time-resolved emission spectra of Laurdan probe and derived parameters: integrated relaxation time related to local lipid mobility, and total emission shift reflecting membrane polarity and hydration) with molecular dynamics simulations to determine the effect of the increasing CaCl₂ concentration on model lipid membranes containing POPC, POPS, and cholesterol. On top of that, the impact of calcium on the plasma membranes isolated from HEK293 cells was investigated using the steady-state fluorescence of Laurdan. We found that calcium increases rigidity of all the model lipid membranes used, elevates their thickness, increases lipid packing and ordering, and impedes the local lipid mobility. All these effects were to a great extent similar to those elicited by cholesterol. However, the changes of the membrane properties induced by calcium and cholesterol seem largely independent from each other. At sufficiently high concentrations of calcium or cholesterol, the steric effects hindered a further alteration of membrane organization, i.e., the compressibility limit of membrane structures was reached. We found no indication for mutual interaction between Ca²⁺ and cholesterol, nor competition of Ca²⁺ ions and hydroxyl groups of cholesterol for binding to phospholipids. Fluorescence measurements indicated that Ca²⁺ adsorption decreases mobility within the carbonyl region of model bilayers more efficiently than monovalent ions do (Ca²⁺ ≫ Li⁺ > Na⁺ > K⁺ > Cs⁺). The effects of calcium ions were to a great extent mitigated in the plasma membranes isolated from HEK293 cells when compared to the model lipid membranes. Noticeably, the plasma membranes showed remarkably higher resistance toward rigidification induced by calcium ions even when compared with the model membranes containing cholesterol.

Molecular dynamic simulations of oxidized skin lipid bilayer and permeability of reactive oxygen species

Lipid peroxidation by reactive oxygen species (ROS) during oxidative stress is non-enzymatic damage that affects the integrity of biological membrane, and alters the fluidity and permeability. We conducted molecular dynamic simulation studies to evaluate the structural properties of the bilayer after lipid peroxidation and to measure the permeability of distinct ROS. The oxidized membrane contains free fatty acid, ceramide, cholesterol, and 5α-hydroperoxycholesterol (5α-CH). The result of unconstrained molecular dynamic simulations revealed that lipid peroxidation causes area-per-lipid of the bilayer to increase and bilayer thickness to decrease. The simulations also revealed that the oxidized group of 5α-CH (-OOH) moves towards the aqueous layer and its backbone tilts causing lateral expansion of the bilayer membrane. These changes are detrimental to structural and functional properties of the membrane. The measured free energy profile for different ROS (H₂O₂, HO₂, HO, and O₂) across the peroxidized lipid bilayer showed that the increase in lipid peroxidation resulted in breaching barrier decrease for all species, allowing easy traversal of the membrane. Thus, lipid peroxidation perturbs the membrane barrier and imposes oxidative stress resulting into apoptosis. The collective insights increase the understanding of oxidation stress at the atomic level.

Lipid lateral self-diffusion drop at liquid-gel phase transition

A drop of lipid lateral self-diffusion coefficient at the liquid-gel phase transition in lipid membranes is calculated. So far this drop was missing theoretical description. Our microscopic model captures so-called subdiffusion regime, which takes place on 1 ps-100 ns timescale and reveals a jump of self-diffusion coefficient. Calculation of the jump is based on our recent study of liquid-gel phase transition. Subdiffusive regime is described within the free volume theory. Calculated values of self-diffusion coefficient are in agreement with quasielastic neutron scattering measurements. Self-diffusion coefficient is found to be composed of two factors: one is related to an area per lipid change at the phase transition, and the other one is due to an order of magnitude change in the stiffness of entropic repulsive potential.

Cholesterol in phospholipid bilayers: positions and orientations inside membranes with different unsaturation degrees

Cholesterol is an essential component of all animal cell membranes and plays an important role in maintaining the membrane structure and physical-chemical properties necessary for correct cell functioning. The presence of cholesterol is believed to be responsible for domain formation (lipid rafts) due to different interactions of cholesterol with saturated and unsaturated lipids. In order to get detailed atomistic insight into the behaviour of cholesterol in bilayers composed of lipids with varying degrees of unsaturation, we have carried out a series of molecular dynamics simulations of saturated and polyunsaturated lipid bilayers with different contents of cholesterol, as well as well-tempered metadynamics simulations with a single cholesterol molecule in these bilayers. From these simulations we have determined distributions of cholesterol across the bilayer, its orientational properties, free energy profiles, and specific interactions of molecular groups able to form hydrogen bonds. Both molecular dynamics and metadynamics simulations showed that the most unsaturated bilayer with 22:6 fatty acid chains shows behaviour which is most different from other lipids. In this bilayer, cholesterol is relatively often found in a "flipped" configuration with the hydroxyl group oriented towards the membrane middle plane. This bilayer has also the highest (least negative) binding free energy among liquid phase bilayers, and the lowest reorientation barrier. Furthermore, cholesterol molecules in this bilayer are often found to form head-to-tail contacts which may lead to specific clustering behaviour. Overall, our simulations support ideas that there can be a subtle interconnection between the contents of highly unsaturated fatty acids and cholesterol, deficiency or excess of each of them is related to many human afflictions and diseases.

Effect of general anesthetics on the properties of lipid membranes of various compositions

Computer simulations of four lipid membranes of different compositions, namely neat DPPC and PSM, and equimolar DPPC-cholesterol and PSM-cholesterol mixtures, are performed in the presence and absence of the general anesthetics diethylether and sevoflurane both at 1 and 600 bar. The results are analyzed in order to identify membrane properties that are potentially related to the molecular mechanism of anesthesia, namely that change in the same way in any membrane with any anesthetics, and change oppositely with increasing pressure. We find that the lateral lipid density satisfies both criteria: it is decreased by anesthetics and increased by pressure. This anesthetic-induced swelling is attributed to only those anesthetic molecules that are located close to the boundary of the apolar phase. This lateral expansion is found to lead to increased lateral mobility of the lipids, an effect often thought to be related to general anesthesia; to an increased fraction of the free volume around the outer preferred position of anesthetics; and to the decrease of the lateral pressure in the nearby range of the ester and amide groups, a region into which anesthetic molecules already cannot penetrate. All these changes are reverted by the increase of pressure. Another important finding of this study is that cholesterol has an opposite effect on the membrane properties than anesthetics, and, correspondingly, these changes are less marked in the presence of cholesterol. Therefore, changes in the membrane that can lead to general anesthesia are expected to occur in the membrane domains of low cholesterol content.

Effects of cholesterol on the binding of the precursor neurotransmitter tryptophan to zwitterionic membranes

The characterization of the microscopical forces between the essential α-amino-acid tryptophan, precursor of the neurotransmitter serotonin and of the hormone melatonin, and the basic components of cell membranes and their environments (phospholipids, cholesterol, ionic species, and water) is of central importance to elucidate their local structure and dynamics as well as the mechanisms responsible for the access of tryptophan to the interior of the cell. We have performed nanosecond molecular dynamics simulations of tryptophan embedded in model zwitterionic bilayer membranes made by di-palmitoyl-phosphatidyl-choline and cholesterol inside aqueous sodium-chloride solution in order to systematically examine tryptophan-lipid, tryptophan-cholesterol, and tryptophan-water interactions under liquid-crystalline phase conditions. Microscopic properties such as the area per lipid, lipid thickness, radial distribution functions, hydrogen-bonding lengths, atomic spectral densities, and self-diffusion coefficients have been evaluated. Our results show that the presence of tryptophan significantly affects the structure and dynamics of the membrane. Tryptophan spends long periods of time at the water-membrane interface, and it plays a central role by bridging a few lipids and cholesterol chains by means of hydrogen-bonds. The computed spectral densities, in excellent agreement with experimental infrared and Raman data, revealed the participation of each atomic site of tryptophan to the complete spectrum of the molecule. Tryptophan self-diffusion coefficients have been found to be in between 10^-7 and 10^-6 cm²/s and strongly depending of the concentration of cholesterol in the system.

Ion channels can be allosterically regulated by membrane domains near a de-mixing critical point

Ion channels are embedded in the plasma membrane, a compositionally diverse two-dimensional liquid that has the potential to exert profound influence on their function. Recent experiments suggest that this membrane is poised close to an Ising critical point, below which cell-derived plasma membrane vesicles phase separate into coexisting liquid phases. Related critical points have long been the focus of study in simplified physical systems, but their potential roles in biological function have been underexplored. Here we apply both exact and stochastic techniques to the lattice Ising model to study several ramifications of proximity to criticality for idealized lattice channels, whose function is coupled through boundary interactions to critical fluctuations of membrane composition. Because of diverging susceptibilities of system properties to thermodynamic parameters near a critical point, such a lattice channel's activity becomes strongly influenced by perturbations that affect the critical temperature of the underlying Ising model. In addition, its kinetics acquire a range of time scales from its surrounding membrane, naturally leading to non-Markovian dynamics. Our model may help to unify existing experimental results relating the effects of small-molecule perturbations on membrane properties and ion channel function. We also suggest ways in which the role of this mechanism in regulating real ion channels and other membrane-bound proteins could be tested in the future.

Hydrophobic Mismatch Modulates Stability and Plasticity of Human Mitochondrial VDAC2

The human mitochondrial outer membrane protein voltage-dependent anion channel isoform 2 (hVDAC2) is a β-barrel metabolite flux channel that is indispensable for cell survival. It is well established that physical forces imposed on a transmembrane protein by its surrounding lipid environment decide protein structure and stability. Yet, how the mitochondrial membrane and protein-lipid interplay together regulate hVDAC2 stability is unknown. Here, we combine experimental biophysical investigations of protein stability with all-atom molecular dynamics simulations to study the effect of the most abundant mitochondrial phosphocholine (PC) lipids on hVDAC2. We demonstrate experimentally that increasing the PC lipid acyl chain length from diC14:0 to diC18:0-PC has a nonlinear effect on the β-barrel. We show that protein stability is highest in diC16:0-PC, which exhibits a negative mismatch with the hVDAC2 barrel. Our simulations also reveal that structural rigidity of hVDAC2 is highest under optimal negative mismatch provided by diC16:0-PC bilayers. Further, we validate our observations by altering the physical properties of PC membranes indirectly using cholesterol. We propose that VDAC plasticity and stability in the mitochondrial outer membrane are modulated by physical properties of the bilayer.

Spatially Resolving the Condensing Effect of Cholesterol in Lipid Bilayers

We study the effect of cholesterol on the structure of dipalmitoylphosphatidylcholine phospholipid bilayers. Using extensive molecular dynamics computer simulations at atomistic resolution, we observe and quantify several structural changes upon increasing cholesterol content that are collectively known as the condensing effect: a thickening of the bilayer, an increase in lipid tail order, and a decrease in lateral area. We also observe a change in leaflet interdigitation and a lack thereof in the distributions of dipalmitoylphosphatidylcholine headgroup orientations. These results, obtained over a wide range of cholesterol mole fractions, are then used to calibrate the analysis of phospholipid properties in bilayers containing a single cholesterol molecule per leaflet, which we perform in a spatially resolved way. We find that a single cholesterol molecule affects phospholipids in its first and second solvation shells, which puts the range of this effective interaction to be on the order of 1-2 nm. We also observe a tendency of phospholipids to orient their polar headgroups toward the cholesterol, which provides additional support for the umbrella model of bilayer organization.

Rationalizing Steroid Interactions with Lipid Membranes: Conformations, Partitioning, and Kinetics

Steroids have numerous physiological functions associated with cellular signaling or modulation of the lipid membrane structure and dynamics, and as such, they have found broad pharmacological applications. Steroid-membrane interactions are relevant to multiple steps of steroid biosynthesis and action, as steroids are known to interact with neurotransmitter or membrane steroid receptors, and steroids must cross lipid membranes to exert their physiological functions. Therefore, rationalizing steroid function requires understanding of steroid-membrane interactions. We combined molecular dynamics simulations and isothermal titration calorimetry to characterize the conformations and the energetics of partitioning, in addition to the kinetics of flip-flop transitions and membrane exit, of 26 representative steroid compounds in a model lipid membrane. The steroid classes covered in this study include birth control and anabolic drugs, sex and corticosteroid hormones, neuroactive steroids, as well as steroids modulating the lipid membrane structure. We found that the conformational ensembles adopted by different steroids vary greatly, as quantified by their distributions of tilt angles and insertion depths into the membrane, ranging from well-defined steroid conformations with orientations either parallel or normal to the membrane, to wide conformational distributions. Surprisingly, despite their chemical diversity, the membrane/water partition coefficient is similar among most steroids, except for structural steroids such as cholesterol, leading to similar rates for exiting the membrane. By contrast, the rates of steroid flip-flop vary by at least 9 orders of magnitude, revealing that flip-flop is the rate-limiting step during cellular uptake of polar steroids. This study lays the ground for a quantitative understanding of steroid-membrane interactions, and it will hence be of use for studies of steroid biosynthesis and function as well as for the development and usage of steroids in a pharmacological context.

Insight from Molecular dynamic simulation of reactive oxygen species in oxidized skin membrane

Non-enzymatic lipid peroxidation of the skin-lipid bilayer causes perturbations that affect the biomembrane structure, function, and permeability of reactive oxygen species (ROS). In the present study, we employed molecular dynamics simulations to study the effect of lipid peroxidation on the bilayer structural properties and permeability of various ROS. The oxidized skin-lipid bilayer was composed of ceramide, cholesterol, free fatty acid, and 5α-hydroperoxycholesterol (5α-CH). The simulation showed that, upon oxidation, the oxidized group (-OOH) of 5α-CH migrates towards the aqueous phase and the backbone of 5α-CH tilts, which causes the membrane to expand laterally. Measurements of the permeability of all ROS along the oxidized skin-lipid bilayer revealed a decreased breaching barrier for all the species as the degree of peroxidation increased, with a resulting easy passage across the membrane. The insights from the simulations indicate that lipid peroxidation might perturb the membrane barrier, thereby inflicting oxidative stress that leads to apoptosis. This study helps to understand oxidative stress at the atomic level. To our knowledge, this is the first reported molecular dynamics simulation study on oxidized skin-lipid bilayer and permeability of ROS.

Generalization of the swelling method to measure the intrinsic curvature of lipids

Via computer simulation of a coarse-grained model of two-component lipid bilayers, we compare two methods of measuring the intrinsic curvatures of the constituting monolayers. The first one is a generalization of the swelling method that, in addition to the assumption that the spontaneous curvature linearly depends on the composition of the lipid mixture, incorporates contributions from its elastic energy. The second method measures the effective curvature-composition coupling between the apposing leaflets of bilayer structures (planar bilayers or cylindrical tethers) to extract the spontaneous curvature. Our findings demonstrate that both methods yield consistent results. However, we highlight that the two-leaflet structure inherent to the latter method has the advantage of allowing measurements for mixed lipid systems up to their critical point of demixing as well as in the regime of high concentration (of either species).

Hampering Effect of Cholesterol on the Permeation of Reactive Oxygen Species through Phospholipids Bilayer: Possible Explanation for Plasma Cancer Selectivity

In recent years, the ability of cold atmospheric pressure plasmas (CAPS) to selectively induce cell death in cancer cells has been widely established. This selectivity has been assigned to the reactive oxygen and nitrogen species (RONS) created in CAPs. To provide new insights in the search for an explanation for the observed selectivity, we calculate the transfer free energy of multiple ROS across membranes containing a varying amount of cholesterol. The cholesterol fraction is investigated as a selectivity parameter because membranes of cancer cells are known to contain lower fractions of cholesterol compared to healthy cells. We find that cholesterol has a significant effect on the permeation of reactive species across a membrane. Indeed, depending on the specific reactive species, an increasing cholesterol fraction can lead to (i) an increase of the transfer free energy barrier height and width, (ii) the formation of a local free energy minimum in the center of the membrane and (iii) the creation of extra free energy barriers due to the bulky sterol rings. In the context of plasma oncology, these observations suggest that the increased ingress of RONS in cancer cells can be explained by the decreased cholesterol fraction of their cell membrane.

Inclusion of lipopeptides into the DMPC lipid bilayers prevents Aβ peptide insertion

Lipopeptides prevent penetration of Alzheimer's Aβ peptides into lipid bilayers.

DPPC-cholesterol phase diagram using coarse-grained Molecular Dynamics simulations

Cholesterol-phospholipid bilayers continue to be the current state of the art in membrane models and serve as representative systems for studying the effect of cholesterol on the cell membrane. As the mixing of different lipid species requires long spatio-temporal scales, coarse-grained models have gained increasing popularity in modeling such membrane systems. In this paper, a systematic study of the MARTINI coarse-grained model for the DPPC-cholesterol binary system has been performed. We construct the phase diagram of DPPC lipid bilayers in the presence of different cholesterol concentrations and at different temperatures using coarse-grained Molecular Dynamics (MD) simulations with the MARTINI force field. The phase diagram based on the condensation effect is directly comparable to available experimental data and demonstrates qualitative agreement over all cholesterol concentrations. Self-assembled bilayers quantitatively reproduce experimental observables, such as lateral diffusion of lipids, electron density, area per lipid and lipid order parameters. The phase diagram of the DPPC-cholesterol binary system also reveals the profound effect of cholesterol on the physical properties of phospholipid bilayers such lipid order, diffusion, and fluidity. Cholesterol induces the liquid-ordered phase, which increases the fluidity of the phospholipid hydrocarbon chains above the gel to liquid-crystalline phase transition temperature and decreases it below the phase transition. The present study suggests that the MARTINI force field can be successfully used to obtain molecular level insights into cholesterol-DPPC model membranes.

Mimicking Photosynthesis with Supercomplexed Lipid Nanoassemblies: Design, Performance, and Enhancement Role of Cholesterol

We report here a new approach to mimicking photosynthesis that relies on supercomplexed lipid nanoassemblies to organize small organic species for coordinated light harvesting, energy/electron transfer, and photo-to-electrochemical energy conversion. Specifically, we demonstrate efficient photoinduced electron transfer (PeT) between rhodamine and fullerene assembled together via electrostatically bound liposome and lipid bilayer hosts. The remarkable impact of the lipid matrix on the photoconversion efficiency is further revealed by cholesterol, whose addition is found to modify the distribution and organization of the coassembled rhodamine dyes and thus their photodynamics. This significantly expedites the energy transfer (ET) among rhodamine dyes, as well as the PeT between rhodamines and fullerenes. A respectable 14% photon-to-electron conversion efficiency was achieved for this supercomplexed system containing 5% rhodamines, 5% fullerenes, and 30% cholesterol. The morphology, photodynamics, and photoelectrochemical behavior of these lipid supercomplexes were thoroughly characterized using atomic force microscopy (AFM), fluorescence microscopy, steady-state and time-resolved fluorescence spectroscopy, and transient absorption (TA) and photoaction spectroscopy. A detailed discussion on enhancement mechanisms of cholesterol in this lipid-complexed photosynthesis-mimicking system is provided at the end.

The effect of hydrostatic pressure on model membrane domain composition and lateral compressibility

We distinguish the liquid ordered and liquid disordered phases in diffraction patterns of biphasic mixtures, comparing their lateral compressibility and report the variations in the two phase region with increasing hydrostatic pressure.

Effect of lipid peroxidation on membrane permeability of cancer and normal cells subjected to oxidative stress

We performed molecular dynamics simulations to investigate the effect of lipid peroxidation products on the structural and dynamic properties of the cell membrane. Our simulations predict that the lipid order in a phospholipid bilayer, as a model system for the cell membrane, decreases upon addition of lipid peroxidation products. Eventually, when all phospholipids are oxidized, pore formation can occur. This will allow reactive species, such as reactive oxygen and nitrogen species (RONS), to enter the cell and cause oxidative damage to intracellular macromolecules, such as DNA or proteins. On the other hand, upon increasing the cholesterol fraction of lipid bilayers, the cell membrane order increases, eventually reaching a certain threshold, from which cholesterol is able to protect the membrane against pore formation. This finding is crucial for cancer treatment by plasma technology, producing a large number of RONS, as well as for other cancer treatment methods that cause an increase in the concentration of extracellular RONS. Indeed, cancer cells contain less cholesterol than their healthy counterparts. Thus, they will be more vulnerable to the consequences of lipid peroxidation, eventually enabling the penetration of RONS into the interior of the cell, giving rise to oxidative stress, inducing pro-apoptotic factors. This provides, for the first time, molecular level insight why plasma can selectively treat cancer cells, while leaving their healthy counterparts undamaged, as is indeed experimentally demonstrated.

Amyloid-β (1-40) restores adhesion properties of pulmonary surfactant, counteracting the effect of cholesterol

A pulmonary surfactant (PS) is a thin lipid-protein film covering the surface of the lung alveoli at the air/liquid interface. The primary purpose of a PS is to control the surface tension of the air/liquid interface and to reduce the work of breathing. High levels of cholesterol in a PS are associated with life-threatening acute respiratory distress syndrome (ARDS) and acute lung injury (ALI). Finding therapeutics to counteract the effect of cholesterol in a PS is a matter of contemporary research. In our earlier work, we showed that the addition of amyloid-β (1-40) (Aβ40), the protein implicated in Alzheimer's disease, can reverse the detrimental effects of cholesterol in surfactants by improving multilayer formation and restoring PS surface active properties. We hypothesized that this phenomenon was due to Aβ40 improving adhesion properties of a surfactant. In this work we used atomic force spectroscopy to demonstrate that Aβ40 counteracts the adhesive properties of a PS compromised by high levels of cholesterol in a PS and helps to restore the functionality of a PS.

Direct in situ measurement of specific capacitance, monolayer tension, and bilayer tension in a droplet interface bilayer

Thickness and tension are important physical parameters of model cell membranes. However, traditional methods to measure these quantities require multiple experiments using separate equipment. This work introduces a new multi-step procedure for directly accessing in situ multiple physical properties of droplet interface bilayers (DIB), including specific capacitance (related to thickness), lipid monolayer tension in the Plateau-Gibbs border, and bilayer tension. The procedure employs a combination of mechanical manipulation of bilayer area followed by electrowetting of the capacitive interface to examine the sensitivities of bilayer capacitance to area and contact angle to voltage, respectively. These data allow for determining the specific capacitance of the membrane and surface tension of the lipid monolayer, which are then used to compute bilayer thickness and tension, respectively. The use of DIBs affords accurate optical imaging of the connected droplets in addition to electrical measurements of bilayer capacitance, and it allows for reversibly varying bilayer area. After validating the accuracy of the technique with diphytanoyl phosphatidylcholine (DPhPC) DIBs in hexadecane, the method is applied herein to quantify separately the effects on membrane thickness and tension caused by varying the solvent in which the DIB is formed and introducing cholesterol into the bilayer. Because the technique relies only on capacitance measurements and optical images to determine both thickness and tension, this approach is specifically well-suited for studying the effects of peptides, biomolecules, natural and synthetic nanoparticles, and other species that accumulate within membranes without altering bilayer conductance.

Properties of Langmuir and solid supported lipid films with sphingomyelin

Biological cell membranes play a crucial role in various biological processes and their functionality to some extent is determined by the hydrophilic/hydrophobic balance. A significant progress in understanding the membrane structure was the discovery of laterally segregated lipid domains, called the lipid rafts. These raft domains are of ordered lamellar liquid-crystalline phase, while rest of the membrane exists in a relatively disordered lamellar liquid-crystalline phase. Moreover, the chemical constitution of the lipid rafts consists of a higher content (up to 50%) of cholesterol (Chol) and sphingomyelin (SM). Sphingomyelin also plays a significant role in the red cells of blood and nerves, in some diseases, as a precursor to ceramides, and other sphingolipid metabolites. In this paper properties of Langmuir and solid supported mixed lipid films of DPPC/SM, DOPC/SM, and Chol/SM are described. Special attention has been paid to wetting properties (hydrophobic/hydrophilic balance) of these films transferred onto a hydrophilic glass surface. To our knowledge such results have not yet been published in the literature. The properties were determined via contact angle measurements and then calculation of the films' apparent surface free energy. The films' wettability and their apparent surface free energy strongly depend on their composition. The energy is affected by both the structure of hydrocarbon chains of glycerophospholipids (DPPC and DOPC) and their interactions with SM. Properties of mixed Chol/SM monolayer depend also on the film stoichiometry. At a low Chol content (XChol=0.25) the interactions between SM and Chol are strong and hence the formation of binary complex is possible. This is accompanied by a decrease in the film surface free energy in comparison to that of pure SM monolayer, contrary to a higher Chol content where the monolayer energy increases. This suggests that cholesterol is excluded from the membrane thus increasing the film hydrophilicity. These results are consistent with the literature data and somehow confirm the hypothesis of lipid raft formation. The roughness of the investigated monolayer surfaces was also determined using optical profilometry. The roughness parameters of the DPPC, SM, and mixed DPPC/SM generally correlate with the changes of their apparent surface free energy, i.e. with the decreasing roughness the apparent surface free energy also decreases. However, this is not the case for mixed DOPC/SM monolayers. Although the roughness increases with SM content the apparent surface free energy decreases. Therefore some other factors, like the presence of unsaturated bonds in the DOPC molecule, influence the film phase state and the energy too. More experiments are needed to explain this hypothesis.