Simulating induced interdigitation in membranes

Investigation of miltefosine-model membranes interactions at the molecular level for two different PS levels modeling cancer cells

Miltefosine (MLT) is a broad-spectrum drug included in the alkylphospholipids (APL) used against leishmania and various types of cancer. The most crucial feature of APLs is that they are thought to only kill cancerous cells without harming normal cells. However, the molecular mechanism of action of APLs is not completely understood. The increase in the phosphatidylserine (PS) ratio is a marker showing the stage of cancer and even metastasis. The goal of this research was to investigate the molecular effects of miltefosine at the molecular level in different PS ratios. The effects of MLT on membrane phase transition, membrane orders, and dynamics were studied using DPPC/DPPS (3:1) and DPPC/DPPS (1:1) multilayer (MLV) vesicles mimicking DPPS ratio variation, Differential Scanning Calorimetry (DSC), and Fourier Transform Infrared spectroscopy (FTIR). Our findings indicate that miltefosine is evidence at the molecular level that it is directed towards the tumor cell and that the drug's effect increases with the increase of anionic lipids in the membrane depending on the stage of cancer.

Advances on nanoformulation approaches for delivering plant-derived antioxidants: A case of quercetin

Oxidative stress has been implicated in tumorigenic, cardiovascular, neuro-, and age-related degenerative changes. Antioxidants minimize the oxidative damage through neutralization of reactive oxygen species (ROS) and other causative agents. Ever since the emergence of COVID-19, plant-derived antioxidants have received enormous attention, particularly in the Indian subcontinent. Quercetin (QCT), a bio-flavonoid, exists in the glycosylated form in fruits, berries and vegetables. The antioxidant potential of QCT analogs relates to the number of free hydroxyl groups in their structure. Despite presence of these groups, QCT exhibits substantial hydrophobicity. Formulation scientists have tested nanotechnology-based approaches for its improved solubilization and delivery to the intended site of action. By the virtue of its hydrophobicity, QCT gets encapsulated in nanocarriers carrying hydrophobic domains. Apart from passive accumulation, active uptake of such formulations into the target cells can be facilitated through well-studied functionalization strategies. In this review, we have discussed the approaches of improving solubilization and bioavailability of QCT with the use of nanoformulations.

Is Lipid Specificity Key to the Potential Antiviral Activity of Mouthwash Reagent Chlorhexidine against SARS-CoV-2?

Chlorhexidine (CHX), a popular antibacterial drug, is widely used for oral health. Emerging pieces of evidence suggest that commercially available chlorhexidine mouthwash formulations are effective in suppressing the spread of SARS-CoV-2, possibly through destabilization of the viral lipid envelope. CHX is known for its membrane-active properties; however, the molecular mechanism revealing how it damages the viral lipid envelope is yet to be understood. Here we used extensive conventional and umbrella sampling simulations to quantify the effects of CHX on model membranes mimicking the composition of the SARS-CoV-2 outer lipid membrane as well as the host plasma membrane. Our results show that the lipid composition and physical properties of the membrane play an important role in binding and insertion, with CHX binding favorably to the viral membrane over the plasma membrane. Among the simulated lipids, CHX preferentially binds to anionic lipids, PS and PI, which are more concentrated in the viral membrane. The deeper and stable binding of CHX to the viral membrane results in more pronounced swelling of the membrane laterally with a thinning of the bilayer. The overall free energies of pore formation are strongly reduced for the viral membrane compared to the plasma membrane; however, CHX has a larger concentration-dependent effect on free energies of pore formation in the plasma membrane than the viral membrane. The results indicate that CHX is less toxic to the human plasma membrane at low concentrations. Our simulations reveal that CHX facilitates pore formation by the combination of thinning the membrane and accumulation at the water defect. This study provides insights into the mechanism underlying the anti-SARS-CoV-2 potency of CHX, supporting its potential for application as an effective and safe oral rinse agent for preventing viral transmission.

Structural properties of cationic surfactant-fatty alcohol bilayers: insights from dissipative particle dynamics

Bilayers, self-assembled by cationic surfactants and fatty alcohols in water, are the basic units of lamellar gel networks - creamy formulations extensively used in cosmetics and pharmaceutics. Mesoscopic modelling and study of the bilayers formed by single- or double-tail cationic surfactants (CTAC or DHDAC), and fatty alcohols (FAs) in the lamellar fluid and gel phases were employed. Fatty alcohols with alkyl tail equal to or greater than the surfactant alkyl tail, i.e., C₁₆FA or C₁₈FA and C₂₂FA, were considered. A model formulation was explored with the FA concentration greater than that of the surfactant and the structure of the fluid and gel bilayers in tensionless state characterised via the density profiles across the bilayers, orientational order parameters of the surfactant and FA chains, intrinsic analysis of the bilayer interfaces, and bending rigidity. The intrinsic analysis allows identification and quantification of the coexistence of the interdigitated and non-interdigitated phases present within the gel bilayers. The FA chains were found to conform the primary scaffolding of the bilayers while the surfactant chains tessellate bilayer monolayers from their water-hydrophobic interface. Further, the overlap of the FA chains from the apposed monolayers of the fluid bilayers rises with increasing FA length. Finally, the prevalence of the non-interdigitated phase over the interdigitated phase within the gel bilayers becomes enhanced upon the FA length increase with a preference of the surfactant chains to reside in the non-interdigitated phase rather than the interdigitated phase.

Lipid Composition Analysis Reveals Mechanisms of Ethanol Tolerance in the Model Yeast Saccharomyces cerevisiae

Saccharomyces cerevisiae is an important unicellular yeast species within the biotechnological and the food and beverage industries. A significant application of this species is the production of ethanol, where concentrations are limited by cellular toxicity, often at the level of the cell membrane. Here, we characterize 61 S. cerevisiae strains for ethanol tolerance and further analyze five representatives with various ethanol tolerances. The most tolerant strain, AJ4, was dominant in coculture at 0 and 10% ethanol. Unexpectedly, although it does not have the highest noninhibitory concentration or MIC, MY29 was the dominant strain in coculture at 6% ethanol, which may be linked to differences in its basal lipidome. Although relatively few lipidomic differences were observed between strains, a significantly higher phosphatidylethanolamine concentration was observed in the least tolerant strain, MY26, at 0 and 6% ethanol compared to the other strains that became more similar at 10%, indicating potential involvement of this lipid with ethanol sensitivity. Our findings reveal that AJ4 is best able to adapt its membrane to become more fluid in the presence of ethanol and that lipid extracts from AJ4 also form the most permeable membranes. Furthermore, MY26 is least able to modulate fluidity in response to ethanol, and membranes formed from extracted lipids are least leaky at physiological ethanol concentrations. Overall, these results reveal a potential mechanism of ethanol tolerance and suggest a limited set of membrane compositions that diverse yeast species use to achieve this. IMPORTANCE Many microbial processes are not implemented at the industrial level because the product yield is poorer and more expensive than can be achieved by chemical synthesis. It is well established that microbes show stress responses during bioprocessing, and one reason for poor product output from cell factories is production conditions that are ultimately toxic to the cells. During fermentative processes, yeast cells encounter culture media with a high sugar content, which is later transformed into high ethanol concentrations. Thus, ethanol toxicity is one of the major stresses in traditional and more recent biotechnological processes. We have performed a multilayer phenotypic and lipidomic characterization of a large number of industrial and environmental strains of Saccharomyces to identify key resistant and nonresistant isolates for future applications.

Effects of ethanol and n-butanol on the fluidity of supported lipid bilayers

The interactions of molecules such as short-chain alcohols with the mammalian plasma membrane are thought to play a role in anesthetic effects. We have examined the concentration-dependent effects of ethanol and n-butanol on the fluidity of planar model lipid bilayer structures supported on mica. The supported model bilayer was composed of 1,2-dioleoyl-sn-phosphatidylcholine (DOPC), cholesterol, and sphingomyelin, and the bilayers were formed by vesicle fusion from extruded unilamellar vesicles (133 nm diameter, polydispersity index of 0.17). Controlled amounts of ethanol and n-butanol were added during vesicle deposition. Translational diffusion constants were obtained utilizing fluorescence recovery after photobleaching (FRAP) measurements on the micrometer scale with perylene as the fluorophore. The translational diffusion constants increased and then decreased with increasing ethanol concentration, with the bilayer structure degrading at ca. 0.8 M ethanol. A similar trend was observed for n-butanol at lower alcohol concentrations owing to greater interactions with phospholipid bilayer constituents. For n-butanol, the integrity of the planar bilayer structure deteriorated at ca. 0.4 M n-butanol. The results are consistent with bilayer interdigitation.

Thermodynamic and structural study of DMPC-alkanol systems

The thermodynamic and structural behaviors of lamellar dimyristoylphosphatidylcholine-alkanol (abbreviation DMPC-CnOH, n = 8-18 is the even number of carbons in the alkyl chain) systems were studied by using DSC and SAXD/WAXD methods at a 0-0.8 CnOH : DMPC molar ratio range. Up to n≤ 10 a significant biphasic effect depending on the main transition temperature t_m on the CnOH concentration was observed. Two breakpoints were revealed: turning point (TP), corresponding to the minimum, and threshold concentration (c_T), corresponding to the end of the biphasic tendency. These breakpoints were also observed in the alkanol concentration dependent change in the enthalpy of the main transition ΔH_m. In the case of CnOHs with n > 10 we propose a marked shift of TP and c_T to very low concentrations; consequently, only increase of t_m is observed. A partial phase diagram was constructed for a pseudo-binary DMPC-C12OH system. We suggest a fluid-fluid immiscibility of the DMPC-C12OH system above c_T with a consequent formation of domains with different C12OH contents. At a constant CnOH concentration, the effects of CnOHs on ΔH_m and bilayer repeat distance were found to depend predominantly on the mismatch between CnOH and lipid chain lengths. Observed effects are suggested to be underlined by a counterbalancing effect of interchain van der Waals interactions and headgroup repulsion.

Free Energy Cost of Interdigitation of Lamellar Bilayers of Fatty Alcohols with Cationic Surfactants from Molecular Dynamics Simulations

Cationic surfactant mixed with fatty alcohol as cosurfactant in excess water can form stable emulsions, known as "lamellar gel networks," that contain extended and interconnected networks of swollen bilayers, including ones with in-plane liquidlike disorder (L_α phase) and solidlike order (L_β phase). To study their structure and thermodynamics, molecular dynamics (MD) simulations with lateral pressure and temperature scans along reversible pathways were used to drive reversible phase changes, including formation at negative lateral pressure of the L_βI phase with interdigitated tails of opposing leaflets. Thermodynamic integration, with extrapolations to infinitely slow scans, yielded a free energy difference between the interdigitated L_βI and non-interdigitated L_β phases of 2.4 ± 0.5 kJ/mol, which is consistent with the spontaneous formation of the L_β phase under atmospheric pressure in simulation. Thermodynamic cycles involving temperature and lateral pressure for which the free energy difference is identically zero were constructed as negative controls to verify the method. Using lateral pressure, including negative lateral pressure, helps avoid kinetic bottlenecks that occur when temperature alone is used as the control variable. The method, using negative lateral pressure, should be widely applicable to other bilayers to identify molecular properties that control interdigitation and other bilayer properties.

Activity of the Gramicidin A Ion Channel in a Lipid Membrane with Switchable Physical Properties

Lipid bilayer membranes formed from the artificial 1,3-diamidophospholipid Pad-PC-Pad have the remarkable property that their hydrophobic thickness can be modified in situ: the particular arrangement of the fatty acid chains in Pad-PC-Pad allows them to fully interdigitate below 37 °C, substantially thinning the membrane with respect to the noninterdigitated state. Two stimuli, traversing the main phase transition temperature of the lipid or addition of cholesterol, have previously been shown to disable the interdigitated state. Both manipulations cause an increase in hydrophobic thickness of about 25 Å due to enhanced conformational entropy of the lipids. Here, we characterize the interdigitated state using electrophysiological recordings from free-standing lipid-membranes formed on micro structured electrode cavity arrays. Compared to standard membranes made from 1,2-diphytanoyl-sn-glycero-3-phosphocholin (DPhPC), pure Pad-PC-Pad membranes at room temperature had lowered electroporation threshold and higher capacitance. Ion channel formation by the peptide Gramicidin A was clearly facilitated in pure Pad-PC-Pad membranes at room temperature, with activity occurring at significantly lower peptide concentrations and channel dwell times increased by 2 orders of magnitude with respect to DPhPC-membranes. Both elevation of temperature beyond the phase transition and addition of cholesterol reduced channel dwell times, as expected if the reduced membrane thickness stabilized channel formation due to decreased hydrophobic mismatch.

Response of microbial membranes to butanol: interdigitation vs. disorder

Biobutanol production by fermentation is potentially a sustainable alternative to butanol production from fossil fuels. However, the toxicity of butanol to fermentative bacteria, resulting largely from cell membrane fluidization, limits production titers and is a major factor limiting the uptake of the technology. Here, studies were undertaken, in vitro and in silico, on the butanol effects on a representative bacterial (i.e. Escherichia coli) inner cell membrane. A critical butanol : lipid ratio for stability of 2 : 1 was observed, computationally, consistent with complete interdigitation. However, at this ratio the bilayer was ∼20% thicker than for full interdigitation. Furthermore, butanol intercalation induced acyl chain bending and increased disorder, measured as a 27% lateral diffusivity increase experimentally in a supported lipid bilayer. There was also a monophasic Tm reduction in butanol-treated large unilamellar vesicles. Both behaviours are inconsistent with an interdigitated gel. Butanol thus causes only partial interdigitation at physiological temperatures, due to butanol accumulating at the phospholipid headgroups. Acyl tail disordering (i.e. splaying and bending) fills the subsequent voids. Finally, butanol short-circuits the bilayer and creates a coupled system where interdigitated and splayed phospholipids coexist. These findings will inform the design of strategies targeting bilayer stability for increasing biobutanol production titers.

Biophysical Mechanisms of Membrane-Thickness-Dependent MscL Gating: An All-Atom Molecular Dynamics Study

The bacterial mechanosensitive channel, MscL, is activated by membrane tension, acting as a safety valve to prevent cell lysis against hypotonic challenge. It has been established that its activation threshold decreases with membrane thickness, while the underlying mechanism remains to be solved. We performed all-atom molecular dynamics (MD) simulations for the initial opening process of MscL embedded in four different types of lipid bilayers with different thicknesses: 1,2-dilauroyl- sn-glycero-3-phosphocholine (DLPC)), 1,2-dimyristoyl-glycero-3-phosphorylcholine (DMPC), 1,2-dipalmitoyl- sn-glycero-3-phosphocholine (DPPC), and 1,2-distearoyl- sn-glycero-3-phosphocholine (DSPC). In response to membrane stretching, channel opening occurred only in the thinner membranes (DLPC and DMPC) in a thickness-dependent way. We found that the MscL opening was governed by the rate and degree of membrane thinning and that the channel opening was tightly associated with the tilting of transmembrane (TM) helices of MscL toward the membrane plane. Upon membrane stretching, the order parameter of acyl chains of thinner membranes (DLPC and DMPC) became smaller, whereas other thicker membranes (DPPC and DSPC) showed interdigitation with little changes in the order parameter. The decreased order parameter contributed much more to membrane thinning than did interdigitation. We conclude that the membrane-thickness-dependent MscL opening mainly arises from structural changes in MscL to match the altered membrane thickness by stretching.

Role of lipid composition on the structural and mechanical features of axonal membranes: a molecular simulation study

The integrity of cellular membranes is critical for the functionality of axons. Failure of the axonal membranes (plasma membrane and/or myelin sheath) can be the origin of neurological diseases. The two membranes differ in the content of sphingomyelin and galactosylceramide lipids. We investigate the relation between lipid content and bilayer structural-mechanical properties, to better understand the dependency of membrane properties on lipid composition. A sphingomyelin/phospholipid/cholesterol bilayer is used to mimic a plasma membrane and a galactosylceramide/phospholipid/cholesterol bilayer to mimic a myelin sheath. Molecular dynamics simulations are performed at atomistic and coarse-grained levels to characterize the bilayers at equilibrium and under deformation. For comparison, simulations of phospholipid and phospholipid/cholesterol bilayers are also performed. The results clearly show that the bilayer biomechanical and structural features depend on the lipid composition, independent of the molecular models. Both galactosylceramide or sphingomyelin lipids increase the order of aliphatic tails and resistance to water penetration. Having 30% galactosylceramide increases the bilayers stiffness. Galactosylceramide lipids pack together via sugar-sugar interactions and hydrogen-bond phosphocholine with a correlated increase of bilayer thickness. Our findings provide a molecular insight on role of lipid content in natural membranes.

Ethanol- and trifluoroethanol-induced changes in phase states of DPPC membranes. Prodan emission-excitation fluorescence spectroscopy supported by PARAFAC analysis

It has been shown that Prodan emission-excitation fluorescence spectroscopy supported by Parallel Factor (PARAFAC) analysis is a fast, simple and sensitive method used in the study of the phase transition from the noninterdigitated gel (L_β') state to the interdigitated gel (L_βI) phase, triggered by ethanol and 2,2,2-trifluoroethanol (TFE) molecules in dipalmitoylphosphatidylcholines (DPPC) membranes. The relative contribution of lipid phases with spectral characteristics of each pure phase component has been presented as a function of an increase in alcohol concentration. It has been stated that both alcohol molecules can induce a formation of the L_βI phase, but TFE is over six times stronger inducer of the interdigitated phase in DPPC membranes than ethanol molecules. Moreover, in the TFE-mixed DPPC membranes, the transition from the L_β' to L_βI phase is accompanied by a formation of the fluid phase, which most probably serves as a boundary phase between the L_β' and L_βI regions. Contrary to the three phase-state model of TFE-mixed DPPC membranes, in ethanol-mixed DPPC membranes only the two phase-state model has been detected.

Effect of Vitamin E and a Long-Chain Alcohol n-Octanol on the Carbohydrate-Based Nonionic Amphiphile Sucrose Monolaurate-Formulation of Newly Developed Niosomes and Application in Cell Imaging

We have introduced new niosome formulations using sucrose monolaurate, vitamin E and n-octanol as independent additives. Detailed characterization techniques including turbidity, dynamic light scattering, transmission electron microscopy, ξ potential, and proton nuclear magnetic resonance measurements have been introduced to monitor the morphological transition of the carbohydrate-based micellar assembly into niosomal aggregates. Moreover, microheterogeneity of these niosomal aggregates has been investigated through different fluorescence spectroscopic techniques using a hydrophobic probe molecule coumarin 153 (C153). Further, it has been observed that vitamin E and octanol have an opposing effect on the rotational motion of C153 in the respective niosome assemblies. The time-resolved anisotropy studies suggest that incorporation of vitamin E and octanol into the surfactant aggregates results in slower and faster rotational motion of C153, respectively, compared to the micellar assemblies. Moreover, the ability to entrap a probe molecule by these niosomes is utilized to encapsulate and deliver the anticancer drug doxorubicin inside the mammalian cells which is monitored through fluorescence microscopic images. Interestingly, the niosome composed of vitamin E demonstrated better cytocompatibility toward primary chondrocyte cell lines compared to the octanol-forming niosome.

Anesthetic-dependent changes in the chain-melting phase transition of DPPG liposomes studied using near-infrared spectroscopy supported by PCA

The effect of inhalation anesthetics (enflurane, isoflurane, sevoflurane or halothane) on the lipid chain-melting phase transition of negatively charged phospholipid membranes was studied using near-infrared (NIR) spectroscopy supported by Principal Component Analysis (PCA). NIR spectra of anesthetics-mixed dipalmitoylphosphatidylglycerol (DPPG) membranes were recorded in a range of the first overtone of the symmetric and antisymmetric stretching vibrations of CH₂ groups of lipid aliphatic chains as a function of increasing temperature. Anesthetic-dependent changes in the trans to gauche conformers ratio of CH₂ groups in the hydrocarbon lipid chains were characterized in detail and compared with the zwitterionic lipid membranes, which were built of dipalmitoylphosphatidylcholine (DPPC) molecules.

Artificial biomembrane morphology: a dissipative particle dynamics study

Artificial membranes mimicking biological structures are rapidly breaking new ground in the areas of medicine and soft-matter physics. In this endeavor, we use dissipative particle dynamics simulation to investigate the morphology and behavior of lipid-based biomembranes under conditions of varied lipid density and self-interaction. Our results show that a less-than-normal initial lipid density does not create the traditional membrane; but instead results in the formation of a 'net', or at very low densities, a series of disparate 'clumps' similar to the micelles formed by lipids in nature. When the initial lipid density is high, a membrane forms, but due to the large number of lipids, the naturally formed membrane would be larger than the simulation box, leading to 'rippling' behavior as the excess repulsive force of the membrane interior overcomes the bending energy of the membrane. Once the density reaches a certain point however, 'bubbles' appear inside the membrane, reducing the rippling behavior and eventually generating a relatively flat, but thick, structure with micelles of water inside the membrane itself. Our simulations also demonstrate that the interaction parameter between individual lipids plays a significant role in the formation and behavior of lipid membrane assemblies, creating similar structures as the initial lipid density distribution. This work provides a comprehensive approach to the intricacies of lipid membranes, and offers a guideline to design biological or polymeric membranes through self-assembly processes as well as develop novel cellular manipulation and destruction techniques.

Effect of head group orientation on phospholipid assembly

The relationship between bilayer stability and lipid head group orientation is reported. In this work, molecular-dynamics simulations are performed to analyze the structure-property relationship of lipid biomembranes, taking into account coarse-grained model lipid interactions. The work explains the molecular scale mechanism of the phase behavior of lipid systems due to ion-lipid or anesthetic-lipid interactions, where reorientations of dipoles play a key role in modifying lipid phases and thereby alter biomembrane function. Our study demonstrates that simple dipolar reorientation is indeed sufficient in tuning a bilayer to a randomly flipped nonbilayer lamellar phase. This study may be used to assess the impact of changes in lipid phase characteristics on biomembrane structure due to the presence of anesthetics and ions.

Organic solvent-induced changes in membrane geometry in human SH-SY5Y neuroblastoma cells - a common narcotic effect?

Exposure to organic solvents may cause narcotic effects. At the cellular level, these narcotic effects have been associated with a reduction in neuronal excitability caused by changes in membrane structure and function. In order to critically test whether changes in membrane geometry contribute to these narcotic effects, cultured human SH-SY5Y neuroblastoma cells have been exposed to selected organic solvents. The solvent-induced changes in cell membrane capacitance were investigated using the whole-cell patch clamp technique for real-time capacitance measurements. Exposure of SH-SY5Y cells to the cyclic hydrocarbons m-xylene, toluene, and cyclohexane caused a rapid and reversible increase of membrane capacitance. The aliphatic, nonpolar n-hexane did not cause a detectable change of whole-cell membrane capacitance, whereas the amphiphiles n-hexanol and n-hexylamine caused an increase of membrane capacitance and a concomitant reduction in membrane resistance. Despite a large difference in dielectric properties, the chlorinated hydrocarbons 1,1,2,2-tetrachoroethane and tetrachloroethylene caused a similar magnitude increase in membrane capacitance. The theory on membrane capacitance has been applied to deduce changes in membrane geometry caused by solvent partitioning. Although classical observations have shown that solvents increase the membrane capacitance per unit area of membrane, i.e., increase membrane thickness, the present results demonstrate that solvent partitioning predominantly leads to an increase in membrane surface area and to a lesser degree to an increase in membrane thickness. Moreover, the present results indicate that the physicochemical properties of each solvent are important determinants for its specific effects on membrane geometry. This implies that the hypothesis that solvent partitioning is associated with a common perturbation of membrane structure needs to be revisited and cannot account for the commonly observed narcotic effects of different organic solvents.

The organization of melatonin in lipid membranes

Melatonin is a hormone that has been shown to have protective effects in several diseases that are associated with cholesterol dysregulation, including cardiovascular disease, Alzheimer's disease, and certain types of cancers. We studied the interaction of melatonin with model membranes made of dimyristoylphosphatidylcholine (DMPC) at melatonin concentrations ranging from 0.5mol% to 30mol%. From 2-dimensional X-ray diffraction measurements, we find that melatonin induces a re-ordering of the lipid membrane that is strongly dependent on the melatonin concentration. At low melatonin concentrations, we observe the presence of melatonin-enriched patches in the membrane, which are significantly thinner than the lipid bilayer. The melatonin molecules were found to align parallel to the lipid tails in these patches. At high melatonin concentrations of 30mol%, we observe a highly ordered melatonin structure that is uniform throughout the membrane, where the melatonin molecules align parallel to the bilayers and one melatonin molecule associates with 2 lipid molecules. Understanding the organization and interactions of melatonin in membranes, and how these are dependent on the concentration, may shed light into its anti-amyloidogenic, antioxidative and photoprotective properties and help develop a structural basis for these properties.

Long-timescale motions in glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulation

The occurrence of long-timescale motions in glycerol-1-monopalmitate (GMP) lipid bilayers is investigated based on previously reported 600 ns molecular dynamics simulations of a 2×8×8 GMP bilayer patch in the temperature range 302-338 K, performed at three different hydration levels, or in the presence of the cosolutes methanol or trehalose at three different concentrations. The types of long-timescale motions considered are: (i) the possible phase transitions; (ii) the precession of the relative collective tilt-angle of the two leaflets in the gel phase; (iii) the trans-gauche isomerization of the dihedral angles within the lipid aliphatic tails; and (iv) the flipping of single lipids across the two leaflets. The results provide a picture of GMP bilayers involving a rich spectrum of events occurring on a wide range of timescales, from the 100-ps range isomerization of single dihedral angles, via the 100-ns range of tilt precession motions, to the multi-μs range of phase transitions and lipid-flipping events.

Phase segregation in bio-inspired multi-component vesicles encompassing double tail phospholipid species

Our aim is to investigate the phase segregation and the structure of multi-component bio-inspired phospholipid vesicles via dissipative particle dynamics. The chemical distinction in the phospholipid species arises due to different head and tail group moieties, and molecular stiffness of the hydrocarbon tails. The individual amphiphilic phospholipid molecular species are represented by a hydrophilic head group and two hydrophobic tails. The distinct chemical nature of the moieties is modeled effectively via soft repulsive interaction parameters, and the molecular rigidity is tuned via suitable three-body potential constants. We demonstrate the formation of a stable hybrid vesicle through the self-assembly of the amphiphilic phospholipid molecules in the presence of a hydrophilic solvent. We investigate and characterize the phase segregation and the structure of the binary vesicles for different phospholipid mixtures. Our results demonstrate macroscopic phase separation for phospholipid mixtures composed of species with different hydrocarbon tail groups. We also investigate the relationship between the phase segregation and thermodynamic variables such as interfacial line tension and surface tension, and obtain correspondence between existing theory and experiments, and our simulation results. We report variations in the molecular chain stiffness to have negligible contributions to the phase segregation in the mixed bilayer, and to demonstrate shape transformations of the hybrid vesicle. Our results can be used to design novel bio-inspired hybrid vehicles for potential applications in biomedicine, sensing, imaging and sustainability.

Lipid oxidation induces structural changes in biomimetic membranes

Oxidation can intimately influence and structurally compromise the levels of biological self-assembly embodied by intracellular and plasma membranes. Lipid peroxidation, a natural metabolic outcome of life with oxygen under light, is also a salient oxidation reaction in photomedicine treatments. However, the effect of peroxidation on the fate of lipid membranes remains elusive. Here we use a new photosensitizer that anchors and disperses in the membrane to achieve spatial control of the oxidizing species. We find, surprisingly, that the integrity of unsaturated unilamellar vesicles is preserved even for fully oxidized membranes. Membrane survival allows for the quantification of the transformations of the peroxidized bilayers, providing key physical and chemical information to understand the effect of lipid oxidation on protein insertion and on other mechanisms of cell function. We anticipate that spatially controlled oxidation will emerge as a new powerful strategy for tuning and evaluating lipid membranes in biomimetic media under oxidative stress.

Structural disruption of phospholipid bilayers over a range of length scales by n-butanol

We report on the exposure of planar multicomponent lipid bilayers supported on mica to n-butanol. The bilayer contains 49 mol % 1,2-dioleoyl-sn-phosphatidylcholine (DOPC), 10 mol % cholesterol, 40 mol % sphingomyelin, and 1 mol % sulforhodamine-tagged 1,2-dioleoyl-sn-phosphatidylethanolamine (SR-DOPE). Phase separation of the cholesterol domains is seen within the bilayer structure, and exposure of this supported bilayer to controlled amounts of n-butanol in the aqueous overlayer produces morphological changes over a range of length scales. We report steady state fluorescence imaging, fluorescence lifetime imaging, and fluorescence anisotropy decay imaging for these bilayers. These data are consistent with literature reports on the interactions of lipid bilayers with n-butanol and provide molecular-scale insight relative to bilayer organization that has not been available to date. The exposure of these bilayers to n-butanol leads to more extensive disruption of the bilayer than is seen for their exposure to ethanol.

Lipid compositions modulate fluidity and stability of bilayers: characterization by surface pressure and sum frequency generation spectroscopy

Cell membranes are crucial to many biological processes. Because of their complexity, however, lipid bilayers are often used as model systems. Lipid structures influence the physical properties of bilayers, but their interplay, especially in multiple-component lipid bilayers, has not been fully explored. Here, we used the Langmuir-Blodgett method to make mono- and bilayers of 1,2-dihexadecanoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DPPG), 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG), and 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phospho-L-serine (POPS) as well as their 1:1 binary mixtures. We studied the fluidity, stability, and rigidity of these structures using sum frequency generation (SFG) spectroscopy combined with analyses of surface pressure-area isotherms, compression modulus, and stability. Our results show that single-component bilayers, both saturated and unsaturated, may not be ideal membrane mimics because of their low fluidity and/or stability. However, the binary saturated and unsaturated DPPG/POPG and DPPG/POPS systems show not only high stability and fluidity but also high resistance to changes in surface pressure, especially in the range of 25-35 mN/m, the range typical of cell membranes. Because the ratio of saturated to unsaturated lipids is highly regulated in cells, our results underline the possibility of modulating biological properties using lipid compositions. Also, our use of flat optical windows as solid substrates in SFG experiments should make the SFG method more compatible with other techniques, enabling more comprehensive future surface characterizations of bilayers.

n-Butanol partitioning into phase-separated heterogeneous lipid monolayers

Cellular adaptation to elevated alcohol concentration involves altering membrane lipid composition to counteract fluidization. However, few studies have examined the biophysical response of biologically relevant heterogeneous membranes. Lipid phase behavior, molecular packing, and elasticity have been examined by surface pressure-area (π-A) analysis in mixed monolayers composed of saturated dipalmitoylphosphatidylcholine (DPPC) and unsaturated dioleoylphosphatidylcholine (DOPC) as a function of DOPC and n-butanol concentration. n-Butanol partitioning into DPPC monolayers led to lipid expansion and increased elasticity. Greater lipid expansion occurred with increasing DOPC concentration, and a maximum was observed at equimolar DPPC:DOPC consistent with n-butanol partitioning between coexisting liquid expanded (LE, DOPC) phases and liquid condensed (LC, DPPC) domains. This led to distinct changes in the size and morphology of LC domains. In DOPC-rich monolayers the effect of n-butanol adsorption on π-A behavior was less pronounced due to DOPC tail kinking. These results point to the importance of lipid composition and phase coexistence on n-butanol partitioning and monolayer restructuring.

α-Synuclein senses lipid packing defects and induces lateral expansion of lipids leading to membrane remodeling

There is increasing evidence for the involvement of lipid membranes in both the functional and pathological properties of α-synuclein (α-Syn). Despite many investigations to characterize the binding of α-Syn to membranes, there is still a lack of understanding of the binding mode linking the properties of lipid membranes to α-Syn insertion into these dynamic structures. Using a combination of an optical biosensing technique and in situ atomic force microscopy, we show that the binding strength of α-Syn is related to the specificity of the lipid environment (the lipid chemistry and steric properties within a bilayer structure) and to the ability of the membranes to accommodate and remodel upon the interaction of α-Syn with lipid membranes. We show that this interaction results in the insertion of α-Syn into the region of the headgroups, inducing a lateral expansion of lipid molecules that can progress to further bilayer remodeling, such as membrane thinning and expansion of lipids out of the membrane plane. We provide new insights into the affinity of α-Syn for lipid packing defects found in vesicles of high curvature and in planar membranes with cone-shaped lipids and suggest a comprehensive model of the interaction between α-Syn and lipid bilayers. The ability of α-Syn to sense lipid packing defects and to remodel membrane structure supports its proposed role in vesicle trafficking.

The quantum casimir effect may be a universal force organizing the bilayer structure of the cell membrane

A mathematic–physical model of the interaction between cell membrane bilayer leaflets is proposed based on the Casimir effect in dielectrics. This model explains why the layers of a lipid membrane gently slide one past another rather than penetrate each other. The presented model reveals the dependence of variations in the free energy of the system on the membrane thickness. This function is characterized by the two close minima corresponding to the different levels of interdigitation of the lipids from neighbor layers. The energy barrier of the compressing transition between the predicted minima is estimated to be 5.7 kT/lipid, and the return energy is estimated to be 3.1 kT/lipid. The proposed model enables estimation of the value of the membrane elastic thickness modulus of compressibility, which is 1.7 × 10⁹ N/m², and the value of the interlayer friction coefficient, which is 1.9 × 10⁸ Ns/m³.

An introduction to dissipative particle dynamics

Dissipative particle dynamics (DPD) is a particle-based mesoscopic simulation method, which facilitates the studies of thermodynamic and dynamic properties of soft matter systems at physically interesting length and time scales. In this method, molecule groups are clustered into the dissipative beads, and this coarse-graining procedure is a very important aspect of DPD as it allows significant computational speed-up. In this chapter, we introduce the DPD methodology, including its theoretical foundation and its parameterization. With this simulation technique, we can study complex behaviors of biological systems, such as the formation of vesicles and their fusion and fission processes, and the phase behavior of lipid membranes.

Role of unsaturated lipid and ergosterol in ethanol tolerance of model yeast biomembranes

We present a combined atomic force microscopy and fluorescence microscopy study of the behavior of a ternary supported lipid bilayer system containing a saturated lipid (DPPC), an unsaturated lipid (DOPC), and ergosterol in the presence of high ethanol (20 vol %). We find that the fluorescent probe Texas Red DHPE preferentially partitions into the ethanol-induced interdigitated phase, which allows the use of fluorescence imaging to investigate the phase behavior of the system. Atomic force microscopy and fluorescence images of samples with the same lipid mixture show good agreement in sample morphology and area fractions of the observed phases. Using area fractions obtained from fluorescence images over a broad range of compositions, we constructed a phase diagram of the DPPC/DOPC/ergosterol system at 20 vol % ethanol. The phase diagram clearly shows that increasing unsaturated lipid and/or ergosterol protects the membrane by preventing the formation of the interdigitated phase. This result supports the hypothesis that yeast cells increase ergosterol and unsaturated lipid content to prevent interdigitation and maintain an optimal membrane thickness as ethanol concentration increases during anaerobic fermentations. Changes in plasma membrane composition provide an important survival factor for yeast cells to deter ethanol toxicity.

VISUALIZING SOFT MATTER: MESOSCOPIC SIMULATIONS OF MEMBRANES, VESICLES AND NANOPARTICLES

Biological membranes have properties and behavior that emerge from the propagation of the molecular characteristics of their components across many scales. Artificial smart materials, such as drug delivery vehicles and nanoparticles, often rely on modifying naturally-occurring soft matter, such as polymers and lipid vesicles, so that they possess useful behavior. Mesoscopic simulations allow in silico experiments to be easily and cheaply performed on complex, soft materials requiring as input only the molecular structure of the constituents at a coarse-grained level. They can therefore act as a guide to experimenters prior to performing costly assays. Additionally, mesoscopic simulations provide the only currently feasible window on the length and time scales relevant to important biophysical processes such as vesicle fusion. We describe here recent work using Dissipative Particle Dynamics simulations to explore the structure and behavior of amphiphilic membranes, the fusion of vesicles, and the interactions between rigid nanoparticles and soft surfaces.

Pore-spanning lipid membrane under indentation by a probe tip: a molecular dynamics simulation study

We study the indentation of a free-standing lipid membrane suspended over a nanopore on a hydrophobic substrate by means of molecular dynamics simulations. We find that in the course of indentation the membrane bends at the point of contact and the fringes of the membrane glide downward intermittently along the pore edges and stop gliding when the fringes reach the edge bottoms. The bending continues afterward, and the large strain eventually induces a phase transition in the membrane, transformed from a bilayered structure to an interdigitated structure. The membrane is finally ruptured when the indentation goes deep enough. Several local physical quantities in the pore regions are calculated, which include the tilt angle of lipid molecules, the nematic order, the included angle, and the distance between neighboring lipids. The variations of these quantities reveal many detailed, not-yet-specified local structural transitions of lipid molecules under indentation. The force-indentation curve is also studied and discussed. The results make a connection between the microscopic structure and the macroscopic properties and provide deep insight into the understanding of the stability of a lipid membrane spanning over nanopore.

Self-assembly, foaming, and emulsifying properties of sodium alkyl carboxylate/guanidine hydrochloride aqueous mixtures

Unsaturated fatty acids may be extracted from various agricultural resources and are widely used as soaps in the industry. However, there also exist a large variety of saturated and hydroxy fatty acids in nature, but their metal salts crystallize at room temperature in water, hampering their use in biological and chemical studies or for industrial applications. Addition of guanidine hydrochloride (GuHCl) to sodium salt of myristic acid has been shown to prevent its crystallization in water, forming stable flat bilayers at room temperature. Herein, we extend this finding to two other saturated fatty acids (palmitic and stearic acids) and two hydroxyl fatty acids (juniperic and 12 hydroxy stearic acids) and study more deeply (by using small angle neutron scattering) the supramolecular assemblies formed in both saturated and hydroxyl fatty acid systems. In addition, we take the advantage that crystallization no longer occurs at room temperature in the presence of GuHCl to study the foaming and emulsifying properties of those fatty acid dispersions. Briefly, our results show that all fatty acids, even juniperic acid, which is a bola lipid, are arranged in a bilayer structure that may be interdigitated. Depending on the nature of the fatty acid, the systems exhibit good foamability and foam stability (except for juniperic acid), and emulsion stability was good. Those findings should be of interest for using saturated long chain (and hydroxyl) fatty acids as surfactants for detergency or even materials chemistry.

Influence of ethanol on lipid/sterol membranes: phase diagram construction from AFM imaging

Herein we develop a sample preparation approach that enables the use of supported lipid bilayers for the quantitative study of the influence of ethanol (0-20 vol %) on the phase behavior of phospholipid (DPPC)/sterol (ergosterol, 0-20 mol %) bilayers. Three coexisting phases were observed with tapping-mode atomic force microscopy: gel (L(beta)'), liquid-ordered (L(o)), and interdigitated (L(beta)'I). High-resolution imaging permitted the construction of a refined phase diagram for DPPC/ergosterol/ethanol and the observation of L(o)-L(beta)' phase separation that has not been observed using optical techniques. Our results quantitatively show the concentration regime where ergosterol protects the membrane by reducing the membrane fraction that is interdigitated in the presence of ethanol.

Cluster formation of anchored proteins induced by membrane-mediated interaction

Computer simulations were used to study the cluster formation of anchored proteins in a membrane. The rate and extent of clustering was found to be dependent upon the hydrophobic length of the anchored proteins embedded in the membrane. The cluster formation mechanism of anchored proteins in our work was ascribed to the different local perturbations on the upper and lower monolayers of the membrane and the intermonolayer coupling. Simulation results demonstrated that only when the penetration depth of anchored proteins was larger than half the membrane thickness, could the structure of the lower monolayer be significantly deformed. Additionally, studies on the local structures of membranes indicated weak perturbation of bilayer thickness for a shallowly inserted protein, while there was significant perturbation for a more deeply inserted protein. The origin of membrane-mediated protein-protein interaction is therefore due to the local perturbation of the membrane thickness, and the entropy loss-both of which are caused by the conformation restriction on the lipid chains and the enhanced intermonolayer coupling for a deeply inserted protein. Finally, in this study we addressed the difference of cluster formation mechanisms between anchored proteins and transmembrane proteins.