Comparison of Ternary Bilayer Mixtures with Asymmetric or Symmetric Unsaturated Phosphatidylcholine Lipids by Coarse Grained Molecular Dynamics Simulations

Molecular modulating of amylopectin's structure promoted the formation of starch-unsaturated fatty acids complexes with controlled digestibility and improved stability to oxidation

In this study, waxy corn starch (WCS) was modified by amylosucrase and pullulanase, producing linear starch chains with elongated length that favored the complexation with unsaturated fatty acids (uFAs). Compared to native WCS, the amylosucrase-modified WCS with an average chain length of 47.8 was easier to form V-type complexes with oleic acid, while increasing the degree of unsaturation impeded the formation of V-type complexes. The pullulanase treatment hydrolyzed the branching points of amylosucrase-modified WCS and the linear starch chains could forme V-type complexes with oleic acid, linoleic acid, and linolenic acid, with V-type crystallinity decreasing from 38.2 % to 20.1 %. V-type complexes had a lower thermal stability than the B-type starch crystallites, and their peak melting temperature ranged from 67.2 to 79.0 °C. The content of resistant starch in the complexes was in the range of 21.8 %-40.9 % and the formation of V-type complexes decreased the susceptibility of uFAs to oxygen.

Atomistic Insight into the Lipid Nanodomains of Synaptic Vesicles

Membrane curvature, once regarded as a passive consequence of membrane composition and cellular architecture, has been shown to actively modulate various properties of the cellular membrane. These changes could also lead to segregation of the constituents of the membrane, generating nanodomains with precise biological properties. Proteins often linked with neurodegeneration (e.g., tau, alpha-synuclein) exhibit an unintuitive affinity for synaptic vesicles in neurons, which are reported to lack distinct, ordered nanodomains based on their composition. In this study, all-atom molecular dynamics simulations are used to study a full-scale synaptic vesicle of realistic Gaussian curvature and its effect on the membrane dynamics and lipid nanodomain organization. Compelling indicators of nanodomain formation, from the perspective of composition, surface areas per lipid, order parameter, and domain lifetime, are identified in the vesicle membrane, which are absent in a flat bilayer of the same lipid composition. Therefore, our study supports the idea that curvature may induce phase separation in an otherwise fluid, disordered membrane.

Data-driven equation for drug-membrane permeability across drugs and membranes

Drug efficacy depends on its capacity to permeate across the cell membrane. We consider the prediction of passive drug-membrane permeability coefficients. Beyond the widely recognized correlation with hydrophobicity, we additionally consider the functional relationship between passive permeation and acidity. To discover easily interpretable equations that explain the data well, we use the recently proposed sure-independence screening and sparsifying operator (SISSO), an artificial-intelligence technique that combines symbolic regression with compressed sensing. Our study is based on a large in silico dataset of 0.4 × 10⁶ small molecules extracted from coarse-grained simulations. We rationalize the equation suggested by SISSO via an analysis of the inhomogeneous solubility-diffusion model in several asymptotic acidity regimes. We further extend our analysis to the dependence on lipid-membrane composition. Lipid-tail unsaturation plays a key role but surprisingly contributes stepwise rather than proportionally. Our results are in line with previously observed changes in permeability, suggesting the distinction between liquid-disordered and liquid-ordered permeation. Together, compressed sensing with analytically derived asymptotes establish and validate an accurate, broadly applicable, and interpretable equation for passive permeability across both drug and lipid-tail chemistry.

Effect of alcohol on the phase separation in model membranes

The discovery of coexisting liquid-ordered and liquid-disordered phases in multicomponent lipid bilayers has received widespread attention due to its potential relevance for biological systems. One of the many open questions is how the presence of additional components affects the nature of the coexisting phases. Of particular interest is the addition of alcohols because their anesthetic properties may arise from modulating bilayer behavior. We use coarse-grained Molecular Dynamics simulations to gain insight into the partitioning preferences of linear n-alcohols into ordered and disordered bilayers alongside their effects on local membrane structure. We find that alcohols cause only small changes to membrane composition alongside a lack of significant effects on membrane thickness and lipid tail order. Cholesterol and n-alcohol trans-bilayer motion is measured and found to be near or within the range of previous atomistic results. The cholesterol flip-flop rates increase with both n-alcohol length and concentration for octanol, dodecanol, and hexadecanol, indicating a decrease in lipid order. Umbrella sampling simulations of removing cholesterol from tertiary membranes find no significant difference with or without n-alcohols at various concentrations. Simulations of a phase-separated bilayer show that octanol preferentially partitions into the liquid-disordered phase in a ratio of approximately 3:1 over the liquid-ordered phase. Furthermore, partition coefficients of alcohol in single-phase membranes show a preference for longer alcohols (dodecanol and hexadecanol) to partition preferentially into the liquid-ordered phase, while decreasing the length of the alcohol reverses this trend. Our work tests experimental results while also investigating the ability for coarse-grained MARTINI simulations to capture minute differences in model membrane spatial arrangements on the nanoscale level.

Structure and Dynamics of GPCRs in Lipid Membranes: Physical Principles and Experimental Approaches

Over the past decade, the vast amount of information generated through structural and biophysical studies of GPCRs has provided unprecedented mechanistic insight into the complex signalling behaviour of these receptors. With this recent information surge, it has also become increasingly apparent that in order to reproduce the various effects that lipids and membranes exert on the biological function for these allosteric receptors, in vitro studies of GPCRs need to be conducted under conditions that adequately approximate the native lipid bilayer environment. In the first part of this review, we assess some of the more general effects that a membrane environment exerts on lipid bilayer-embedded proteins such as GPCRs. This is then followed by the consideration of more specific effects, including stoichiometric interactions with specific lipid subtypes. In the final section, we survey a range of different membrane mimetics that are currently used for in vitro studies, with a focus on NMR applications.

Computational Modeling of Realistic Cell Membranes

Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.

The asymmetry of plasma membranes and their cholesterol content influence the uptake of cisplatin

The composition of the plasma membrane of malignant cells is thought to influence the cellular uptake of cisplatin and to take part in developing resistance to this widespread anti-cancer drug. In this work we study the permeation of cisplatin through the model membranes of normal and cancer cells using molecular dynamics simulations. A special attention is paid to lipid asymmetry and cholesterol content of the membranes. The loss of lipid asymmetry, which is common for cancer cells, leads to a decrease in their permeability to cisplatin by one order of magnitude in comparison to the membranes of normal cells. The change in the cholesterol molar ratio from 0% to 33% also decreases the permeability of the membrane by approximately one order of magnitude. The permeability of pure DOPC membrane is 5-6 orders of magnitude higher than one of the membranes with realistic lipid composition, which makes it as an inadequate model for the studies of drug permeability.

Regimes of Complex Lipid Bilayer Phases Induced by Cholesterol Concentration in MD Simulation

Cholesterol is essential to the formation of phase-separated lipid domains in membranes. Lipid domains can exist in different thermodynamic phases depending on the molecular composition and play significant roles in determining structure and function of membrane proteins. We investigate the role of cholesterol in the structure and dynamics of ternary lipid mixtures displaying phase separation using molecular dynamics simulations, employing a physiologically relevant span of cholesterol concentration. We find that cholesterol can induce formation of three regimes of phase behavior: 1) miscible liquid-disordered bulk, 2) phase-separated, domain-registered coexistence of liquid-disordered and liquid-ordered domains, and 3) phase-separated, domain-antiregistered coexistence of liquid-disordered and newly identified nanoscopic gel domains composed of cholesterol threads we name "cholesterolic gel" domains. These findings are validated and discussed in the context of current experimental knowledge, models of cholesterol spatial distributions, and models of ternary lipid-mixture phase separation.

Relating the structure factors of two-dimensional materials in planar and spherical geometries

Scattering structure factors provide essential insight into material properties and are routinely obtained in experiments, computer simulations, and theoretical analyses. Different approaches favor different geometries of the material. In case of lipid bilayers, scattering experiments can be performed on spherical vesicles, while simulations and theory often consider planar membrane patches. We derive an approximate relationship between the structure functions of such a material in planar and spherical geometries. We illustrate the usefulness of this relationship in a case study of a Gaussian material that supports both homogeneous and microemulsion phases. Within its range of applicability, this relationship enables a model-free comparison of structure factors of the same material in different geometries.

Regulation of phase boundaries and phase-segregated patterns in model membranes

Demixing of components has long been described in model membranes. It is a consequence of non-ideal lateral interactions between membrane components, and it causes the presence of segregated phases, forming patches (domains) of different properties, thus introducing heterogeneity into the membrane. In the present review we first describe the processes through which domains are generated, how they grow, and why they are rounded, striped or fractal-like, as well as why they get distributed forming defined patterns. Next, we focus on the effect of an additive on a lipid mixture, which usually induces shifts in demixing points, thus stabilizing or destabilizing the phase-segregated state. Results found for different model membranes are summarized, detailing the ways in which phase segregation and the generated patterns may be modulated. We focus on which are, from our viewpoint, the most relevant regulating factors affecting the surface texture observed in model membranes. This article is part of a Special Issue entitled: Emergence of Complex Behavior in Biomembranes edited by Marjorie Longo.

Composition Fluctuations in Lipid Bilayers

Cell membranes contain multiple lipid and protein components having heterogeneous in-plane (lateral) distribution. Nanoscale rafts are believed to play an important functional role, but their phase state—domains of coexisting phases or composition fluctuations—is unknown. As a step toward understanding lateral organization of cell membranes, we investigate the difference between nanoscale domains of coexisting phases and composition fluctuations in lipid bilayers. We simulate model lipid bilayers with the MARTINI coarse-grained force field on length scales of tens of nanometers and timescales of tens of microseconds. We use a binary and a ternary mixture: a saturated and an unsaturated lipid, or a saturated lipid, an unsaturated lipid, and cholesterol, respectively. In these mixtures, the phase behavior can be tuned from a mixed state to a coexistence of a liquid-crystalline and a gel, or a liquid-ordered and a liquid-disordered phase. Transition from a two-phase to a one-phase state is achieved by raising the temperature and adding a hybrid lipid (with a saturated and an unsaturated chain). We analyze the evolution of bilayer properties along this transition: domains of two phases transform to fluctuations with local ordering and compositional demixing. Nanoscale domains and fluctuations differ in several properties, including interleaflet overlap and boundary length. Hybrid lipids show no enrichment at the boundary, but decrease the difference between the coexisting phases by ordering the disordered phase, which could explain their role in cell membranes.

Critical size dependence of domain formation observed in coarse-grained simulations of bilayers composed of ternary lipid mixtures

Model cellular membranes are known to form micro- and macroscale lipid domains dependent on molecular composition. The formation of macroscopic lipid domains by lipid mixtures has been the subject of many simulation investigations. We present a critical study of system size impact on lipid domain phase separation into liquid-ordered and liquid-disordered macroscale domains in ternary lipid mixtures. In the popular di-C16:0 PC:di-C18:2 PC:cholesterol at 35:35:30 ratio mixture, we find systems with a minimum of 1480 lipids to be necessary for the formation of macroscopic phase separated domains and systems of 10 000 lipids to achieve structurally converged conformations similar to the thermodynamic limit. To understand these results and predict the behavior of any mixture forming two phases, we develop and investigate an analytical Flory-Huggins model which is recursively validated using simulation and experimental data. We find that micro- and macroscale domains can coexist in ternary mixtures. Additionally, we analyze the distributions of specific lipid-lipid interactions in each phase, characterizing domain structures proposed based on past experimental studies. These findings offer guidance in selecting appropriate system sizes for the study of phase separations and provide new insights into the nature of domain structure for a popular ternary lipid mixture.

Molecular Insight into the Line Tension of Bilayer Membranes Containing Hybrid Polyunsaturated Lipids

Line tension (γ) is a key parameter for the structure and dynamics of membrane domains. It was proposed that hybrid lipids, with mixed saturated and unsaturated acyl chains, participate in the relaxation of γ through different mechanisms. In this work, we used molecular dynamics simulations of the coarse-grained MARTINI model to measure γ in liquid-ordered-liquid-disordered (Lo-Ld) membranes, with increasingly larger relative proportion of the hybrid polyunsaturated lipid PAPC (4:0-5:4PC) to DAPC (di5:4PC) (i.e., X_H). We also calculated an elastic contribution to γ by the Lo-Ld thickness mismatch, tilt moduli, and bending moduli, as predicted by theory. We found that an increase in X_H decreased the overall γ value and the elastic contribution to line tension. The effect on the elastic line tension is driven by a reduced hydrophobic mismatch. Changes in the elastic constants of the phases due to an increase in X_H produced a slightly larger elastic γ term. In addition to this elastic energy, other major contributions to γ are found in these model membranes. Increasing X_H decreases both elastic and nonelastic contributions to γ. Finally, PAPC also behaves as a linactant, relaxing γ through an interfacial effect, as predicted by theoretical results. This study gives insight into the actual contribution of distinct energy terms to γ in bilayers containing polyunsaturated hybrid lipids.

Domain Stability in Biomimetic Membranes Driven by Lipid Polyunsaturation

Biological membranes contain a broad variety of lipid species whose individual physicochemical properties and collective interactions ultimately determine membrane organization. A key aspect of the organization of cellular membranes is their lateral subdivision into domains of distinct structure and composition. The most widely studied membrane domains are lipid rafts, which are the biological manifestations of liquid-ordered phases that form in sterol-containing membranes. Detailed studies of biomimetic membrane mixtures have yielded wide-ranging insights into the physical principles behind lipid rafts; however, these simplified models do not fully capture the diversity and complexity of the mammalian lipidome, most notably in their exclusion of polyunsaturated lipids. Here, we assess the role of lipid acyl chain unsaturation as a driving force for phase separation using coarse-grained molecular dynamics (CGMD) simulations validated by model membrane experiments. The clear trends in our observations and good qualitative agreements between simulations and experiments support the conclusions that highly unsaturated lipids promote liquid-liquid domain stability by enhancing the differences in cholesterol content and lipid chain order between the coexisting domains. These observations reveal the important role of noncanonical biological lipids in the physical properties of membranes, showing that lipid polyunsaturation is a driving force for liquid-liquid phase separation.

Model parameters for simulation of physiological lipids

Coarse grain simulation of proteins in their physiological membrane environment can offer insight across timescales, but requires a comprehensive force field. Parameters are explored for multicomponent bilayers composed of unsaturated lipids DOPC and DOPE, mixed-chain saturation POPC and POPE, and anionic lipids found in bacteria: POPG and cardiolipin. A nonbond representation obtained from multiscale force matching is adapted for these lipids and combined with an improved bonding description of cholesterol. Equilibrating the area per lipid yields robust bilayer simulations and properties for common lipid mixtures with the exception of pure DOPE, which has a known tendency to form nonlamellar phase. The models maintain consistency with an existing lipid-protein interaction model, making the force field of general utility for studying membrane proteins in physiologically representative bilayers.

Effects of Transmembrane α-Helix Length and Concentration on Phase Behavior in Four-Component Lipid Mixtures: A Molecular Dynamics Study

We used coarse-grained molecular dynamics simulations to examine the effects of transmembrane α-helical WALP peptides on the behavior of four-component lipid mixtures. These mixtures contain a high-melting temperature (high-Tm) lipid, a nanodomain-inducing low-Tm lipid, a macrodomain-inducing low-Tm lipid and cholesterol to model the outer leaflet of cell plasma membranes. In a series of simulations, we incrementally replace the nanodomain-inducing low-Tm lipid by the macrodomain-inducing low-Tm lipid and measure how lipid and phase properties are altered by the addition of WALPs of different length. Regardless of the ratio of the two low-Tm lipids, shorter WALPs increase domain size and all WALPs increase domain alignment between the two leaflets. These effects are smallest for the longest WALP tested, and increase with increasing WALP concentration. Thus, our simulations explain the experimental observation that WALPs induce macroscopic domains in otherwise nanodomain-forming lipid-only mixtures (unpublished). Since the cell plasma membrane contains a large fraction of transmembrane proteins, these findings link the behavior of lipid-only model membranes in vitro to phase behavior in vivo.

Lipid Raft Size and Lipid Mobility in Non-raft Domains Increase during Aging and Are Exacerbated in APP/PS1 Mice Model of Alzheimer's Disease. Predictions from an Agent-Based Mathematical Model

A connection between lipid rafts and Alzheimer's disease has been studied during the last decades. Mathematical modeling approaches have recently been used to correlate the effects of lipid composition changes in the physicochemical properties of raft-like membranes. Here we propose an agent based model to assess the effect of lipid changes in lipid rafts on the evolution and progression of Alzheimer's disease using lipid profile data obtained in an established model of familial Alzheimer's disease. We have observed that lipid raft size and lipid mobility in non-raft domains are two main factors that increase during age and are accelerated in the transgenic Alzheimer's disease mouse model. The consequences of these changes are discussed in the context of neurotoxic amyloid β production. Our agent based model predicts that increasing sterols (mainly cholesterol) and long-chain polyunsaturated fatty acids (LCPUFA) (mainly DHA, docosahexaenoic acid) proportions in the membrane composition might delay the onset and progression of the disease.

Force Field Development for Lipid Membrane Simulations

With the rapid development of computer power and wide availability of modelling software computer simulations of realistic models of lipid membranes, including their interactions with various molecular species, polypeptides and membrane proteins have become feasible for many research groups. The crucial issue of the reliability of such simulations is the quality of the force field, and many efforts, especially in the latest several years, have been devoted to parametrization and optimization of the force fields for biomembrane modelling. In this review, we give account of the recent development in this area, covering different classes of force fields, principles of the force field parametrization, comparison of the force fields, and their experimental validation. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Measuring the composition-curvature coupling in binary lipid membranes by computer simulations

The coupling between local composition fluctuations in binary lipid membranes and curvature affects the lateral membrane structure. We propose an efficient method to compute the composition-curvature coupling in molecular simulations and apply it to two coarse-grained membrane models-a minimal, implicit-solvent model and the MARTINI model. Both the weak-curvature behavior that is typical for thermal fluctuations of planar bilayer membranes as well as the strong-curvature regime corresponding to narrow cylindrical membrane tubes are studied by molecular dynamics simulation. The simulation results are analyzed by using a phenomenological model of the thermodynamics of curved, mixed bilayer membranes that accounts for the change of the monolayer area upon bending. Additionally the role of thermodynamic characteristics such as the incompatibility between the two lipid species and asymmetry of composition are investigated.

Multiscale modeling of four-component lipid mixtures: domain composition, size, alignment, and properties of the phase interface

Simplified lipid mixtures are often used to model the complex behavior of the cell plasma membrane. Indeed, as few as four components-a high-melting lipid, a nandomain-inducing low-melting lipid, a macrodomain-inducing low-melting lipid, and cholesterol (chol)-can give rise to a wide range of domain sizes and patterns that are highly sensitive to lipid compositions. Although these systems are studied extensively with experiments, the molecular-level details governing their phase behavior are not yet known. We address this issue by using molecular dynamics simulations to analyze how phase separation evolves in a four-component system as it transitions from small domains to large domains. To do so, we fix concentrations of the high-melting lipid 16:0,16:0-phosphatidylcholine (DPPC) and chol, and incrementally replace the nanodomain-inducing low-melting lipid 16:0,18:2-PC (PUPC) by the macrodomain-inducing low-melting lipid 18:2,18:2-PC (DUPC). Coarse-grained simulations of this four-component system reveal that lipid demixing increases as the amount of DUPC increases. Additionally, we find that domain size and interleaflet alignment change sharply over a narrow range of replacement of PUPC by DUPC, indicating that intraleaflet and interleaflet behaviors are coupled. Corresponding united atom simulations show that only lipids within ∼2 nm of the phase interface are significantly perturbed regardless of domain composition or size. Thus, whereas the fraction of interface-perturbed lipids is negligible for large domains, it is significant for smaller ones. Together, these results reveal characteristic traits of bilayer thermodynamic behavior in four-component mixtures, and provide a baseline for investigation of the effects of proteins and other lipids on membrane phase properties.

Modeling lipid raft domains containing a mono-unsaturated phosphatidylethanolamine species

An advanced coarse-grained model for “atypical” lipid rafts was built and validated to be employed in studies of membrane-protein interactions.

Computer simulations of phase separation in lipid bilayers and monolayers

Studying phase coexistence in lipid bilayers and monolayers is important for understanding lipid-lipid interactions underlying lateral organization in biological membranes. Computer simulations follow experimental approaches and use model lipid mixtures of simplified composition. Atomistic simulations give detailed information on the specificity of intermolecular interactions, while coarse-grained simulations achieve large time and length scales and provide a bridge towards state-of-the-art experimental techniques. Computer simulations allow characterizing the structure and composition of domains during phase transformations at Angstrom and picosecond resolution, and bring new insights into phase behavior of lipid membranes.

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

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

Prediction of the dependence of the line tension on the composition of linactants and the temperature in phase separated membranes

We calculate the line tension between domains in phase separated, ternary membranes that comprise line active molecules (linactants) that tend to increase the compatibility of the two phase separating species. The predicted line tension, which depends explicitly on the linactant composition and temperature, is shown to decrease significantly as the fraction of linactants in the membrane increases toward a Lifshitz point, above which the membrane phase separates into a modulated phase. We predict regimes of zero line tension at temperatures close to the mixing transition and clarify the two different ways in which the line tension can be reduced: (1) The linactants uniformly distribute in the system and reduce the compositional mismatch between the two bulk domains. (2) The linactants accumulate at the interface with a preferred orientation. Both of these mechanisms have been observed in recent experiments and simulations. The second one is unique to line active molecules, and our work shows that it is increasingly important at large fraction of linactants and is necessary for the emergence of a regime of zero line tension. The methodology is based on the ternary mixture model proposed by Palmieri and Safran [Palmieri, B.; Safran, S. A. Langmuir 2013, 29, 5246], and the line tension is calculated via variationally derived, self-consistent profiles for the local variation of composition and linactant orientation in the interface region.

Line active molecules promote inhomogeneous structures in membranes: theory, simulations and experiments

We review recent theoretical efforts that predict how line-active molecules can promote lateral heterogeneities (or domains) in model membranes. This fundamental understanding may be relevant to membrane composition in living cells, where it is thought that small domains, called lipid rafts, are necessary for the cells to be functional. The theoretical work reviewed here ranges in scale from coarse grained continuum models to nearly atomistic models. The effect of line active molecules on domain sizes and shapes in the phase separated regime or on fluctuation length scales and lifetimes in the single phase, mixed regime, of the membrane is discussed. Recent experimental studies on model membranes that include line active molecules are also presented together with some comparisons with the theoretical predictions.

Interactions between fengycin and model bilayers quantified by coarse-grained molecular dynamics

Bacteria, particularly of the genus Bacillus, produce a wide variety of antifungal compounds. They act by affecting the lipid bilayers of fungal membranes, causing curvature-induced strain and eventual permeabilization. One class of these, known as fengycins, has been commercialized for treating agricultural infections and shows some promise as a possible antifungal pharmaceutical. Understanding the mechanism by which fengycins damage lipid bilayers could prove useful to the future development of related antifungal treatments. In this work, we present multi-microsecond-long simulations of fengycin interacting with different lipid bilayer systems. We see fengycin aggregation and uncover a clear aggregation pattern that is partially influenced by bilayer composition. We also quantify some local bilayer perturbations caused by fengycin binding, including curvature of the lipid bilayer and local electrostatic-driven reorganization.

Pairing of cholesterol with oxidized phospholipid species in lipid bilayers

We claim that (1) cholesterol protects bilayers from disruption caused by lipid oxidation by sequestering conical shaped oxidized lipid species such as 1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine (PZPC) away from phospholipid, because cholesterol and the oxidized lipid have complementary shapes and (2) mixtures of cholesterol and oxidized lipids can self-assemble into bilayers much like lysolipid–cholesterol mixtures. The evidence for bilayer protection comes from molecular dynamics (MD) simulations and dynamic light scattering (DLS) measurements. Unimodal size distributions of extruded vesicles (LUVETs) made up of a mixture of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and PZPC containing high amounts of PZPC are only obtained when cholesterol is present in high concentrations. In simulations, bilayers containing high amounts of PZPC become porous, unless cholesterol is also present. The protective effect of cholesterol on oxidized lipids has been observed previously using electron paramagnetic resonance (EPR) and electron microscopy imaging of vesicles. The evidence for the pairing of cholesterol and PZPC comes mainly from correlated 2-D density and thickness plots from simulations, which show that these two molecules co-localize in bilayers. Further evidence that the two molecules can cohabitate comes from self-assembly simulations, where we show that cholesterol-oxidized lipid mixtures can form lamellar phases at specific concentrations, reminiscent of lysolipid–cholesterol mixtures. The additivity of the packing parameters of cholesterol and PZPC explains their cohabitation in a planar bilayer. Oxidized lipids are ubiquitously present in significant amounts in high- and low-density lipoprotein (HDL and LDL) particles, diseased tissues, and in model phospholipid mixtures containing polyunsaturated lipids. Therefore, our hypothesis has important consequences for cellular cholesterol trafficking; diseases related to oxidized lipids, and to biophysical studies of phase behaviour of cholesterol-containing phospholipid mixtures.

Hybrid lipids increase nanoscale fluctuation lifetimes in mixed membranes

A recently proposed ternary mixture model is used to predict fluctuation domain lifetimes in the one phase region. The membrane is made of saturated, unsaturated, and hybrid lipids that have one saturated and one unsaturated hydrocarbon chain. The hybrid lipid is a natural linactant which can reduce the packing incompatibility between saturated and unsaturated lipids. The fluctuation lifetimes are predicted as a function of the hybrid lipid fraction and the fluctuation domain size. These lifetimes can be increased by up to three orders of magnitude compared to the case of no hybrids. With hybrid, small length scale fluctuations have sizable amplitudes even close to the critical temperature and, hence, benefit from enhanced critical slowing down. The increase in lifetime is particularly important for nanometer scale fluctuation domains where the hybrid orientation and the other lipids composition are highly coupled.