Phase behavior and dynamic heterogeneities in lipids: A coarse-grained simulation study of DPPC–DPPE mixtures

Quantification of spatio-temporal scales of dynamical heterogeneity of water near lipid membranes above supercooling

A hydrated 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) lipid membrane is investigated using an all atom molecular dynamics simulation at 308 K to determine the physical sources of universal slow relaxations of hydration layers and length-scale of the spatially heterogeneous dynamics. Continuously residing interface water (IW) molecules hydrogen bonded to different moieties of lipid heads in the membrane are identified. The non-Gaussian parameters of all classes of IW molecules show a cross-over from cage vibration to translational diffusion. A significant non-Gaussianity is observed for the IW molecules exhibiting large length correlations in translational van Hove functions. Two time-scales for the ballistic motions and hopping transitions are obtained from the self intermediate scattering functions of the IW molecules with an additional long relaxation, which disappears for bulk water. The long relaxation time-scales for the IW molecules obtained from the self intermediate scattering functions are in good accordance with the hydrogen bond relaxation time-scales irrespective of the nature of the chemical confinement and the confinement lifetime. Employing a block analysis approach, the length-scale of dynamical heterogeneities is captured from a transition from non-Gaussianity to Gaussianity in van Hove correlation functions of the IW molecules. The heterogeneity length-scale is comparable to the wave-length of the small and weak undulations of the membrane calculated by Fourier transforms of lipid tilts. This opens up a new avenue towards a possible correlation between heterogeneity length-scale and membrane curvature more significant for rippled membranes. Thus, our analyses provide a measure towards the spatio-temporal scale of dynamical heterogeneity of confined water near membranes.

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.

Bilayer structure and lipid dynamics in a model stratum corneum with oleic acid

The stratum corneum is the uppermost layer of the skin and acts as a barrier to keep out contaminants and retain moisture. Understanding the molecular structure and behavior of this layer will provide guidance for optimizing its biological function. In this study we use a model mixture comprised of equimolar portions of ceramide NS (24:0), lignoceric acid, and cholesterol to model the effect of the addition of small amounts of oleic acid to the bilayer at 300 and 340 K. Five systems at each temperature have been simulated with concentrations between 0 and 0.1 mol % oleic acid. Our major finding is that subdiffusive behavior over the 200 ns time scale is evident in systems at 340 K, with cholesterol diffusion being enhanced with increased oleic acid. Importantly, cholesterol and other species diffuse faster when radial densities indicate nearest neighbors include more cholesterol. We also find that, with the addition of oleic acid, the bilayer midplane and interfacial densities are reduced and there is a 3% decrease in total thickness occurring mostly near the hydrophilic interface at 300 K with reduced overall density at 340 K. Increased interdigitation occurs independent of oleic acid with a temperature increase. Slight ordering of the long non-hydroxy fatty acid of the ceramide occurs near the hydrophilic interface as a function of the oleic acid concentration, but no significant impact on hydrogen bonding is seen in the chosen oleic acid concentrations.

Lateral heterogeneities in supported bilayers from pure and mixed phosphatidylethanolamine demonstrating hydrogen bonding capacity

The phase behavior and lateral organization of saturated phosphatidylethanolamine (PE) and phosphatidylcholine (PC) bilayers were investigated using atomic force microscopy (AFM) and force-volume (FV) imaging for both pure and two component mixed layers. The results demonstrated the existence of unexpected segregated domains in pure PE membranes at temperatures well below the transition temperature (T(m)) of the component phospholipid. These domains were of low mechanical stability and lacked the capacity for hydrogen bonding between lipid headgroups. Temperature dependent studies for different PC/PE ratios using AFM also demonstrated the mixing of these phospholipid bilayers to exhibit only a single gel to liquid transition temperature. Further work performed using FV imaging and chemically modified probes established that no lipid segregation exists at the PC/PE ratios investigated.

Dynamics of vesicle formation from lipid droplets: mechanism and controllability

A coarse-grained model developed by Marrink et al. [J. Phys. Chem. B 111, 7812 (2007)] is applied to investigate vesiculation of lipid [dipalmitoylphosphatidylcholine (DPPC)] droplets in water. Three kinds of morphologies of micelles are found with increasing lipid droplet size. When the initial lipid droplet is smaller, the equilibrium structure of the droplet is a spherical micelle. When the initial lipid droplet is larger, the lipid ball starts to transform into a disk micelle or vesicle. The mechanism of vesicle formation from a lipid ball is analyzed from the self-assembly of DPPC on the molecular level, and the morphological transition from disk to vesicle with increasing droplet size is demonstrated. Importantly, we discover that the transition point is not very sharp, and for a fixed-size lipid ball, the disk and vesicle appear with certain probabilities. The splitting phenomenon, i.e., the formation of a disk/vesicle structure from a lipid droplet, is explained by applying a hybrid model of the Helfrich membrane theory. The elastic module of the DPPC bilayer and the smallest size of a lipid droplet for certain formation of a vesicle are successfully predicted.

Coarse-grained modeling of lipids

Molecular modeling of phospholipids on many scales has progressed significantly over the last years. Here we review several membrane models on intermediate to large length scales restricting ourselves to particle based coarse-grained models with implicit and explicit solvent. We explain similarities and differences as well as their connection to experiments and fine-grained models. We neglect any field descriptions on larger scales. We discuss then a few examples where we focus on studies of lipid phase behavior as well as supported lipid bilayers as these examples can only be meaningfully studied using large-scale models to date.

The influence of size, lipid composition and bilayer fluidity of cationic liposomes on the transfection efficiency of nanolipoplexes

Among non-viral vectors, cationic liposomes are the most promising carriers in gene delivery. But the most critical issue about their application is their low transfection efficiency compared to viral vectors. In this study, we tried to make a comparison between transfection efficiency of different liposomal formulations and to investigate the effect of membrane fluidity and other physical properties of liposomes and lipoplexes such as size and charge ratio on the transfection efficiency in in vitro environment. Different gene delivery systems were developed by using liposomes composed of 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) or 3-beta-[N-(N'N'-dimethylaminoethane)-carbamoyl] cholesterol (DC-CHOL) in combination with other lipids including 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), egg L-alpha-phosphatidylcholine (EPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE). These multilamellar vesicle (MLV) liposomes were extruded through 100 nm polycarbonate filters to produce small unilamellar vesicles (SUVs). Transfection activity of these lipoplexes in Neuro2A cells was tested using pRL-CMV encoding Renilla luciferase. We could not establish any direct correlation between high fluid membranes and high transfection efficiency because DOTAP:DPPE had a better result than DOTAP:DOPE while DC-CHOL:DOPE was more successful in gene transfer than DC-CHOL:DPPE. It was revealed that the use of these two helper lipids with different Tm (DPPE: 64 degrees C and DOPE: -11 degrees C) along with DOTAP increased transfection efficiency but formulation of these phospholipids with DC-CHOL was led to a significant reduction in transfection activity. Generally, DOTAP:DPPE, DC-CHOL:DOPE and DOTAP:DOPE:DPPE formulations showed the highest transfection activity. The results of this study showed that, in designing of liposome based non-viral vectors, different parameters such as size, lipid composition and the use of helper lipid should be considered.

Phase and mixing behavior in two-component lipid bilayers: a molecular dynamics study in DLPC/DSPC mixtures

Phase and mixing behavior of dilauroylphosphatidylcholine (DLPC)/distearoylphosphatidylcholine (DSPC) lipid mixtures are studied by molecular dynamics simulations with use of a coarse-grained model over a wide range of concentrations. The results reveal that phase transformations from the fluid to the gel state can be followed over a microsecond time scale. The changes in structure suggest regions of phase coexistence allowing us to outline the entire phase diagram for this lipid mixture using a molecular based model. We show that simulations yield good agreement with the experimental phase diagram. We also address the effect of macroscopic phase separation on the determination of the transition temperature, different leaflet composition, and finite size effects. This study may have implications on lateral membrane organization and the associated processes dependent on these membrane regions on different time and length scales.