A molecular-dynamics study of lipid bilayers: effects of the hydrocarbon chain length on permeability

In this paper, we investigate the effects of the hydrocarbon chain length of lipid molecules on the permeation process of small molecules through lipid bilayers. We perform molecular-dynamics simulations using three kinds of lipid molecules with different chain length: dilauroylphosphatidylcholine, dimyristoylphosphatidylcholine, and dipalmiltoylphosphatidylcholine. Free-energy profiles of O2, CO, NO, and water molecules are calculated by means of the cavity insertion Widom method and the probability ratio method. We show that the lipid membrane with longer chains has a larger and wider energy barrier. The local diffusion coefficients of water across the bilayers are also calculated by the force autocorrelation function method and the velocity autocorrelation function method. The local diffusion coefficients in the bilayers are not altered significantly by the chain length. We estimate the permeability coefficients of water across the three membranes according to the solubility-diffusion model; we find that the water permeability decreases modestly with increasing chain length of the lipid molecules.     

Stearic acid spin labels in lipid bilayers: insight through atomistic simulations

Spin-labeled stearic acid species are commonly used for electron paramagnetic resonance (EPR) studies of cell membranes to investigate phase transitions, fluidity, and other physical properties. In this paper, we use large-scale molecular dynamics simulations to investigate the position and behavior of nitroxide spin labels attached to stearic acid molecules in dipalmitoylphosphatidylcholine (DPPC) bilayers. The results of these studies are potentially very important for the interpretation of EPR spectra, which rely on assumptions about the position of the label in the membrane. Additionally, we investigate the effect of chirality and ionization of the carboxyl group of the label. For a non-ionized species, we observe that spin-label molecules are even able to make flip-flop transitions between the leaflets of the bilayer. Such transitions have been previously observed only in very rare cases in molecular simulations.     

Controlling the charge and organization of anionic lipid bilayers: effect of monovalent and divalent ions

It is shown that the organization of lipid bilayers containing phosphatidic acid (PA) and phosphatidlycholine (PC) can be controlled by altering the monovalent and divalent ion concentrations. At high pH and/or calcium concentration, 1:1 Ca(2+)-PA(2-) complexes form; these complexes demix, and PA-rich and PC-rich regions are observable with epifluorescence microscopy. The results are compared with predictions from electrostatic theory. It is noted that the complex formation correlates in a roughly linear fashion with the monovalent/divalent ion ratio, a parameter that cells adjust.     

Fusion of lipid vesicles with planar lipid bilayers induced by a combination of peptides

We studied the peptide-induced membrane fusion process between small unilamellar vesicles (SUVs) and supported planar bilayers (SPBs) with the aim of developing a method for incorporating membrane components into SPBs. As fusogenic peptides, two analogues of the N-terminal region of an influenza membrane fusion protein hemaggulutinin, anionic E5 and cationic K5, were synthesized, and the membrane fusion was investigated using SPB and SUVs composed of phosphatidylcholine from egg yolk (EggPC). We directly visualized the process of lipid transfer from SUVs to SPB by total internal reflection fluorescence (TIRF) microscopy. The transfer of fluorescent lipids was effectively induced only by the combination of two peptides. The TIRF microscopy observations of single SUV fusion events also revealed that lipid membranes from SUV could completely fuse into the SPB. However, the presence of single peptide (either E5 or K5) rather inhibited the lipid transfer, presumably due to the electrostatic repulsion between SUVs and SPB. The opposite effects induced by the peptides indicate the possibility for a designed application of two peptides as a means to control the membrane fusion spatially and temporally.     

Anomalous diffusion in supported lipid bilayers induced by oxide surface nanostructures

Hierarchic structure and anomalous diffusion on submicrometer scale were introduced into an artificial cell membrane, and the spatiotemporal dependence of lipid diffusion was visualized on nanostructured oxide surfaces. We observed the lipid diffusion in supported lipid bilayers (SLBs) on step-and-terrace TiO(2)(100) and amorphous SiO(2)/Si surfaces by single molecule tracking (SMT) method. The SMT at the time resolution of 500 μs to 30 ms achieved observation of the lipid diffusion over the spatial and temporal ranges of 100 nm/millisecond to 1 μm/second. The temporal dependence of the diffusion coefficient in the SLB on TiO(2)(100) showed that the crossover from anomalous diffusion to random diffusion occurred around 10 ms. The surface fine architecture on substrates will be applicable to induce hierarchic structures on the order of 100 nm or less, which correspond to the microcompartment size in vivo.     

Pore formation coupled to ion transport through lipid membranes as induced by transmembrane ionic charge imbalance: atomistic molecular dynamics study

We have employed atomic-scale molecular dynamics simulations to address ion transport through transient water pores in phospholipid membranes. The formation of a water pore is induced by a transmembrane ionic charge imbalance, which gives rise to a significant potential difference across the membrane. The subsequent transport of ions through the pore discharges the transmembrane potential and makes the water pore metastable, leading eventually to its sealing. The findings highlight the importance of ionic charge fluctuations in spontaneous pore formation and their role in ion leakage through protein-free lipid membranes.     

On possible microscopic origins of the swelling of neutral lipid bilayers induced by simple salts

It was recently suggested that the swelling of neutral multilipid bilayers upon addition of a salt can be simply explained only by the electrolyte screening of the van der Waals attractions, while assuming that the hydration force and the repulsion due to thermal undulations of membranes are unaffected by the salt. While we agree that the screening of the van der Waals interactions plays a role, we suggest that the increase in the hydration force upon addition of a salt has also to be taken into account. In a statistical model, which accounts for the membrane undulations, parameters could be found to explain the multibilayer swelling even when the van der Waals attraction is considered unaffected by the electrolyte screening. These results point out that the decrease by a factor of three of the Hamaker constant upon addition of a salt, suggested recently to be responsible for the swelling of neutral multilipid bilayers, is perhaps too large, and a smaller decrease in Hamaker constant, coupled with the above mentioned effects might explain the swelling.     

A study of reconstituted anion channels using lipid bilayers

A chloride channel from impermeant sarcoplasmic reticulum (SR) was embedded in a planar lipid bilayer (BLM) and its electrical properties determined. Studies using ER-derived vesicles fused with BLMs have shown that they are permeable to Na⁺, K⁺, choline and Cl⁻ but less permeable to Ca²⁺ and Mg²⁺. Though highly permeable to K⁺, the liver ER membrane has been postulated to a lack of an efficient ion-conducting structure for K⁺ channel in the SR. The present study was undertaken with the aim to look at the anionic, Ca²⁺ and K⁺ permeability pathways present in the ER membrane. Our reconstituted system exhibits considerable anionic permeability following the sequence: SCN⁻>I⁻>Br⁻Cl⁻>gluconate. The findings suggest the chloride channels have low field-strength sites. It can be pharmacologically dissected to Zn²⁺-sensitive and DIDS-sensitive types. The gating of the channel is weakly voltage-dependent and at higher positive or negative voltages the channel prefers the low sub-conductance states.     

Thermodynamic study of benzocaine insertion into different lipid bilayers

Despite the general consensus concerning the role played by sodium channels in the molecular mechanism of local anesthetics, the potency of anaesthetic drugs also seems to be related with their solubility in lipid bilayers. In this respect, this work represents a thermodynamic study of benzocaine insertion into lipid bilayers of different compositions by means of molecular dynamics simulation. Thus, the free energy profiles associated with benzocaine insertion into symmetric lipid bilayers composed of different proportions of dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine were studied. From the simulation results, a maximum in the free energy (ΔG) profile was measured in the region of the lipid/solution interface. This free energy barrier appears to be very much dependent on the lipid composition of the membrane. On the other hand, the minimum free energy (ΔG) within the bilayer remained almost independent of the lipid composition of the bilayer. By repeating the study at different temperatures, it was seen how the spontaneity of benzocaine insertion into the lipid bilayer is due to an increase in the entropy associated with the process.     

Flexoelectricity of lipid bilayers

Abstract

The direct flexoeffect in single lipid bilayers in the form of black lipid membranes has been investigated experimentally by the oscillating pressure technique in the regime of voltage measurement. Black lipid membranes of various composition have been studied in order to check the effect of lipid surface charge on the curvature-electric response and its frequency dependence; these include egg yolk lecithin (low negative charge); egg yolk lecithin plus phosphatidyl serine (high negative charge); egg yolk lecithin with surface adsorbed ions of uranyl acetate (high positive charge). An increase of the response has been found by increasing the surface charge and a reversal of the sign of the flexoelectric coefficient from positive to negative has been obtained by changing the sign of the surface charge from negative to positive. These results underline the leading role of the contribution of the surface charge to the flexoelectricity of lyotropics. Their theoretical interpretation provides further insight into the molecular mechanism of this phenomenon.     

Interactions of lipid bilayers with supports: a coarse-grained molecular simulation study

The study of lipid structure and phase behavior at the nanoscale is of utmost importance due to implications in understanding the role of the lipids in biochemical membrane processes. Supported lipid bilayers play a key role in understanding real biological systems, but they are vastly underrepresented in computational studies. In this paper, we discuss molecular dynamics simulations of supported lipid bilayers using a coarse-grained model. We first focus on the technical implications of modeling solid supports for biomembrane simulations. We then describe noticeable influences of the support on the systems. We are able to demonstrate that the bilayer system behavior changes when supported by a hydrophilic surface. We find that the thickness of the water layer between the support and the bilayer (the inner-water region in the latter part of this paper) adapts through water permeation on the microsecond time scale. Additionally, we discuss how different surface topologies affect the bilayer. Finally, we point out the differences between the two leaflets induced by the support.     

Disruption of supported lipid bilayers by semihydrophobic nanoparticles

Understanding the interaction between functional nanoparticles and cell membranes is critical to use nanomaterials for broad biomedical applications with minimal cytotoxicity. In this work, we have investigated the effect of adsorbed semihydrophobic nanoparticles (NPs) on the dynamics and morphology of model cell membranes. We have systematically varied the degree of surface hydrophobicity of carboxyl end-functionalized polystyrene NPs of varied size in buffer solutions with varied ionic strength. It is observed that semihydrophobic NPs can readily adsorb on neutral SLBs and drag lipids from SLBs to NP surfaces. Above a critical NP concentration, the disruption of SLBs is observed, accompanied with the formation and rapid growth of lipid-poor regions on NP-adsorbed SLBs. In the study of the effect of solution ionic strength on NP surface hydrophobic degree and the growth of lipid-poor regions, we have concluded that the hydrophobic interaction enhanced by screened electrostatic interaction underlies the envelopment of NPs by lipids that are attracted from SLBs to the surface of NPs or their aggregates. Hence, the formation and growth of lipid-poor regions, or vaguely referred as "pores" or "holes" in the literature, can be controlled by NP concentration, size, and surface hydrophobicity, which is critical to design functional nanomaterials for effective nanomedicine while minimizing possible cytotoxicity.     

PEG-covered lipid surfaces: bilayers and monolayers

In this review paper we survey the ways in which various micropipet techniques have been used to study the mechanochemical and interactive features of lipid bilayer vesicles and monolayer-coated gas bubbles. Special emphasis will be made on characterizing the barrier properties of grafted PEG layers and how a hierarchical approach that uses a short barrier and extended ligand allows us to start to mimic nature's own solution to the problem of ubiquitous repulsion and specific attraction. The information gained from such studies not only characterizes the membrane and other lipid surfaces and their intersurface interactions from a fundamental materials science perspective, but also provides essential materials property data that are required for the successful design and deployment of lipid-based carriers and other capsules in applications involving this so-called ‘stealthy’ surface.     

Preparation of aqueous gel beads coated by lipid bilayers

Novel giant liposome microcapsules have been fabricated based on aqueous gel cores encapsulated with a lipid bilayer. The method involves templating of lipid-stabilised water-in-oil emulsions after gelling the aqueous phase with a suitable hydrocolloid.     

A simulation study on nanoscale holes generated by gold nanoparticles on negative lipid bilayers

Understanding the interactions of gold nanoparticles (AuNPs) with cellular compartments, especially cell membranes, is of fundamental importance in obtaining their control in biomedical applications. An effort is made in this paper to investigate the interactions of 2.2 nm core AuNPs with negative model bilayer membranes by coarse-grained (CG) molecular dynamics (MD) simulation. The CG model of lipid bilayer was taken from Marrink et al. ( J. Phys. Chem. B 2004, 108, 750-760 ), whereas the CG AuNPs model was developed on the basis of both atomistic MD simulations and experimental data. It was found that AuNPs functionalized with cationic ligands penetrated into the negative bilayer membranes and generated significant disruptions on bilayers. The lipids surrounding the nanoparticle were highly disordered and the bulk surface of the bilayer exhibits some defective areas. Most importantly, it is observed that a nanoscale hole can be formed and expanded spontaneously on the peripheral regions of the 20 × 20 nm bilayer. The expansion of the hole is on the time scale of hundreds of nanosceonds. The fully expanded hole had a radius of ～5.5 nm and could transport water molecules at a rate of up to ～1100 molecule/ns. However holes could not be formed on a larger bilayer (28 × 28 nm). The factors that can eliminate hole formation on the bilayer also include the decrease of cationic lignads on the AuNP, the reduction of negative lipids in the bilayer, the release of bilayer surface tension, the lowering of temperature, and the addition of a high concentration of salt. The results suggest that a hole can only be formed on living cell membranes under extreme conditions.     

Solvent and lipid dynamics of hydrated lipid bilayers by incoherent quasielastic neutron scattering

The microscopic dynamics of the planar, multilamellar lipid bilayer system 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) has been investigated using quasielastic neutron scattering. The DMPC was hydrated to a level corresponding to approximately nine water molecules per lipid molecule. Selective deuteration has been used to separately extract the dynamics of the water, the acyl chains, and the polar head groups from the strong incoherent scattering of the remaining hydrogen atoms. Furthermore, the motions parallel and perpendicular to the bilayers were probed by using two different sample orientations relative to the incident neutron beam. For both sample orientations, the results showed an onset of water motions at 260 K on the experimental time scale of about 100 ps. From lack of wave-vector dependence of the onset temperature for water motions, it is evident that the observed water dynamics is of mainly rotational character at such low temperatures. At 290 K, i.e., slightly below the gel-to-liquid transition around 295 K, the nature of the water dynamics had changed to a more translational character, well described by a jump-diffusion model. On the limited experimental time and length (about 10 A) scales, this jump-diffusion process was isotropic, despite the very anisotropic system. The acyl chains exhibited a weak onset of anharmonic motions already at 120 K, probably due to conformational changes (trans-gauche and/or syn-anti) in the plane of the lipid bilayers. Other anharmonic motions were not observed on the experimental time scale until temperature had been reached above the gel-to-liquid transition around 295 K, where the acyl chains start to show more substantial motions.     

Computer simulation study of intermolecular voids in unsaturated phosphatidylcholine lipid bilayers

Computer simulation of the liquid crystalline phase of five different hydrated unsaturated phosphadidylcholine (PC) lipid bilayers, i.e., membranes built up by 18:0/18:1omega9cis PC, 18:0/18:2omega6cis PC, 18:0/18:3omega3cis PC, 18:0/20:4omega6cis PC, and 18:0/22:6omega3cis PC molecules have been performed on the isothermal-isobaric ensemble at 1 atm and 303 K. (The notation n:domegapcis specifies the lipid tails: n refers to the total number of carbon atoms in the chain, d is the number of the methylene-interrupted double bonds, p denotes the number of carbons between the chain terminal CH(3) group and the nearest double bond, and cis refers to the conformation around the double bonds.) The characteristics of the free volume in these systems have been analyzed by means of a generalized version of the Voronoi-Delaunay method [M. G. Alinchenko et al., J. Phys. Chem. B 108, 19056 (2004)]. As a reference system, the hydrated bilayer of the saturated 14:014:0 PC molecules (dimyristoylphosphatidylcholine) has also been analyzed. It has been found that the profiles of the fraction of the free volume across the membrane exhibit a rather complex pattern. This fine structure of the free volume fraction profiles can be interpreted by dividing the membrane into three separate major zones (i.e., zones of the aqueous, polar, and apolar parts of the membrane) and defining five subzones within these zones according to the average position of various atomic groups in the membrane. The fraction of the free volume in the middle of the membrane is found to increase with increasing unsaturation of the sn-2 chain of the lipid molecule. This is due to the fact that with increasing number of methylene-interrupted double bonds the lipid tails become more flexible, and hence they do not extend to the middle of the membrane. It is found that there are no broad enough preformed channels in the bilayers through which small penetrants, such as water molecules, can readily go through; however, the existing channels can largely facilitate the permeation of these molecules.