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1.
Conventional molecular dynamics (MD) simulations are seriously limited by the slow rate of diffusive mixing in their ability to predict lateral distributions of different lipid types within mixed-lipid bilayers using atomistic models. A method to overcome this limitation, using configuration-bias Monte Carlo (MC) "mutation" moves to transform lipids from one type to another in dynamic equilibrium, is demonstrated in binary fluid-phase mixtures of lipids whose tails differ in length by four carbons. The hybrid MC-MD method operates within a semigrand canonical ensemble, so that an equilibrium composition of the mixture is determined by a constant difference in chemical potential (Delta(mu)) chosen for the components. Within several nanoseconds, bilayer structures initiated as pure dipalmitoyl phosphatidylcholine (DPPC) or pure dilauroyl phosphatidylcholine (DLPC) converge to a common composition and structure in independent simulations conducted at the same Delta(mu). Trends in bilayer thickness, area per lipid, density distributions across the bilayer, and order parameters have been investigated at three mixture compositions and compared with results from the pure bilayers at 323 K. The mixtures showed a moderate increase in DPPC acyl tail sites crossing the bilayer midplane relative to pure DPPC. Correlations between lateral positions of the two lipid types within or across the bilayer were found to be weak or absent. While the lateral distribution is consistent with nearly ideal mixing, the dependence of composition on Delta(mu) indicates a positive excess free energy of mixing.  相似文献   

2.
This paper records what is believed to be the first evidence for the reorganization of the liquid-ordered phase by ethanol. Specifically, ethanol has been found to significantly enhance sterol-phospholipid association in liquid-ordered bilayers derived from 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) plus cholesterol and also 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) plus cholesterol. The evidence for such reorganization comes from a series of nearest-neighbor recognition (NNR) experiments that have been carried out, where low concentrations of equilibrating lipid dimers (i.e., "reporter molecules") have been used to detect changes in the phase composition of host membranes made from varying mixtures of DPPC/cholesterol, and also DSPC/cholesterol, in the presence and in the absence of ethanol. These findings have important biological implications, which are briefly discussed.  相似文献   

3.
We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane, where the individual lipid and sterol molecules are described by pointlike particles. The effective intermolecular interactions used in the model are systematically derived from detailed atomic-scale molecular dynamics simulations using the Inverse Monte Carlo technique, which guarantees that the radial distribution properties of the CG model are consistent with those given by the corresponding atomistic system. We find that the coarse-grained model for the DPPC/cholesterol bilayer is substantially more efficient than atomistic models, providing a speedup of approximately eight orders of magnitude. The results are in favor of formation of cholesterol-rich and cholesterol-poor domains at intermediate cholesterol concentrations, in agreement with the experimental phase diagram of the system. We also explore the limits of the coarse-grained model, and discuss the general validity and applicability of the present approach.  相似文献   

4.
In order to investigate experimentally inaccessible, molecular-level detail regarding interleaflet interaction in membranes, we have run an extensive series of coarse-grained molecular dynamics simulations of phase separated lipid bilayers. The simulations are motivated by differences in lipid and cholesterol composition in the inner and outer leaflets of biological membranes. Over the past several years, this phenomenon has inspired a series of experiments in model membrane systems which have explored the effects of lipid compositional asymmetry in the two leaflets. The simulations are directed at understanding one potential consequence of compositional asymmetry, that being regions of bilayers where liquid-ordered (L(o)) domains in one leaflet are opposite liquid-disordered (L(d)) domains in the other leaflet (phase asymmetry). The simulated bilayers are of two sorts: 1) Compositionally symmetric leaflets where each of the two leaflets contains an identical, phase separated (L(o)/L(d)) mixture of cholesterol, saturated and unsaturated phospholipid; and 2) Compositionally asymmetric leaflets, where one leaflet contains a phase separated (L(o)/L(d)) mixture while the other contains only unsaturated lipid, which on its own would be in the L(d) phase. In addition, we have run simulations where the lengths of the saturated lipid chains as well as the mole ratios of the three lipid components are varied. Collectively, we report on three types of interleaflet coupling within a bilayer. First, we show the effects of compositional asymmetry on acyl chain tilt and order, lipid rotational dynamics, and lateral diffusion in regions of leaflets that are opposite L(o) domains. Second, we show substantial effects of compositional asymmetry on local bilayer curvature, with the conclusion that phase separated leaflets resist curvature, while inducing large degrees of curvature in an opposing L(d) leaflet. Finally, in compositionally symmetric, phase separated bilayers, we find phase asymmetry (domain antiregistration) between the two leaflets occurs as a consequence of mismatched acyl chain-lengths in the saturated and unsaturated lipids.  相似文献   

5.
The influence of selected perfluorinated compounds (PFCs), perfluorooctanoic acid (PFOA) or perfluorooctanesulfonic acid (PFOS), on the structure and organization of lipid membranes was investigated using model membranes-lipid monolayers and bilayers. The simplest model--a lipid monolayer--was studied at the air-water interface using the Langmuir-Blodgett technique with surface pressure and surface potential measurements. Lipid bilayers were characterized by NMR techniques and molecular dynamics simulations. Two phospholipids, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), characterized by different surface properties have been chosen as components of the model membranes. For a DPPC monolayer, a phase transition from the liquid-expanded state to the liquid-condensed state can be observed upon compression at room temperature, while a DMPC monolayer under the same conditions remains in the liquid-expanded state. For each of the two lipids, the presence of both PFOA and PFOS leads to the formation of a more fluidic layer at the air-water interface. Pulsed field gradient NMR measurements of the lateral diffusion coefficient (DL) of DMPC and PFOA in oriented bilayers reveal that, upon addition of PFOA to DMPC bilayers, DL of DMPC decreases for small amounts of PFOA, while larger additions produce an increased DL. The DL values of PFOA were found to be slightly larger than those for DMPC, probably as a consequence of the water solubility of PFOA. Furthermore, 31P and 2H NMR showed that the gel-liquid crystalline phase transition temperature decreased by the addition of PFOA for concentrations of 5 mol % and above, indicating a destabilizing effect of PFOA on the membranes. Deuterium order parameters of deuterated DMPC were found to increase slightly upon increasing the PFOA concentration. The monolayer experiments reveal that PFOS also penetrates slowly into already preformed lipid layers, leading to a change of their properties with time. These experimental observations are in qualitative agreement with the computational results obtained from the molecular dynamics simulations showing a slow migration of PFCs from the surrounding water phase into DPPC and DMPC bilayers.  相似文献   

6.
Computer simulations have been performed for fluids with van der Waals potential, that is, hard spheres with attractive inverse power tails, to determine the equation of state and the excess energy. On the other hand, the first- and second-order perturbative contributions to the energy and the zero- and first-order perturbative contributions to the compressibility factor have been determined too from Monte Carlo simulations performed on the reference hard-sphere system. The aim was to test the reliability of this "exact" perturbation theory. It has been found that the results obtained from the Monte Carlo perturbation theory for these two thermodynamic properties agree well with the direct Monte Carlo simulations. Moreover, it has been found that results from the Barker-Henderson [J. Chem. Phys. 47, 2856 (1967)] perturbation theory are in good agreement with those from the exact perturbation theory.  相似文献   

7.
The effect of hydrophobic alkylated gold nanoparticles (Au NPs) on the phase behavior and structure of Langmuir monolayers of dipalmitoylphosphatidylcholine (DPPC) and Survanta, a naturally derived commercial pulmonary surfactant that contains DPPC as the main lipid component and hydrophobic surfactant proteins SP-B and SP-C, has been investigated in connection with the potential implication of inorganic NPs in pulmonary surfactant dysfunction. Hexadecanethiolate-capped Au NPs (C(16)SAu NPs) with an average core diameter of 2 nm have been incorporated into DPPC monolayers in concentrations ranging from 0.1 to 0.5 mol %. Concentrations of up to 0.2 mol % in DPPC and 16 wt % in Survanta do not affect the monolayer phase behavior at 20 °C, as evidenced by surface pressure-area (π-A) and ellipsometric isotherms. The monolayer structure at the air/water interface was imaged as a function of the surface pressure by Brewster angle microscopy (BAM). In the liquid-expanded/liquid-condensed phase coexistence region of DPPC, the presence of 0.2 mol % C(16)SAu NPs causes the formation of many small, circular, condensed lipid domains, in contrast to the characteristic larger multilobes formed by pure lipid. Condensed domains of similar size and shape to those of DPPC with 0.2 mol % C(16)SAu NPs are formed by compressing Survanta, and these are not affected by the C(16)SAu NPs. Atomic force microscopy images of Langmuir-Schaefer-deposited films support the BAM observations and reveal, moreover, that at high surface pressures (i.e., 35 and 45 mN m(-1)) the C(16)SAu NPs form honeycomb-like aggregates around the polygonal condensed DPPC domains. In the Survanta monolayers, the C(16)SAu NPs were found to accumulate together with the proteins in the liquid-expanded phase around the circular condensed lipid domains. In conclusion, the presence of hydrophobic C(16)SAu NPs in amounts that do not influence the π-A isotherm alters the nucleation, growth, and morphology of the condensed domains in monolayers of DPPC but not of those of Survanta. Systematic investigations of the effect of the interaction of chemically defined NPs with the lipid and protein components of lung surfactant on the physicochemical properties of surfactant films are pertinent to understanding how inhaled NPs impact pulmonary function.  相似文献   

8.
The influence of silicalite-1 pores on the reaction equilibria and the selectivity of the propene metathesis reaction system in the temperature range between 300 and 600 K and the pressure range from 0.5 to 7 bars has been investigated with molecular simulations. The reactive Monte Carlo (RxMC) technique was applied for bulk-phase simulations in the isobaric-isothermal ensemble and for two phase systems in the Gibbs ensemble. Additionally, Monte Carlo simulations in the grand-canonical ensemble (GCMC) have been carried out with and without using the RxMC technique. The various simulation procedures were combined with the configurational-bias Monte Carlo approach. It was found that the GCMC simulations are superior to the Gibbs ensemble simulations for reactions where the bulk-phase equilibrium can be calculated in advance and does not have to be simulated simultaneously with the molecules inside the pore. The confined environment can increase the conversion significantly. A large change in selectivity between the bulk phase and the pore phase is observed. Pressure and temperature have strong influences on both conversion and selectivity. At low pressure and temperature both conversion and selectivity have the highest values. The effect of confinement decreases as the temperature increases.  相似文献   

9.
Raman spectroscopy has been used to obtain thermal phase transition profiles for recombinant particles composed of 1,2-dipalmitoylphosphatidylcholine (DPPC) and apolipoprotein A—I. Comparison of these profiles with unilamellar vesicles of DPPC indicates that lateral packing of DPPC acyl chains is tighter in recombinant DPPC/apolipoporotein A—I particles than in uncomplexed lipid of unilamellar vesicles. Consequently, the magnitude of the entropy change associated with acyl chain melting in the recombinants at the main lipid phase transition is almost twice that of unilamellar DPPC. In addition, a second phase transition has been observed for the DPPC/apolipoprotein A—I complex and has been assigned to the acyl chain melting of DPPC molecules which are bound to the apolipoprotein annulus on the periphery of the discoidal complexes. A combination of results from Raman spectroscopy, electron micrograph measurements and chemical analysis leads to the conclusion that these protein-bound lipids, the “boundary layer”, account for about 20% of the total lipid in the recombinant material. Calculations indicate that there are about 55 protein-bound lipid molecules per apolipoprotein A—I molecule in the DPPC/apolipoprotein A—I discoidal complexes prepared for this study.  相似文献   

10.
The effect of four general anesthetic molecules, i.e., chloroform, halothane, diethyl ether and enflurane, on the properties of a fully hydrated dipalmitoylphosphatidylcholine (DPPC) membrane is studied in detail by long molecular dynamics simulations. Furthermore, to address the problem of pressure reversal, the effect of pressure on the anesthetic containing membranes is also investigated. In order to ensure sufficient equilibration and adequate sampling, the simulations performed have been at least an order of magnitude longer than the studies reported previously in the literature on general anesthetics. The results obtained can help in resolving several long-standing contradictions concerning the effect of anesthetics, some of which were the consequence of too short simulation time used in several previous studies. More importantly, a number of seeming contradictions are found to originate from the fact that different anesthetic molecules affect the membrane structure differently in several respects. In particular, halothane, being able to weakly hydrogen bound to the ester group of the lipid tails, is found to behave in a markedly different way than the other three molecules considered. Besides, we also found that two changes, namely lateral expansion of the membrane and increasing local disorder in the lipid tails next to the anesthetic molecules, are clearly induced by all four anesthetic molecules tested here in the same way, and both of these effects are reverted by the increase in pressure.  相似文献   

11.
Liquid crystal phases formed by bent-shaped (or "banana") molecules are currently of great interest. Here we investigate by Monte Carlo computer simulations the phases formed by rigid banana molecules modeled combining three Gay-Berne sites and containing either one central or two lateral and transversal dipoles. We show that changing the dipole position and orientation has a profound effect on the mesophase stability and molecular organization. In particular, we find a uniaxial nematic phase only for off-center dipolar models and tilted phases only for the one with terminal dipoles.  相似文献   

12.
To understand more fully the effect of polyunsaturated fatty acids (PUFAs) on lipid bilayers, we investigated the effects of treatment with fatty acids on the properties of a model membrane. Three kinds of liposomes comprising dipalmitoylphosphatidylcholine (DPPC), dioleylphosphatidylcholine (DOPC), and cholesterol (Ch) were used as the model membrane, and the fluorescence anisotropy of 1,6-diphenyl-1,3,5-hexatriene (DPH) and detergent insolubility were determined. Characterization of the liposomes clarified that DPPC, DPPC/Ch, and DPPC/DOPC/Ch existed as solid-ordered phase (L beta), liquid-ordered phase (l o), and a mixture of l o and liquid-disordered phase (L alpha) membranes at room temperature. Treatment with unsaturated fatty acids such as oleic acid (OA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) markedly decreased the fluorescence anisotropy value and detergent insolubility. PUFAs and OA had different effects on the model membranes. In DPPC liposomes, the most prominent change was induced by PUFAs, whereas, in DPPC/Ch and DPPC/DOPC/Ch liposomes, OA had a stronger effect than PUFAs. The effect of PUFAs was strongly affected by the amount of Ch in the membrane, which confirmed a specific effect of PUFAs on the Ch-poor membrane domain. We further explored the effect of fatty acids dispersed in a water-in-oil-in-water multiple emulsion and found that unsaturated fatty acids acted on the membranes even when incorporated in emulsion form. These findings suggest that treatment with PUFAs increases the segregation of ordered and disordered phase domains in membranes.  相似文献   

13.
We investigate the effect of three-body correlations on the phase behavior of hard rectangle two-dimensional fluids. The third virial coefficient B3 is incorporated via an equation of state that recovers scaled particle theory for parallel hard rectangles. This coefficient, a functional of the orientational distribution function, is calculated by Monte Carlo integration, using an accurate parametrized distribution function, for various particle aspect ratios in the range of 1-25. A bifurcation analysis of the free energy calculated from the obtained equation of state is applied to find the isotropic (I)-uniaxial nematic (N(u)) and isotropic-tetratic nematic (N(t)) spinodals and to study the order of these phase transitions. We find that the relative stability of the N(t) phase with respect to the isotropic phase is enhanced by the introduction of B3. Finally, we have calculated the complete phase diagram using a variational procedure and compared the results with those obtained from scaled particle theory and with Monte Carlo simulations carried out for hard rectangles with various aspect ratios. The predictions of our proposed equation of state as regards the transition densities between the isotropic and orientationally ordered phases for small aspect ratios are in fair agreement with simulations. Also, the critical aspect ratio below which the N(t) phase becomes stable is predicted to increase due to three-body correlations, although the corresponding value is underestimated with respect to simulation.  相似文献   

14.
The adsorbate dynamics during simultaneous action of desorption and lateral adsorbate diffusion is studied in a simple lattice-gas model by kinetic Monte Carlo simulations. It is found that the action of the coverage-conserving diffusion process during the course of the desorption has two distinct, competing effects: a general acceleration of the desorption process, and a coarsening of the adsorbate configuration through Ostwald ripening. The balance between these two effects is governed by the structure of the adsorbate layer at the beginning of the desorption process.  相似文献   

15.
A lattice-gas model is described for the adsorption of halides on single-crystal electrodes. The lateral interactions between the adsorbed halides include a short-range nearest-neighbor interaction and a long-range electrostatic interaction. By Monte Carlo simulations the model is used to fit the experimental isotherm of bromide adsorption on Ag(100), giving information about the relative importance of the long-range and short-range interactions. The model reproduces the order–disorder transition observed experimentally, and the way in which the long-ranged interactions influence the properties of this phase transition is discussed. The Monte Carlo simulations are also compared to analytical mean-field and quasi-chemical approximations to the isotherm. Finally, the kinetics of the disorder–order transition are studied by dynamic Monte Carlo simulations, and some results on isotherms and ordered phases on (110) and (111) surfaces are described.  相似文献   

16.
Monte Carlo simulations have been performed to determine the excess energy and the equation of state of fcc solids with Sutherland potentials for wide ranges of temperatures, densities, and effective potential ranges. The same quantities have been determined within a perturbative scheme by means of two procedures: (i) Monte Carlo simulations performed on the reference hard-sphere system and (ii) second-order Barker-Henderson perturbation theory. The aim was twofold: on the one hand, to test the capability of the "exact" MC-perturbation theory of reproducing the direct MC simulations and, on the other hand, the reliability of the Barker-Henderson perturbation theory, as compared with direct MC simulations and MC-perturbation theory, to determine the thermodynamic properties of these solids depending on temperature, density, and potential range. We have found that the simulation data for the excess energy obtained from the two procedures are in close agreement with each other. For the equation of state, the results from the MC-perturbation procedure also agree well with the direct MC simulations except for very low temperatures and extremely short-ranged potentials. Regarding the Barker-Henderson perturbation theory, we have found that in general the second-order approximation does not provide significant improvement over the first-order one.  相似文献   

17.
We have carried out atomic level molecular dynamics and Monte Carlo simulations of hydrated 18:0 sphingomyelin (SM)-cholesterol (CHOL) bilayers at temperatures of 20 and 50 degrees C. The simulated systems each contained 266 SM, 122 CHOL, and 11861 water molecules. Each simulation was run for 10 ns under semi-isotropic pressure boundary conditions. The particle-mesh Ewald method was used for long-range electrostatic interactions. Properties of the systems were calculated over the final 3 ns. We compare the properties of 20 and 50 degrees C bilayer systems with each other, with experimental data, and with experimental and simulated properties of pure SM bilayers and dipalmitoyl phospatidyl choline (DPPC)-CHOL bilayers. The simulations reveal an overall similarity of both systems, despite the 30 degrees C temperature difference which brackets the pure SM main phase transition. The area per molecule, lipid chain order parameter profiles, atom distributions, and electron density profiles are all very similar for the two simulated systems. Consistent with simulations from our lab and others, we find strong intramolecular hydrogen bonding in SM molecules between the phosphate ester oxygen and the hydroxyl hydrogen atoms. We also find that cholesterol hydroxyl groups tend to form hydrogen bonds primarily with SM carbonyl, methyl, and amide moieties and to a lesser extent methyl and hydroxyl oxygens.  相似文献   

18.
In this study, two-photon fluorescence microscopy on giant unilamellar vesicles and tapping-mode atomic force microscopy (AFM) are applied to follow the insertion of a fluorescently (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene, BODIPY) labeled and completely lipidated (hexadecylated and farnesylated) N-Ras protein into heterogeneous lipid bilayer systems. The bilayers consist of the canonical raft mixture 1-palmitoyl-2-oleoylphosphatidylcholine (POPC), sphingomyelin, and cholesterol, which-depending on the concentration of the constituents-separates into liquid-disordered (l(d)), liquid-ordered (l(o)), and solid-ordered (s(o)) phases. The results provide direct evidence that partitioning of N-Ras occurs preferentially into liquid-disordered lipid domains, which is also reflected in a faster kinetics of incorporation into the fluid lipid bilayers. The phase sequence of preferential binding of N-Ras to mixed-domain lipid vesicles is l(d) > l(o) > s(o). Intriguingly, we detect, using the better spatial resolution of AFM, also a large proportion of the lipidated protein located at the l(d)/l(o) phase boundary, thus leading to a favorable decrease in line tension that is associated with the rim of the demixed phases. Such an interfacial adsorption effect may serve as an alternative vehicle for association processes of signaling proteins in membranes.  相似文献   

19.
The statistical properties of the bilayer membranes of diparmitoylphosphatidylcholine (DPPC) in the gel and liquid-crystal phases were studied by Monte Carlo (MC) simulation using potential functions of the Lennard-Jones, the simple Coulomb, and the bond torsion. The simulation was undertaken on a two-dimensional periodic condition imposed on the bilayer model consisting of faithfully described molecules. The structure and ordering of the model bilayers accorded well with experiments, and the segment order parameters were in agreement with those of the nuclear magnetic resonance (NMR) experiments. The two kinds of lipid chains of DPPC do not equivalently behave in the bilayers, and chain 2 has lower ordering than chain 1. The order parameters of the first eight segments of chain 2 in the liquid-crystal model are particularly small and are roughly constant. From electron density analysis, it has been observed that the liquid-crystal bilayer has about one excess water molecule per one lipid molecule in comparison with the gel bilayer. The energy difference between the two bilayer models, taking account of the water contribution, is consistent with the latent heat of the phase transition. © 1995 by John Wiley & Sons, Inc.  相似文献   

20.
The current interest in mixed cationic-zwitterionic lipid membranes derives from their potential use as transfer vectors in nonviral gene therapy. Mixed cationic-zwitterionic lipid membranes have a number of structural properties that are distinct from the corresponding anionic-zwitterionic lipid membranes. As known from experiment and reproduced by computer simulations, the average cross-sectional area per lipid changes nonmonotonically with the mole fraction of the charged lipid, passing through a minimum at a roughly equimolar mixture. At the same time, the average orientation of the zwitterionic headgroup dipoles changes from more parallel to the membrane plane to more perpendicular. We suggest a simple mean-field model that reveals the physical mechanisms underlying the observed structural properties. To backup the mean-field calculations, we have also performed Monte Carlo simulations. Our model extends Poisson-Boltzmann theory to include (besides the cationic headgroup charges) the individual charges of the zwitterionic lipid headgroups. We model these charges to be arranged as dipoles of fixed length with rotational degrees of freedom. Our model includes, in a phenomenological manner, the changes in steric headgroup interactions upon reorientation of the zwitterionic headgroups. Our numerical results suggest that two different mechanisms contribute to the observed structural properties: one involves the lateral electrostatic pressure and the other the zwitterionic headgroup orientation, the latter modifying steric headgroup interactions. The two mechanisms operate in parallel as they both originate in the electrostatic properties of the involved lipids. We have also applied our model to a mixed anionic-zwitterionic lipid membrane for which neither a significant headgroup reorientation nor a nonmonotonic change in the average lateral cross-sectional area is predicted.  相似文献   

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