Interleaflet interaction and asymmetry in phase separated lipid bilayers: molecular dynamics simulations

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.     

Molecular dynamics simulations of lipid bilayers

Computer simulation methods are becoming increasingly widespread as tools for studying the structure and dynamics of lipid bilayer membranes. The length scale and time scale accessible to atomic-level molecular dynamics simulations are rapidly increasing, providing insight into the relatively slow motions of molecular reorientation and translation and demonstrating that effects due to the finite size of the simulation cell can influence simulation results. Additionally, significant advances have been made in the complexity of membrane systems studied, including bilayers with cholesterol, small solute molecules, and lipid-protein and lipid-DNA complexes. Especially promising is the progress that continues to be made in the comparison of simulation results with experiment, both to validate the simulation algorithms and to aid in the interpretation of existing experimental data.     

Investigation of finite system-size effects in molecular dynamics simulations of lipid bilayers

In the absence of external stress, the surface tension of a lipid membrane vanishes at equilibrium, and the membrane exhibits long wavelength undulations that can be described as elastic (as opposed to tension-dominated) deformations. These long wavelength fluctuations are generally suppressed in molecular dynamics simulations of membranes, which have typically been carried out on membrane patches with areas <100 nm2 that are replicated by periodic boundary conditions. As a result, finite system-size effects in molecular dynamics simulations of lipid bilayers have been subject to much discussion in the membrane simulation community for several years, and it has been argued that it is necessary to simulate small membrane patches under tension to properly model the tension-free state of macroscopic membranes. Recent hardware and software advances have made it possible to simulate larger, all-atom systems allowing us to directly address the question of whether the relatively small size of current membrane simulations affects their physical characteristics compared to real macroscopic bilayer systems. In this work, system-size effects on the structure of a DOPC bilayer at 5.4 H2O/lipid are investigated by performing molecular dynamics simulations at constant temperature and isotropic pressure (i.e., vanishing surface tension) of small and large single bilayer patches (72 and 288 lipids, respectively), as well as an explicitly multilamellar system consisting of a stack of five 72-lipid bilayers, all replicated in three dimensions by using periodic boundary conditions. The simulation results are compared to X-ray and neutron diffraction data by using a model-free, reciprocal space approach developed recently in our laboratories. Our analysis demonstrates that finite-size effects are negligible in simulations of DOPC bilayers at low hydration, and suggests that refinements are needed in the simulation force fields.     

Improved dissipative particle dynamics simulations of lipid bilayers

The authors introduce a new parameterization for the dissipative particle dynamics simulations of lipid bilayers. In this parameterization, the conservative pairwise forces between beads of the same type in two different hydrophobic chains are chosen to be less repulsive than the water-water interaction, but the intrachain bead interactions are the same as the water-water interaction. For a certain range of parameters, the new bilayer can only be stretched up to 30% before it ruptures. Membrane tension, density profiles, and the in-plane lipid diffusion coefficient of the new bilayer are discussed in detail. They find two kinds of finite size effects that influence the membrane tension: lateral finite size effects, for which larger membranes rupture at a smaller stretch, and transverse finite size effects, for which tensionless bilayers are more compact in larger systems. These finite size effects become rather small when the simulation box is sufficiently large.     

Molecular dynamics simulations of rhodopsin in different one-component lipid bilayers

Four 20 ns molecular dynamic simulations of rhodopsin embedded in different one-component lipid bilayers have been carried out to ascertain the importance of membrane lipids on the protein structure. Specifically, dimyristoyl phosphatidylcholine (DMPC), dipalmitoyl phosphatidylcholine (DPPC), palmitoyl oleoyl phosphatidylcholine (POPC), and palmitoyl linoleyl phosphatidylcholine (PLPC) lipid bilayers have been considered for the present work. The results reported here provide information on the hydrophobic matching between the protein and the bilayer and about the differential effects of the protein on the thickness of the different membranes. Furthermore, a careful analysis of the individual protein-lipid interactions permits the identification of residues that exhibit permanent interactions with atoms of the lipid environment that may putatively act as hooks of the protein to the membrane. The analysis of the trajectories also provides information about the effect of the bilayer on the protein structure, including secondary structural elements, salt bridges, and rigid-body motions.     

Microscopic structure of phospholipid bilayers: comparison between molecular dynamics simulations and wide-angle X-ray spectra

We present results of molecular dynamics simulations of fully hydrated dipalmitoylphosphatidylcholine and dimyristoylphosphatidylcholine bilayers in the disordered liquid crystalline phase (Lalpha) and compare them to wide-angle X-ray scattering experiments. Though we find a generally good agreement between the simulated and experimental spectra, there are some deviations whose origin has been investigated by a reparametrization of the aliphatic chains' force field. A detailed analysis of the various contribution to the X-ray spectra shows that a non-negligible contribution to the total scattered intensity comes from the headgroups and the head-tail cross correlation.     

Structure and phase transformations of DPPC lipid bilayers in the presence of nanoparticles: insights from coarse-grained molecular dynamics simulations

In this article, we investigate fluid-gel transformations of a DPPC lipid bilayer in the presence of nanoparticles, using coarse-grained molecular dynamics. Two types of nanoparticles are considered, specifically a 3 nm hydrophobic nanoparticle located in the core of the bilayer and a 6 nm charged nanoparticle located at the interface between the bilayer and water phase. Both negatively and positively charged nanoparticles at the bilayer interface are investigated. We demonstrate that the presence of all types of nanoparticles induces disorder effects in the structure of the lipid bilayer. These effects are characterized using computer visualization of the gel phase in the presence of nanoparticles, radial distribution functions, and order parameters. The 3 nm hydrophobic nanoparticle immersed in the bilayer core and the positively charged nanoparticle at the bilayer surface have no effect on the temperature of the fluid-gel transformation, compared to the bulk case. Interestingly, a negatively charged hydrophobic nanoparticle located at the surface of the bilayer causes slight shift of the fluid-gel transformation to a lower temperature, compared to the bulk bilayer case.     

Area compressibility and buckling of amphiphilic bilayers in molecular dynamics simulations

The elastic modulus or area compressibility of a membrane is routinely calculated in molecular dynamics simulations as the proportionality constant relating surface tension and projected surface area. Recent studies, however, have revealed a marked system size dependence of these moduli, which we attribute to the neglect of thermal undulations in the area calculation. We discuss several methods, based on the Helfrich model and on numerical triangulation, to remedy this situation, and find a satisfying agreement between them. The Helfrich model also quantitatively describes a buckling transition observed for compressed bilayers.     

Steered molecular dynamics simulations of protein-ligand interactions

Molecular recognition and specific protein-ligandinteractions are central to many biochemical processes,such as enzyme catalysis, assembly of organelles, en-ergy transduction, signaling, diverse control functions,and replication, expression and storage of the geneticmaterial[1]. Moreover, protein-ligand interactions pro-vide the mechanism of many drug therapies and un-derstanding of such interactions is thus significant forrational drug design[1,2]. For the experimental studiesof protein-ligan…     

Molecular interactions between lipid bilayers and a water-soluble polymer

Molecular interactions between lipid bilayers (liposomes) and chondroitin sulfate C (CS), a water soluble polymer, have been investigated in terms of zeta-potential, particle size, microscopic-viscosity, microscopic-polarity of liposomes and permeability of calcein. Microscopic morphology is dramatically changed by the addition of CS to the positively charged liposomes (Pos.L), while it is not changed by the addition to uncharged liposomes (Unc.L) or negatively charged liposomes (Neg.L). The absolute value of the particle size of Pos.L increases with the addition of CS, while the zeta- potential of Pos.L decreases. Permeability of Pos.L decreases with an increase in the concentration of CS. Phase transition temperature of Pos.L is changed after the addition of CS. These values, however, are not changed for the other liposomes by the addition of CS. The results of gel filtration chromatography show that CS is absorbed on the Pos.L surface. Microscopic viscosity is also increased by the addition of CS to Pos.L due to the adsorption of CS.     

Effect of temperature on the interactions between cellulose and lignin via molecular dynamics simulations

Cellulose - Heating is essential in various biomass pre-treatments and thermal conversion processes. It is of practical significance to study the characteristics of cellulose-lignin and...     

Characterizing the dynamics and ligand-specific interactions in the human leukocyte elastase through molecular dynamics simulations

The human leukocyte elastase (HLE), a neutrophil serine protease of the chymotrypsin superfamily, is a major therapeutic target for a number of inflammatory diseases, such as chronic obstructive pulmonary disease (COPD). In this work, we present a comparative explicit water molecular dynamics (MD) study on the free and inhibitor-bound HLE. Knowledge of the flexibility and conformational changes induced by this irreversible inhibitor, whether in a prebound stage or covalently bound at the enzyme binding site, encases fundamental biological interest and is particularly relevant to ongoing structure-based drug design studies. Our results suggest that HLE operates by an induced-fit mechanism with direct intervention of a surface loop which is open toward the solvent in the free enzyme and closed while in the presence of the ligand. MM-PBSA free energy calculations furthermore elucidate the energetic contributions to the distinct conformations adopted by this loop. Additionally, a survey of the major contributions to the inhibitor binding free energies was attained. Our findings enforce the need to account for HLE flexibility, whether through the use of MD-generated ensembles of HLE conformations as targets for molecular docking or via sophisticated flexible-docking algorithms. We anticipate that inclusion of the observed HLE dynamic behavior into future drug design methodologies will have a relevant impact in the development of novel, more efficient, inhibitors.     

Observations concerning the treatment of long-range interactions in molecular dynamics simulations

Molecular dynamics simulations of pure water employing two different empirical water models have been used to study the effects of different methods for truncation of long-range interactions in molecular mechanics calculations. As has been observed previously in integral equation studies, “shifting” these interactions on an atom-by-atom basis was found to produce artificial structuring in the water and affect diffusion rates. In cases where some form of short-range truncation must be used, the ST2 switching function applied on a group-by-group basis was found to be the most realistic procedure. If atom-based shifting must be employed, a cutoff distance greater than or equal to 12.0 Å was found to be required to produce realistic results. © 1993 John Wiley & Sons, Inc.     

Molecular dynamics simulations of hydrophobic associations in aqueous salt solutions indicate a connection between water hydrogen bonding and the Hofmeister effect

Although the often profound effects of neutral salts on protein solubility were first identified over a century ago by Hofmeister, a general molecular explanation of these effects-capable of accounting even for salts with highly anomalous behavior-has yet to be established. As one way toward developing such an explanation, we aim here to quantify how eight simple monovalent salts alter the association thermodynamics of hydrophobic solute-pairs in a series of 1 micros explicit-solvent molecular dynamics simulations. For both methane-methane and neopentane-neopentane associations, the salt-induced strengthening of the hydrophobic interaction observed in the simulations is found to be highly correlated with corresponding experimental solubility data; the computed changes in interaction free energy are also found to be quantitatively predictable using the preferential interaction formalism of Timasheff (Timasheff, S. N. Adv. Protein Chem. 1998, 51, 355-432). From additional simulations of 20 different pure salt solutions-in which no hydrophobic solutes are present-a strong correlation is also observed between the extent of water-water hydrogen bonding and experimental solubility data for hydrophobic solutes; this suggests that the Hofmeister effects of the simple salts investigated here may primarily be a manifestation of salt-induced changes in the water structure. Importantly, all of the strong correlations with experiment obtained here extend even to salts of lithium, whose unusual behavior has previously been unexplained; lithium's anomalous behavior can be rationalized in part by its formation of alternating, linear clusters (strings) with halide anions. The close agreement between simulation and experiment obtained in the present study reinforces previous work, showing that molecular simulations can be a valuable tool for understanding salt-related phenomena and indicating that this can be so even when the simulations employ the simple, nonpolarizable potential functions widely used in simulations of biological macromolecules.     

Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations

We calculated the pressure-area isotherm of a dipalmitoyl-phosphatidylcholine (DPPC) lipid monolayer from molecular dynamics simulations using a coarse-grained molecular model. We characterized the monolayer structure, geometry, and phases directly from the simulations and compared the calculated isotherm to experiments. The calculated isotherm shows liquid-expanded and liquid-condensed phases and their coexistence plateau. At high pressure, the monolayer surface is rippled; upon further compression, the monolayer undergoes a collapse. We studied the effect of temperature and system size on the isotherm slope and phase coexistence region. Thermodynamic and dynamic properties of the monolayer phases were also investigated.     

Communication: consistent picture of lateral subdiffusion in lipid bilayers: molecular dynamics simulation and exact results

This communication presents a molecular dynamics simulation study of a bilayer consisting of 128 dioleoyl-sn-glycero-3-phosphocholine molecules, which focusses on the center-of-mass diffusion of the lipid molecules parallel to the membrane plane. The analysis of the simulation results is performed within the framework of the generalized Langevin equation and leads to a consistent picture of subdiffusion. The mean square displacement of the lipid molecules evolves as ∝ t(α), with α between 0.5 and 0.6, and the fractional diffusion coefficient is close to the experimental value for a similar system obtained by fluorescence correlation spectroscopy. We show that the long-time tails of the lateral velocity autocorrelation function and the associated memory function agree well with exact results which have been recently derived by asymptotic analysis [G. Kneller, J. Chem. Phys. 134, 224106 (2011)]. In this context, we define characteristic time scales for these two quantities.     

Combined Monte Carlo and molecular dynamics simulation of hydrated 18:0 sphingomyelin-cholesterol lipid bilayers

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.     

Communication: Critical dynamics and nuclear relaxation in lipid bilayers

Membrane composition fluctuations affect deuterium nuclear magnetic relaxation in lipid bilayers. The time dependence of the fluctuations depends on lipid diffusion. Near a miscibility critical point this diffusion involves an advective hydrodynamic coupling to the aqueous phase. The corresponding diffusion coefficient depends on both the critical length and the fluctuation wavelength. We calculate the effects of these dynamics on transverse deuterium nuclear relaxation in the 0.1(o)-10(o) range above the critical temperature.     

Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations

Single-chain and single-fragment configurational entropies of lipid tails in hydrated lipid bilayers are evaluated from molecular dynamics simulations using the quasi-harmonic approximation. The entropy distribution along individual acyl tails is obtained and compared to that of corresponding hydrocarbon chains in the liquid phase. We consider pure dipalmitoylphosphatidylcholine and mixed dioleoylphosphatidylcholine/dioleoylphosphatidylethanolamine bilayers. The systems are modeled at different levels of spatial resolution: In an atomic-level (AL) model all (heavy) atoms are explicitly simulated; in a coarse-grained (CG) model particles (beads) representing groups of covalently bound atoms are used, which map approximately four non-hydrogen atoms to one interaction site. Single-chain and single-fragment entropies and correlations between the motions of (single) acyl chains are compared. A good correspondence is found between the flexibility of the AL and CG models. The loss in configurational entropy due to the reduction in the number of degrees of freedom upon coarse-graining of the model is estimated. The CG model shows about 4 times faster convergence of the chain entropies than the more detailed AL model. Corrections to the quasi-harmonic entropy estimates were found to be small for the CG model. For the AL model, the correction due to mode anharmonicities is small, but the correction due to pairwise (supralinear) mode correlations is sizable.     

The hydrophobic effect: molecular dynamics simulations of water confined between extended hydrophobic and hydrophilic surfaces

Structural and dynamic properties of water confined between two parallel, extended, either hydrophobic or hydrophilic crystalline surfaces of n-alkane C(36)H(74) or n-alcohol C(35)H(71)OH, are studied by molecular dynamics simulations. Electron density profiles, directly compared with corresponding experimental data from x-ray reflectivity measurements, reveal a uniform weak de-wetting characteristic for the extended hydrophobic surface, while the hydrophilic surface is weakly wetted. These microscopic data are consistent with macroscopic contact angle measurements. Specific water orientation is present at both surfaces. The ordering is characteristically different between the surfaces and of longer range at the hydrophilic surface. Furthermore, the dynamic properties of water are different at the two surfaces and different from the bulk behavior. In particular, at the hydrophobic surface, time-correlation functions reveal that water molecules have characteristic diffusive behavior and orientational ordering due to the lack of hydrogen bonding interactions with the surface. These observations suggest that the altered dynamical properties of water in contact with extended hydrophobic surfaces together with a partial drying of the surfaces are more indicative of the hydrophobic effect than structural ordering, which we suggest to be independent of surface topology.