Multiscale coupling of mesoscopic- and atomistic-level lipid bilayer simulations

A multiscale method is presented to bridge between the atomistic and mesoscopic membrane systems. The atomistic model in this case is the united atom dimyristoylphosphatidylcholine membrane system, although the method is completely general. Atomistic molecular dynamics provides the expansion modulus which is used to parametrize a mesoscopic elastic membrane model. The resulting elastic membrane model, including explicit mesoscopic solvent, shows appropriate static and dynamic undulation behaviors. Large membranes of approximately 100 nm in length can then be easily simulated using the mesoscopic membrane system. The critical feedback from the mesoscopic system back down to the atomistic-scale system is accomplished by bridging the stress (or surface tension) of a small region in the mesoscopic membrane to the corresponding atomistic membrane system. Because of long length-scale modes of membranes such as undulation and buckling, the local tension responds differently from the frame tension, when subjected to external perturbations. The effect of these membrane modes is shown for the stress response of a local membrane region and therefore the atomistic membrane system. In addition, certain equilibrium static and dynamic properties of stand-alone and multiscale coupled systems are presented for several different membrane sizes. Although static properties such as two-dimensional pair-correlation function and order parameters show no noticeable discrepancy for the different systems, lipid self-diffusion and the rotational relaxation of lipid dipoles have a strong dependence on the membrane size (or long-wavelength membrane motions), which is properly modeled by the present multiscale method.     

Lateral diffusion in lipid membranes through collective flows

There is no comprehensive model for the dynamics of cellular membranes. Even mechanisms of basic dynamic processes, such as lateral diffusion of lipids, are poorly understood. Our atomic-scale molecular dynamics simulations support a novel, concerted mechanism for lipid diffusion. We find that a lipid and its nearest neighbors move in unison, forming loosely defined clusters. What is more, the motions of lipids are correlated over tens of nanometers: the lateral displacements of lipids in a given monolayer produce striking two-dimensional flow patterns. These flow patterns should have wide implications, affecting, for example, the formation of membrane domains, protein functionality, and action of lipases and drugs on membranes.     

Influence of ethanol on lipid membranes: from lateral pressure profiles to dynamics and partitioning

We have combined experiments with atomic-scale molecular dynamics simulations to consider the influence of ethanol on a variety of lipid membrane properties. We first employed isothermal titration calorimetry together with the solvent-null method to study the partitioning of ethanol molecules into saturated and unsaturated membrane systems. The results show that ethanol partitioning is considerably more favorable in unsaturated bilayers, which are characterized by their more disordered nature compared to their saturated counterparts. Simulation studies at varying ethanol concentrations propose that the partitioning of ethanol depends on its concentration, implying that the partitioning is a nonideal process. To gain further insight into the permeation of alcohols and their influence on lipid dynamics, we also employed molecular dynamics simulations to quantify kinetic events associated with the permeation of alcohols across a membrane, and to characterize the rotational and lateral diffusion of lipids and alcohols in these systems. The simulation results are in agreement with available experimental data and further show that alcohols have a small but non-vanishing effect on the dynamics of lipids in a membrane. The influence of ethanol on the lateral pressure profile of a lipid bilayer is found to be prominent: ethanol reduces the tension at the membrane-water interface and reduces the peaks in the lateral pressure profile close to the membrane-water interface. The changes in the lateral pressure profile are several hundred atmospheres. This supports the hypothesis that anesthetics may act by changing the lateral pressure profile exerted on proteins embedded in membranes.     

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.     

Dynamical motions of lipids and a finite size effect in simulations of bilayers

Molecular dynamics (MD) simulations of dipalmitoylphosphatidylcholine bilayers composed of 72 and 288 lipids are used to examine system size dependence on dynamical properties associated with the particle mesh Ewald (PME) treatment of electrostatic interactions. The lateral diffusion constant Dl is 2.92 x 10(-7) and 0.95 x 10(-7) cm2/s for 72 and 288 lipids, respectively. This dramatic finite size effect originates from the correlation length of lipid diffusion, which extends to next-nearest neighbors in the 288 lipid system. Consequently, diffusional events in smaller systems can propagate across the boundaries of the periodic box. The internal dynamics of lipids calculated from the PME simulations are independent of the system size. Specifically, reorientational correlation functions for the slowly relaxing phosphorus-glycerol hydrogen, phosphorus-nitrogen vectors, and more rapidly relaxing CH vectors in the aliphatic chains are equivalent for the 72 and 288 lipid simulations. A third MD simulation of a bilayer with 72 lipids using spherical force-shift electrostatic cutoffs resulted in interdigitated chains, thereby rendering this cutoff method inappropriate.     

Surface tension effect on transmembrane channel stability in a model membrane

The effect of surface tension on the lipid bilayer membrane is a question that has drawn considerable research effort. This interest has been driven both by the desire to determine the surface tension effects on the lipid bilayer and from the suggestion that adding finite surface tension to a small membrane system may provide more realistic lipid properties in molecular dynamics simulations. Here, the effect of surface tension on a palmitololelylphosphatidylcholine (POPC) bilayer membrane containing a four-helix transmembrane alamethicin peptide bundle is investigated. Simulations of 10 ns were undertaken for two different ensembles, NPT and NP(z)gammaT with a surface tension, gamma, of 20 mN m(-1) per interface, which is near the pore-forming region. The significance of differences between the tension-free and surface tension simulations was determined using nonparametric statistical analysis on replicate simulations with different initial conditions. The results suggest that, when the membrane is under surface tension, the peptide helical structure is perturbed from that in the tension-free state but that the bundle conformation is more stable than that in the tension-free state, with hydrogen bonding playing an important stabilizing role. Surface tension counteracts the influence of the transmembrane helix bundle on nearby lipid order, making the lipid order more uniform throughout the membrane in the tension state. Conversely, the lipid mobility was less uniform in the tension state, with lipids far from the bundle being significantly more mobile than those near the bundle. One general implication of the results is that surface tension can affect the membrane nonuniformly, in that the properties of lipids near the peptide are different from those further away.     

Free pyrene probes in gel and fluid membranes: perspective through atomistic simulations

We consider the properties of free pyrene probes inside gel- and fluidlike phospholipid membranes and unravel their influence on membrane properties. For this purpose, we employ atomic-scale molecular dynamics simulations at several temperatures for varying pyrene concentrations. Molecular dynamics simulations show that free pyrene molecules prefer to be located in the hydrophobic acyl chain region close to the glycerol group of lipid molecules. Their orientation is shown to depend on the phase of the membrane. In the fluid phase, pyrenes favor orientations where they are standing upright in parallel to the membrane normal, while, in the gel phase, the orientation is affected by the tilt of lipid acyl chains. Pyrenes are found to locally perturb membrane structure, while the nature of perturbations in the gel and fluid phases is completely different. In the gel phase, pyrenes break the local packing of lipids and decrease the ordering of lipid acyl chains around them, while, in the fluid phase, pyrenes increase the ordering of nearby acyl chains, thus having an opposite effect. Interestingly, this proposes a similarity to effects induced by cholesterol on structural membrane properties above and below the gel-fluid transition temperature. Further studies express a view that the orientational ordering of pyrene is not a particularly good measure of the acyl chain ordering of lipids. While pyrene ordering provides the correct qualitative behavior of acyl chain ordering in the fluid phase, its capability to predict the correct temperature dependence is limited.     

Molecular dynamics simulation of an archaeal lipid bilayer with sodium chloride

We have performed molecular dynamics simulations of a bilayer formed by the synthetic archaeal lipid, diphytanyl phosphatidylcholine, in NaCl electrolyte solution at four different concentrations (0-4 M) to investigate how structural and dynamic properties of the model archaeal membrane are changed due to the ionic strength of the solution. The archaeal lipid bilayer shows minor changes in their physical properties, indicating the unusual high stability of the membrane against salt, though small reductions of molecular area and lateral diffusion of the lipid are detected at the highest electrolyte concentration of 4 M. Sodium ions penetrate to the ether-rich region, where the ions are likely bound to the ether oxygen in the sn-1 chain rather than to that in the sn-2 chain. The observed salt bridges among two or three neighboring lipids account for the small reduction in the molecular area. The bound ions together with the counter (chloride) ions give rise to a diffusive electric double layer; as a result, the membrane dipole potential is slightly increased with increasing NaCl concentration.     

A Mass‐Spectrometry‐Based Approach to Distinguish Annular and Specific Lipid Binding to Membrane Proteins

Membrane proteins engage in a variety of contacts with their surrounding lipids, but distinguishing between specifically bound lipids, and non‐specific, annular interactions is a challenging problem. Applying native mass spectrometry to three membrane protein complexes with different lipid‐binding properties, we explore the ability of detergents to compete with lipids bound in different environments. We show that lipids in annular positions on the presenilin homologue protease are subject to constant exchange with detergent. By contrast, detergent‐resistant lipids bound at the dimer interface in the leucine transporter show decreased k_off rates in molecular dynamics simulations. Turning to the lipid flippase MurJ, we find that addition of the natural substrate lipid‐II results in the formation of a 1:1 protein–lipid complex, where the lipid cannot be displaced by detergent from the highly protected active site. In summary, we distinguish annular from non‐annular lipids based on their exchange rates in solution.     

Cofilin-Membrane Interactions: Electrostatic Effects in Phosphoinositide Lipid Binding

The actin cytoskeleton interacts with the cell membrane primarily through the indirect interactions of actin-binding proteins such as cofilin-1. The molecular mechanisms underlying the specific interactions of cofilin-1 with membrane lipids are still unclear. Here, we performed coarse-grain molecular dynamics simulations of cofilin-1 with complex lipid bilayers to analyze the specificity of protein-lipid interactions. We observed the maximal interactions with phosphoinositide (PIP) lipids, especially PIP₂ and PIP₃ lipids. A good match was observed between the residues predicted to interact and previous experimental studies. The clustering of PIP lipids around the membrane bound protein leads to an overall lipid demixing and gives rise to persistent membrane curvature. Further, through a series of control simulations, we observe that both electrostatics and geometry are critical for specificity of lipid binding. Our current study is a step towards understanding the physico-chemical basis of cofilin-PIP lipid interactions.     

Effect of NaCl and KCl on phosphatidylcholine and phosphatidylethanolamine lipid membranes: insight from atomic-scale simulations for understanding salt-induced effects in the plasma membrane

To gain a better understanding of how monovalent salt under physiological conditions affects plasma membranes, we have performed 200 ns atomic-scale molecular dynamics simulations of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipid bilayers. These two systems provide representative models for the outer and inner leaflets of the plasma membrane, respectively. The implications of cation-lipid interactions in these lipid systems have been considered in two different aqueous salt solutions, namely NaCl and KCl, and the sensitivity of the results on the details of interactions used for ions is determined by repeating the simulations with two distinctly different force fields. We demonstrate that the main effect of monovalent salt on a phospholipid membrane is determined by cations binding to the carbonyl region of a membrane, while chloride anions mostly stay in the water phase. It turns out that the strength and character of the cation-lipid interactions are quite different for different types of lipids and cations. PC membranes and Na+ ions demonstrate strongest interactions, leading to notable membrane compression. This finding was confirmed by both force fields (Gromacs and Charmm) employed for the ions. The binding of potassium ions to PC membranes (and the overall effect of KCl), in turn, was found to be much weaker mainly due to the larger size of a K+ ion compared to Na+. Furthermore, the effect of KCl on PC membranes was found to be force-field sensitive: The binding of a potassium ion was not observed at all in simulations performed with the Gromacs force-field, which seems to exaggerate the size of a K+ ion. As far as PE lipid bilayers are concerned, they are found to be influenced by monovalent salt to a significantly lesser extent compared to PC bilayers, which is a direct consequence of the ability of PE lipids to form both intra- and intermolecular hydrogen bonds and hence to adopt a more densely packed bilayer structure. Whereas for NaCl we observed weak binding of Na+ cations to the PE lipid-water interface, in the case of KCl we witnessed almost complete lack of cation binding. Overall, our findings indicate that monovalent salt ions affect lipids in the inner and outer leaflets of plasma cell membranes in substantially different ways.     

G-Protein-Coupled Receptor–Membrane Interactions Depend on the Receptor Activation State

G-protein-coupled receptors (GPCRs) are the largest family of human membrane proteins and serve as primary targets of approximately one-third of currently marketed drugs. In particular, adenosine A₁ receptor (A₁AR) is an important therapeutic target for treating cardiac ischemia–reperfusion injuries, neuropathic pain, and renal diseases. As a prototypical GPCR, the A₁AR is located within a phospholipid membrane bilayer and transmits cellular signals by changing between different conformational states. It is important to elucidate the lipid–protein interactions in order to understand the functional mechanism of GPCRs. Here, all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method were performed on both the inactive (antagonist bound) and active (agonist and G-protein bound) A₁AR, which was embedded in a 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) lipid bilayer. In the GaMD simulations, the membrane lipids played a key role in stabilizing different conformational states of the A₁AR. Our simulations further identified important regions of the receptor that interacted distinctly with the lipids in highly correlated manner. Activation of the A₁AR led to differential dynamics in the upper and lower leaflets of the lipid bilayer. In summary, GaMD enhanced simulations have revealed strongly coupled dynamics of the GPCR and lipids that depend on the receptor activation state. © 2019 Wiley Periodicals, Inc.     

A Mass-Spectrometry-Based Approach to Distinguish Annular and Specific Lipid Binding to Membrane Proteins

Membrane proteins engage in a variety of contacts with their surrounding lipids, but distinguishing between specifically bound lipids, and non-specific, annular interactions is a challenging problem. Applying native mass spectrometry to three membrane protein complexes with different lipid-binding properties, we explore the ability of detergents to compete with lipids bound in different environments. We show that lipids in annular positions on the presenilin homologue protease are subject to constant exchange with detergent. By contrast, detergent-resistant lipids bound at the dimer interface in the leucine transporter show decreased k_off rates in molecular dynamics simulations. Turning to the lipid flippase MurJ, we find that addition of the natural substrate lipid-II results in the formation of a 1:1 protein–lipid complex, where the lipid cannot be displaced by detergent from the highly protected active site. In summary, we distinguish annular from non-annular lipids based on their exchange rates in solution.     

A molecular dynamics investigation of the influence of hydration and temperature on structural and dynamical properties of a dimyristoylphosphatidylcholine bilayer

A series of molecular dynamics simulations of dimyristoylphosphatidylcholine bilayers, with different levels of hydration and temperature, were performed to examine the influence of hydration on properties of lipid membranes. Structural and dynamical properties such as area per lipid, electron densities, order parameters for all CH bonds and water, diffusion, and reorientation autocorrelation functions were determined and were all found to be affected by changes in the hydration level. The simulations give an overall picture of the bilayer going to a more ordered state when the hydration level is reduced. Lipid headgroups were found to adopt an orientation more parallel to the membrane plane when the water content was decreased. Dynamical properties such as lipid diffusion and relaxation of reorientation time correlation functions were found to become slower with the removal of water. Our simulation results generally agree with experimental data in cases where such data are available. One important conclusion drawn is that while structural properties are affected only moderately dynamical properties are affected very strongly by a decrease of water content.     

Diffusive dynamics of vesicles tethered to a fluid supported bilayer by single-particle tracking

We recently introduced a method to tether intact phospholipid vesicles onto a fluid supported lipid bilayer using DNA hybridization (Yoshina-Ishii, C.; Miller, G. P.; Kraft, M. L; Kool, E. T.; Boxer, S. G. J. Am. Chem. Soc. 2005, 127, 1356-1357). Once tethered, the vesicles can diffuse in two dimensions parallel to the supported membrane surface. The average diffusion coefficient, D, is typically 0.2 microm(2)/s; this is 3-5 times smaller than for individual lipid or DNA-lipid conjugate diffusion in supported bilayers. In this article, we investigate the origin of this difference in the diffusive dynamics of tethered vesicles by single-particle tracking under collision-free conditions. D is insensitive to tethered vesicle size from 30 to 200 nm, as well as a 3-fold change in the viscosity of the bulk medium. The addition of macromolecules such as poly(ethylene glycol) reversibly stops the motion of tethered vesicles without causing the exchange of lipids between the tethered vesicle and supported bilayer. This is explained as a depletion effect at the interface between tethered vesicles and the supported bilayer. Ca ions lead to transient vesicle-vesicle interactions when tethered vesicles contain negatively charged lipids, and vesicle diffusion is greatly reduced upon Ca ion addition when negatively charged lipids are present both in the supported bilayer and tethered vesicles. Both effects are interesting in their own right, and they also suggest that tethered vesicle-supported bilayer interactions are possible; this may be the origin of the reduction in D for tethered vesicles. In addition, the effects of surface defects that reversibly trap diffusing vesicles are modeled by Monte Carlo simulations. This shows that a significant reduction in D can be observed while maintaining normal diffusion behavior on the time scale of our experiments.     

Lipid/protein interactions and the membrane/water interfacial region

Despite the importance of lipid/protein interactions in the folding, assembly, stability, and function of membrane proteins, information at an atomic level on how such proteins interact with the lipids that surround them remains sparse. The dynamics and flexible nature of the protein/bilayer interaction make it difficult to study, for example, by crystallographic means. However, based on recent progress in molecular simulations of membranes it is possible to address this problem computationally. This communication reports one of the first attempts to use multiple ns molecular simulations to establish a qualitative picture of the intermolecular interactions between the lipids of a bilayer and two topologically different membrane proteins for which a high resolution (2 A or better) X-ray structure is available.     

Domain Size and Fluctuations at Domain Interfaces in Lipid Mixtures

Biomembranes consist of a complex mixture of a large number of lipids and proteins. In such mixtures, microscopic domains and macroscopically separated phases may exist. Here, we discuss phase behavior and domains formation of binary lipid mixtures. We show that the domain formation is accompanied by large fluctuations at the domain boundaries, resulting in altered physical properties at the boundaries, for instance in a pronounced increase of the elastic constants. Therefore, we argue that the physics of the membrane depends on the overall length scale of its domains interfaces. We present here confocal microscopy images, calorimetric melting profiles and Monte-Carlo simulations to understand the factors that determine domain formation, their sizes and the role of the domain interfaces.     

Atomistic simulation of lipid and DiI dynamics in membrane bilayers under tension

Membrane tension modulates cellular processes by initiating changes in the dynamics of its molecular constituents. To quantify the precise relationship between tension, structural properties of the membrane, and the dynamics of lipids and a lipophilic reporter dye, we performed atomistic molecular dynamics (MD) simulations of DiI-labeled dipalmitoylphosphatidylcholine (DPPC) lipid bilayers under physiological lateral tensions ranging from -2.6 mN m(-1) to 15.9 mN m(-1). Simulations showed that the bilayer thickness decreased linearly with tension consistent with volume-incompressibility, and this thinning was facilitated by a significant increase in acyl chain interdigitation at the bilayer midplane and spreading of the acyl chains. Tension caused a significant drop in the bilayer's peak electrostatic potential, which correlated with the strong reordering of water and lipid dipoles. For the low tension regime, the DPPC lateral diffusion coefficient increased with increasing tension in accordance with free-area theory. For larger tensions, free area theory broke down due to tension-induced changes in molecular shape and friction. Simulated DiI rotational and lateral diffusion coefficients were lower than those of DPPC but increased with tension in a manner similar to DPPC. Direct correlation of membrane order and viscosity near the DiI chromophore, which was just under the DPPC headgroup, indicated that measured DiI fluorescence lifetime, which is reported to decrease with decreasing lipid order, is likely to be a good reporter of tension-induced decreases in lipid headgroup viscosity. Together, these results offer new molecular-level insights into membrane tension-related mechanotransduction and into the utility of DiI in characterizing tension-induced changes in lipid packing.     

Elastic deformation of membrane bilayers probed by deuterium NMR relaxation

In deuterium ((2)H) NMR spectroscopy of fluid lipid bilayers, the average structure is manifested in the segmental order parameters (S(CD)) of the flexible molecules. The corresponding spin-lattice relaxation rates (R(1Z) depend on both the amplitudes and the rates of the segmental fluctuations, and indicate the types of lipid motions. By combining (2)H NMR order parameter measurements with relaxation studies, we have obtained a more comprehensive picture of lipids in the liquid-crystalline (L(alpha)) state than formerly possible. Our data suggest that a lipid bilayer constitutes an ordered fluid, in which the phospholipids are grafted to the aqueous interface via their polar headgroups, whereas the fatty acyl chains are in effect liquid hydrocarbon. Studies of (2)H-labeled saturated lipids indicate their R(1Z) rates and S(CD) order parameters are correlated by a model-free, square-law functional dependence, signifying the presence of relatively slow bilayer fluctuations. A new composite membrane deformation model explains simultaneously the frequency (magnetic field) dependence and the angular anisotropy of the relaxation. The results imply the R(1Z) rates are due to a broad spectrum of 3-D collective bilayer excitations, together with effective axial rotations of the lipids. For the first time, NMR relaxation studies show that the viscoelastic properties of membrane lipids at megahertz frequencies are modulated by the lipid acyl length (bilayer thickness), polar headgroups (bilayer interfacial area), inclusion of a nonionic detergent (C(12)E(8)), and the presence of cholesterol, leading to a range of bilayer softness. Our findings imply the concept of elastic deformation is relevant on lengths approaching the bilayer thickness and less (the mesoscopic scale), and suggest that application of combined R(1Z) and S(CD) studies of phospholipids can be used as a simple membrane elastometer. Heuristic estimates of the bilayer bending rigidity kappa and the area elastic modulus K(a) enable comparison to other biophysical studies, involving macroscopic deformation of thin membrane lipid films. Finally, the bilayer softness may be correlated with the lipid diversity of biomembranes, for example, with regard to membrane curvature, repulsive interactions between bilayers, and lipid-protein interactions.