CHARMM36 Lipid Force Field Research Articles

Leaflet Asymmetry Modeling in the Lipid Composition of Escherichia coli Cytoplasmic Membranes.

Lipid composition asymmetry between leaflets is important to cell function and plays a key role in the "positive inside" rule in transmembrane proteins. In this work, Escherichia coli inner plasma membrane models reflecting this asymmetry have been investigated at the early-log and stationary stages during the bacterial lifecycle using all-atom molecular dynamics simulations. The CHARMM36 lipid force field is used, and selected membrane properties are tested for variations between two leaflets and whole membranes. Our models include bacterial lipids with a cyclopropane moiety on the sn-2 acyl chain in the stationary membrane model. The PE/PG ratio for two leaflets reflects the "positive inside" rule of membrane proteins, set to 6.8 and 2.8 for the inner and outer leaflets of the two models, respectively. We are the first to model leaflet asymmetry in the lipid composition of E. coli cytoplasmic membranes and observe the effect on membrane properties in leaflets and whole membranes. Specifically, our results show that for the stationary phase bilayer, the surface area per lipid (SA/lipid) is larger, the thickness (2DC and DB) is smaller, the tilt angle is larger, the tilt modulus is smaller, and the deuterium order parameters (SCD) of sn-1 and sn-2 tails are lower, compared to the early-log stage. Moreover, the stationary stage bilayer has a positive spontaneous curvature, while the early-log stage has a near flat spontaneous curvature. For leaflet asymmetry, the inner leaflet has a larger SA/lipid, a smaller thickness, a smaller elastic tilt modulus (a larger tilt angle), and lower SCD, compared to the outer leaflet in both stages. Moreover, an asymmetric membrane involves a lipid tilt and a lateral extension, varying from a reference state of a pre-equilibrium membrane. This work encourages a more profound exploration of leaflet asymmetry in various other membrane models and how this might affect the structure and function of membrane-associated peptides and proteins.

All-Atom Modeling of Complex Cellular Membranes.

Cell membranes are composed of a variety of lipids and proteins where they interact with each other to fulfill their roles. The first step in modeling these interactions in molecular simulations is to have reliable mimetics of the membrane's lipid environment. This Feature Article presents our recent efforts to model complex cellular membranes using all-atom force fields. A short review of the CHARMM36 (C36) lipid force field and its recent update to incorporate the long-range dispersion is presented. Key examples of model membranes mimicking various species and organelles are given. These include single-celled organisms such as bacteria (E. coli., chlamydia, and P. aeruginosa) and yeast (plasma membrane, endoplasmic reticulum, and trans-Golgi network) and more advanced ones such as plants (soybean and Arabidopsis thaliana) and mammals (ocular lens, stratum corneum, and peripheral nerve myelin). Leaflet asymmetry in composition has also been applied to some of these models. With the increased lipid diversity in the C36 lipid FF, these complex models can better reflect the structural, mechanical, and dynamic properties of realistic membranes and open an opportunity to study biological processes involving other molecules.

CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids.

Long-range Lennard-Jones (LJ) interactions have been incorporated into the CHARMM36 (C36) lipid force field (FF) using the LJ particle-mesh Ewald (LJ-PME) method in order to remove the inconsistency of bilayer and monolayer properties arising from the exclusion of long-range dispersion [Yu, Y.; Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion. J. Chem. Theory Comput. 2021, 10.1021/acs.jctc.0c01326. (preceding article in this issue)]. The new FF is denoted C36/LJ-PME. While the first optimization was based on three phosphatidylcholines (PCs), this work extends the validation and parametrization to more lipids including PC, phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and ether lipids. The agreement with experimental structure data is excellent for PC, PE, and ether lipids. C36/LJ-PME also compares favorably with scattering data of PG bilayers but less so with NMR deuterium order parameters of 1,2-dimyristoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DMPG) at 303.15 K, indicating a need for future optimization regarding PG-specific parameters. Frequency dependence of NMR T1 spin-lattice relaxation times is well-described by C36/LJ-PME, and the overall agreement with experiment is comparable to C36. Lipid diffusion is slower than C36 due to the added long-range dispersion causing a higher viscosity, although it is still too fast compared to experiment after correction for periodic boundary conditions. When using a 10 Å real-space cutoff, the simulation speed of C36/LJ-PME is roughly equal to C36. While more lipids will be incorporated into the FF in the future, C36/LJ-PME can be readily used for common lipids and extends the capability of the CHARMM FF by supporting monolayers and eliminating the cutoff dependence.

Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion.

The development of the CHARMM lipid force field (FF) can be traced back to the early 1990s with its current version denoted CHARMM36 (C36). The parametrization of C36 utilized high-level quantum mechanical data and free energy calculations of model compounds before parameters were manually adjusted to yield agreement with experimental properties of lipid bilayers. While such manual fine-tuning of FF parameters is based on intuition and trial-and-error, automated methods can identify beneficial modifications of the parameters via their sensitivities and thereby guide the optimization process. This work introduces a semi-automated approach to reparametrize the CHARMM lipid FF with consistent inclusion of long-range dispersion through the Lennard-Jones particle-mesh Ewald (LJ-PME) approach. The optimization method is based on thermodynamic reweighting with regularization with respect to the C36 set. Two independent optimizations with different topology restrictions are presented. Targets of the optimizations are primarily liquid crystalline phase properties of lipid bilayers and the compression isotherm of monolayers. Pair correlation functions between water and lipid functional groups in aqueous solution are also included to address headgroup hydration. While the physics of the reweighting strategy itself is well-understood, applying it to heterogeneous, complex anisotropic systems poses additional challenges. These were overcome through careful selection of target properties and reweighting settings allowing for the successful incorporation of the explicit treatment of long-range dispersion, and we denote the newly optimized lipid force field as C36/LJ-PME. The current implementation of the optimization protocol will facilitate the future development of the CHARMM and related lipid force fields.

Recent Updates to the Charmm Lipid Force Fields

Since its release in the early 1990s, the CHARMM lipid force field (FF) has been updated frequently to agree with experimental data and to work with state-of-art simulation protocols. The most recent all-atom version, C36, has been heavily used due to the diversity of lipids it covers and the well-designed parameters, but it is not suitable for monolayer simulations due to the inconsistency of surface tension with experiment. To fix this problem, we introduced the long-range Lennard-Jones (LJ) interactions using the LJ Particle Mesh Ewald (LJ-PME) method and optimized the C36 parameter set to work with LJ-PME.

A New Lipid Force Field (FUJI).

To explore inhomogeneous and anisotropic systems such as lipid bilayers, the Lennard-Jones particle mesh Ewald (LJ-PME) method has been applied without a conventional isotropic dispersion correction. As the popular AMBER and CHARMM lipid force fields were developed using a cutoff scheme, their lipid bilayers unacceptably shrink when using the LJ-PME method. In this study, a new all-atom lipid force field (FUJI) was developed on the basis of the AMBER force-field scheme including the Lipid14 van der Waals parameters. Point charges were calculated using the restrained electrostatic potentials of many lipid conformers. Further, torsion energy profiles were calculated using high-level ab initio molecular orbitals (LCCSD(T)/Aug-cc-pVTZ//LMP2/Aug-cc-pVTZ), following which the molecular mechanical dihedral parameters were derived through a fast Fourier transform. By incorporation of these parameters into a new lipid force field without fitting experimental data, the desired lipid characteristics such as the area per lipid and lateral diffusion coefficients were obtained through GROMACS molecular dynamics simulations using the LJ-PME method and virtual hydrogen sites. The calculated area per lipid and lateral diffusion coefficients showed satisfactory agreement with experimental data. Furthermore, the electron-density profiles along the membrane normal were calculated for pure lipid bilayers, and the resulting membrane thicknesses agreed well with the experimental values. As the new lipid force field is compatible with FUJI for protein and small molecules, the new FUJI force field will offer accurate modeling for complex systems consisting of various membrane proteins and lipids.

Modifying the CHARMM36 Lipid Force Field for LJ-PME Simulations

Long-range Lennard-Jones (LJ) interactions were historically excluded from energy calculations in Molecular Dynamics (MD) simulations due to high computational cost. However, these interactions have a significant impact on the properties of nonpolar systems. The LJ particle-mesh Ewald (LJ-PME) method offers a solution to this problem and retains good efficiency. Here we introduce a modification to the additive all-atom CHARMM lipid force field (FF) which makes it compatible with the LJ-PME method. The last generation of the CHARMM36 (C36) lipid FF is suitable for NPT simulations of lipid bilayer systems using the PME method for the nonbonded interactions but systematically yields lower values of surface area per lipid compared to experimental estimates when the long-range LJ interactions are included. Here we develop an automated workflow to optimize the parameters of the nonbonded interactions (partial atomic charges and Lennard-Jones parameters). 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) is used as the prototype and various structural properties (surface area per lipid, NMR deuterium order parameters, radial distribution functions of water for selected atoms) are used as targets. In each optimization step, free energy perturbation theory is used to estimate the properties from trajectories generated by the optimal parameters in the previous step. QM calculations of partial atomic charges are also used to guide the optimization. The parametrization improves the above-mentioned properties significantly with small changes to the C36 lipid FF and allows MD simulations of lipid systems to use the LJ-PME method.

Molecular Ordering in Lipid Monolayers: An Atomistic Simulation.

We report on atomistic simulations of DPPC lipid monolayers using the CHARMM36 lipid force field (and also the Slipid force field as a control case), combined with a four-point OPC water model. The entire two-phase region where domains of the "liquid-condensed" (LC) phase coexist with domains of the "liquid-expanded" (LE) phase has been explored. The simulations are long enough that the complete phase-transition stage, with two domains coexisting in the monolayer, is reached in all cases. Also, system sizes used are larger than those in previous works. As expected, domains of the minority phase are elongated, emphasizing the importance of anisotropic van der Waals and/or electrostatic dipolar interactions in the monolayer plane. The molecular structure is quantified in terms of distribution functions for the hydrocarbon chains and the PN dipoles. In contrast to previous work, where average distributions are calculated, distributions are here extracted for each of the coexisting phases by first identifying lipid molecules that belong to either LC or LE regions. In the case of the CHARMM36 force field, the three-dimensional distributions show that the average tilt angle of the chains with respect to the normal outward direction is (39.0 ± 0.1)° in the LC phase and (48.1 ± 0.5)° in the LC phase. In the case of the PN dipoles, the distributions indicate a tilt angle of (110.8 ± 0.5)° in the LC phase and (112.5 ± 0.5)° in the LE phase. These results are quantitatively different from those in previous works, which indicated a smaller normal component of the PN dipole. Also, the distributions of the monolayer-projected chains and PN dipoles have been calculated. Chain distributions peak along a particular direction in the LC domains, while they are uniform in the LE phase. Long-range ordering associated with the projected PN dipoles is absent in both phases. These results strongly suggest that LC domains do not exhibit dipolar ordering in the plane of the monolayer, the effect of these components being averaged out at short distances. Therefore, the only relevant component of the molecular dipoles, with regard to both intra- and long-range interdomain interactions, is normal to the monolayer. Also, the local orientation of chain projections is almost constant in LC domains and points in the direction along which domains are elongated, suggesting that the line tension driving the phase transition might be anisotropic with respect to the interfacial domain boundary.

Modeling Pseudomonas aeruginosa Inner Plasma Membrane in Planktonic and Biofilm Modes

Pseudomonas aeruginosa changes its growth modes under different conditions. The bacteria in biofilm is more resistant to environmental stress compared to the planktonic mode of growth. The compositions of the inner plasma membrane for the two modes are noticeably different. Major lipid types are chosen from experiment to model the membrane in both modes of growth, and molecular dynamics simulation is used to study the properties of the membrane. The CHARMM36 lipid force field is used and tested against several experimental results. Our models include lipids containing cyclopropane in the middle of the sn-2 tail, namely, 1-palmitoyl-2-cis-11,12-methylene-stearic-acid-sn-glycero-3-phosphoethanolamine and 1-palmitoyl-2-cis-11,12-methylene-stearic-acid-sn-glycero-3-phosphoglycerol. The PE:PG ratio for the two model membranes is close, but the fraction of lipids composed of long-chain and cyclopropane-containing fatty acids changes significantly, causing differences between the two models. Compared to previous model membranes built for Escherichia coli, the inner membrane of P. aeruginosa has a longer averaged lipid tail length and a higher percentage of PG lipids, which are responsible for the changes in membrane properties like membrane thickness and stiffness. Most importantly, the comparison to experiments shows good agreements and encourages the model's use to study the behavior of proteins from P. aeruginosa associated with the membrane.

Ripple and Gel Phases of Saturated Phosphocholine Bilayers Investigated with Simulations

Lipid bilayers with saturated acyl chains typically are in a liquid crystalline (Lα) phase, but can condense to a ripple (Pβ) or gel (Lβ) phase. We focused on 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dipalmitoyl-sn-glycero-phosphocholine (DPPC) lipid bilayers and their mixtures to characterize these lipid phases. MD simulations with the CHARMM36 lipid force field accurately predict the main transition temperature of DMPC and DPPC bilayers. Our MD simulations focused on the less-characterized Pβ phase and compared to x-ray experiments. The Pβ major arm has similar structure to that of the Lβ, while the thinner minor arm has interdigitated chains and the transition region between these two regions has large chain splay and disorder. The length of these major/minor arms are in reasonable agreement with x-ray experiments based on several μs of simulation. The Lβ phase form a chain tilt and lipid packing in good agreement with experiment. This work demonstrates that the CHARMM36 lipid force field can accurately represent more condensed phases and provides insight into the complex structure of the ripple phase.

Modeling Pseudomonas aeruginosa inner plasma membrane in planktonic and biofilm modes.

Pseudomonas aeruginosa changes its growth modes under different conditions. The bacteria in biofilm is more resistant to environmental stress compared to the planktonic mode of growth. The compositions of the inner plasma membrane for the two modes are noticeably different. Major lipid types are chosen from experiment to model the membrane in both modes of growth, and molecular dynamics simulation is used to study the properties of the membrane. The CHARMM36 lipid force field is used and tested against several experimental results. Our models include lipids containing cyclopropane in the middle of the sn-2 tail, namely, 1-palmitoyl-2-cis-11,12-methylene-stearic-acid-sn-glycero-3-phosphoethanolamine and 1-palmitoyl-2-cis-11,12-methylene-stearic-acid-sn-glycero-3-phosphoglycerol. The PE:PG ratio for the two model membranes is close, but the fraction of lipids composed of long-chain and cyclopropane-containing fatty acids changes significantly, causing differences between the two models. Compared to previous model membranes built for Escherichia coli, the inner membrane of P. aeruginosa has a longer averaged lipid tail length and a higher percentage of PG lipids, which are responsible for the changes in membrane properties like membrane thickness and stiffness. Most importantly, the comparison to experiments shows good agreements and encourages the model's use to study the behavior of proteins from P. aeruginosa associated with the membrane.

Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field.

Whether lipid rafts are presentin the membranes of living cells remains hotly disputed despite their incontrovertible existence in liposomes at 298 K. In attempts to resolve this debate, molecular dynamics (MD) simulations have been extensively used to study lipid phase separation at high resolution. However, computation has been of limited utility in this respect because the experimental distributions of phases in lamellar lipid mixtures are poorly reproduced by simulations. In particular, all-atom (AA) approaches suffer from restrictions on accessible time scales and system sizes whereas the more efficient coarse-grained (CG) force fields remain insufficiently accurate to achieve correspondence with experiment. In this work, we refine the CG Martini parameters for the high- and low-melting temperature ( Tm) lipids 1,2-dipalmitoyl- sn-glycero-3-phosphatidylcholine (DPPC) and 1,2-dioleoyl- sn-glycero-3-phosphatidylcholine (DOPC). Our approach involves the modification of bonded Martini parameters based on fitting to atomistic simulations conducted with the CHARMM36 lipid force field. The resulting CG parameters reproduce experimental structural and thermodynamic properties of homogeneous lipid membranes while concurrently improving simulation fidelity to experimental phase diagrams of DPPC, DOPC, and cholesterol lipid mixtures. Importantly, the refined parameters provide much better phase accuracy for regions near the critical point that mimic the lipid concentrations under physiological conditions.

Simulations of lipid bilayers using the CHARMM36 force field with the TIP3P-FB and TIP4P-FB water models.

The CHARMM36 force field for lipids is widely used in simulations of lipid bilayers. The CHARMM family of force fields were developed for use with the mTIP3P water model. This water model has an anomalously high dielectric constant and low viscosity, which limits its accuracy in the calculation of quantities like permeability coefficients. The TIP3P-FB and TIP4P-FB water models are more accurate in terms of the dielectric constant and transport properties, which could allow more accurate simulations of systems containing water and lipids. To test whether the CHARMM36 lipid force field is compatible with the TIP3P-FB and TIP4P-FB water models, we have performed simulations of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers. The calculated headgroup area, compressibility, order parameters, and X-ray form factors are in good agreement with the experimental values, indicating that these improved water models can be used with the CHARMM36 lipid force field without modification when calculating membrane physical properties. The water permeability predicted by these models is significantly different; the mTIP3P-model diffusion in solution and at the lipid–water interface is anomalously fast due to the spuriously low viscosity of mTIP3P-model water, but the potential of mean force of permeation is higher for the TIP3P-FB and TIP4P-FB models due to their high excess chemical potentials. As a result, the rates of water permeation calculated the FB water models are slower than the experimental value by a factor of 15–17, while simulations with the mTIP3P model only underestimate the water permeability by a factor of 3.

Investigation of phase transitions of saturated phosphocholine lipid bilayers via molecular dynamics simulations

Lipid bilayers play an important role in biological systems as they protect cells against unwanted chemicals and provide a barrier for material inside a cell from leaking out. In this paper, nearly 30 μs of molecular dynamics (MD) simulations were performed to investigate phase transitions of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dipalmitoyl-sn-glycero-phosphocholine (DPPC) lipid bilayers from the liquid crystalline (Lα) to the ripple (Pβ) and to the gel phase (Lβ). Our MD simulations accurately predict the main transition temperature for the single-component bilayers. A key focus of this work is to quantify the structure of the Pβ phase for DMPC and compare with measures from x-ray experiments. The Pβ major arm has similar structure to that of the Lβ, while the thinner minor arm has interdigitated chains and the transition region between these two regions has large chain splay and disorder. At lower temperatures, our MD simulations predict the formation of the Lβ phase with tilted fatty acid chains. The Pβ and Lβ phases are studied for mixtures of DMPC and DPPC and compare favorably with experiment. Overall, our MD simulations provide evidence for the relevancy of the CHARMM36 lipid force field for structures and add to our understanding of the less-defined Pβ phase.

Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers.

Lung surfactant and a tear film lipid layer are examples of biologically relevant macromolecular structures found at the air-water interface. Because of their complexity, they are often studied in terms of simplified lipid layers, the simplest example being a Langmuir monolayer. Given the profound biological significance of these lipid assemblies, there is a need to understand their structure and dynamics on the nanoscale, yet there are not many techniques able to provide this information. Atomistic molecular dynamics simulations would be a tool fit for this purpose; however, the simulation models suggested until now have been qualitative instead of quantitative. This limitation has mainly stemmed from the challenge to correctly describe the surface tension of water with simulation parameters compatible with other biomolecules. In this work, we show that this limitation can be overcome by using the recently introduced four-point OPC water model, whose surface tension for water is demonstrated to be quantitatively consistent with experimental data and which is also shown to be compatible with the commonly employed lipid models. We further establish that the approach of combining the OPC four-point water model with the CHARMM36 lipid force field provides nearly quantitative agreement with experiments for the surface pressure-area isotherm for POPC and DPPC monolayers, also including the experimentally observed phase coexistence in a DPPC monolayer. The simulation models reported in this work pave the way for nearly quantitative atomistic studies of lipid-rich biological structures at air-water interfaces.

Simulations of simple linoleic acid-containing lipid membranes and models for the soybean plasma membranes.

The all-atom CHARMM36 lipid force field (C36FF) has been tested with saturated, monounsaturated, and polyunsaturated lipids; however, it has not been validated against the 18:2 linoleoyl lipids with an unsaturated sn-1 chain. The linoleoyl lipids are common in plants and the main component of the soybean membrane. The lipid composition of soybean plasma membranes has been thoroughly characterized with experimental studies. However, there is comparatively less work done with computational modeling. Our molecular dynamics (MD) simulation results show that the pure linoleoyl lipids, 1-stearoyl-2-linoleoyl-sn-glycero-3-phosphocholine (18:0/18:2) and 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (di-18:2), agree very well with the experiments, which demonstrates the accuracy of the C36FF for the computational study of soybean membranes. Based on the experimental composition, the soybean hypocotyl and root plasma membrane models are developed with each containing seven or eight types of linoleoyl phospholipids and two types of sterols (sitosterol and stigmasterol). MD simulations are performed to characterize soybean membranes, and the hydrogen bonds and clustering results demonstrate that the lipids prefer to interact with the lipids of the same/similar tail unsaturation. All the results suggest that these two soybean membrane models can be used as a basis for further research in soybean and higher plant membranes involving membrane-associated proteins.

Lo/Ld Phase Coexistence and Interaction in Model Membranes with IPC Lipids

New computational resources, such as Anton, have allowed the study of Lo/Ld phase coexistence in equimolar mixtures of inositol phosphoceramide (IPC), ergosterol (ERG), and phosphatidylinositol (PI) or phosphatidylcholine (PC) lipids. These models are preliminary studies of representative models for the trans-Golgi network and plasma membrane of yeast (Saccharomyces cerevisiae). Our past research on yeast membrane models lacked IPC lipids because at the time ceramide lipids were not fully parameterized for the CHARMM36 lipid force field. Such parameters have been published for sphingolipids (BJ, 107:134-145) and we have extended their use for various ceramides. Phase segregation was shown in IPC/PI/ERG mixtures obtained from separated total lipid extracts of yeast membranes (JBC, 285:30224-30232). Moreover, IPC/PI/ERG had more order than IPC/PC/ERG mixtures, but the reasoning for this is not known. We present the results of two 6μs trajectories of all-atom simulations for each ternary system to probe the formation of lipid domains as well as the increase in order effect of PI vs. PC lipids. Our studies expand on the work of Sodt et al. (JACS, 136:725-732) from simple model systems (DPPC/DOPC/cholesterol) to understanding the effects of head group on the phase behavior and long-chained IPC lipids on potential interleaflet coupling (BJ, 103:2311-2319). We examined lipid diffusion time scales, deuterium order parameters, electron density profiles, lipid head group interaction mechanisms such as hydrogen bonding, and sterol flip-flop timescales.

Molecular Dynamics Simulations of Sphingomyelin-Cholesterol Bilayers

Sphingolipids are one of the major components in animal cell membranes. One type of sphingolipids is sphingomyelins which are abundant in myelin sheath surrounding nerve cell axons. The two common forms of sphingomyelin targeted in this research are palmitoylsphingomyelin (PSM) and stearoylsphingomyelin (SSM). Another bilayer component included in our membranes that has high affinity to sphingomyelins is cholesterol, which aids in maintaining membrane fluidity and structural integrity. Sphingomyelins and cholesterol make up a great part of highly dynamic membrane domains, termed lipid rafts. With that being said, this work tests the accuracy of molecular dynamics (MD) simulations with the CHARMM36 (C36) lipid force field for PSM and SSM, each SM bilayer has varying concentrations of cholesterol. Properties such as surface area per lipid, x-ray and neutron form factors, and chain deuterium order parameters are to be compared to those yielded from past experiments to prove C36's ability to correctly simulate the mixed SM-cholesterol lipid bilayers. Based on past studies on C36 lipid force field, we expect to see excellent agreement between experimental and MD simulation data for more complex mixtures of membranes that contain SM lipids.

How Does Ethanol Affect the Stability of Simple Model Yeast Membranes?

Biofuels such as biomass-based ethanol (EtOH) have become increasingly popular as a source of renewable energy, but the higher cost of production and lower energy content make the fuel difficult to compete with petroleum gasoline. Cellulosic biomass can be used to produce bioethanol, but process efficiency is limited by ethanol's cytotoxic nature. One proposed mechanism for EtOH inhibition of yield growth suggests that ethanol diffuses through cell membranes, decreasing the lipid bilayer stability. Bilayers comprising various molar concentrations of 1-palmitoyl-2-oleoylphosphatidlyserine (POPS), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipids were simulated using molecular dynamics. Pure POPS, pure POPE, pure POPC, and mixed 30/70 POPS/POPE lipid bilayers were constructed using the CHARMM36 lipid force field. Each lipid bilayer was exposed to molar concentrations of 0.5%, 1%, 2%, 3%, and 4% ethanol EtOH with additional molar concentrations of 5% and 10% EtOH for pure bilayers only. Average bilayer surface area, NMR deuterium order parameters (SCD), and electron density profiles (EDP) were analyzed to interpret bilayer stability. Each analysis indicated decreased membrane stability with increased EtOH concentration, supporting the proposed mechanism. Trends between different lipid bilayer compositions were all similar. Surface area increases resulted from more frequent EtOH bilayer penetrations into the hydrophobic core, causing bilateral expansion of the membrane's walls. SCD values decreased as more EtOH penetrated the bilayer due to the disruption of lipid packing, increasing membrane fluidity and decreasing stabilizing interactions between hydrophobic lipid tails. As overall EtOH concentration increased, EDP plots indicated increased EtOH concentration within the bilayer, past the hydrophilic head region. EDP plots also indicated decreased bilayer thickness. Increased concentration of EtOH within the bilayer is in accordance with SCD results and decreased bilayer thickness supports increased bilayer surface area results.

All-atom lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields.

This communication reports the first example of spontaneous lipid bilayer formation in unbiased all-atom molecular dynamics (MD) simulations. Using two different lipid force fields we show simulations started from random mixtures of lipids and water in which four different types of phospholipids self-assemble into organized bilayers in under 1 microsecond.