Bilayer Midplane Research Articles

An Unexpected Driving Force for Lipid Order Appears in Asymmetric Lipid Bilayers.

An ordered phase in one leaflet of an asymmetric bilayer can induce a precisely superimposed induced order domain in the apposed leaflet. Order is induced in such simple lipid compositions as dioleoylphosphatidylcholine/cholesterol (DOPC)/chol) which is expected to be a uniform and disordered lipid mixture. Dye partitioning can be used to label and identify coexisting liquid-disordered (Ld), liquid-ordered (Lo), or gel-ordered (Lβ) molecules in a phase-separated leaflet. In the other leaflet of an asymmetric bilayer, dye partitioning also labels and identifies any induced order domains created by an Lo or gel phase domain in the apposed leaflet as well as the state of disorder of the lipid surrounding the induced ordered region. We explore a molecular level mechanism by which a disorder-prone uniform mixture of DOPC/chol = 0.8/0.2 would spontaneously separate into ordered regions coexisting with disordered regions. A redistribution of cholesterol seems to take place in the regions apposed to the ordered phase. The precision of the superposition of Lo or gel domains with their induced order domains implies a strong energy penalty that would be incurred if order/disorder interfaces were to form at the bilayer midplane. We conclude that the energy penalty for Lo/Ld or gel/Ld contact in the bilayer midplane is sufficient to drive disorderly DOPC/chol into an ordered state that reduces unfavorable order-disorder contacts at the bilayer midplane interface.

Interdependence of cholesterol distribution and conformational order in lipid bilayers.

We show, via molecular simulations, that not only does cholesterol induce a lipid order, but the lipid order also enhances cholesterol localization within the lipid leaflets. Therefore, there is a strong interdependence between these two phenomena. In the ordered phase, cholesterol molecules are predominantly present in the bilayer leaflets and orient themselves parallel to the bilayer normal. In the disordered phase, cholesterol molecules are mainly present near the center of the bilayer at the midplane region and are oriented orthogonal to the bilayer normal. At the melting temperature of the lipid bilayers, cholesterol concentration in the leaflets and the bilayer midplane is equal. This result suggests that the localization of cholesterol in the lipid bilayers is mainly dictated by the degree of ordering of the lipid bilayer. We validate our findings on 18 different lipid bilayer systems, obtained from three different phospholipid bilayers with varying concentrations of cholesterol. To cover a large temperature range in simulations, we employ the Dry Martini force field. We demonstrate that the Dry and the Wet Martini (with polarizable water) force fields produce comparable results.

Non-Polar Lipids as Regulators of Membrane Properties in Archaeal Lipid Bilayer Mimics.

The modification of archaeal lipid bilayer properties by the insertion of apolar molecules in the lipid bilayer midplane has been proposed to support cell membrane adaptation to extreme environmental conditions of temperature and hydrostatic pressure. In this work, we characterize the insertion effects of the apolar polyisoprenoid squalane on the permeability and fluidity of archaeal model membrane bilayers, composed of lipid analogues. We have monitored large molecule and proton permeability and Laurdan generalized polarization from lipid vesicles as a function of temperature and hydrostatic pressure. Even at low concentration, squalane (1 mol%) is able to enhance solute permeation by increasing membrane fluidity, but at the same time, to decrease proton permeability of the lipid bilayer. The squalane physicochemical impact on membrane properties are congruent with a possible role of apolar intercalants on the adaptation of Archaea to extreme conditions. In addition, such intercalant might be used to cheaply create or modify chemically resistant liposomes (archeaosomes) for drug delivery.

Characterisation of a synthetic Archeal membrane reveals a possible new adaptation route to extreme conditions

It has been proposed that adaptation to high temperature involved the synthesis of monolayer-forming ether phospholipids. Recently, a novel membrane architecture was proposed to explain the membrane stability in polyextremophiles unable to synthesize such lipids, in which apolar polyisoprenoids populate the bilayer midplane and modify its physico-chemistry, extending its stability domain. Here, we have studied the effect of the apolar polyisoprenoid squalane on a model membrane analogue using neutron diffraction, SAXS and fluorescence spectroscopy. We show that squalane resides inside the bilayer midplane, extends its stability domain, reduces its permeability to protons but increases that of water, and induces a negative curvature in the membrane, allowing the transition to novel non-lamellar phases. This membrane architecture can be transposed to early membranes and could help explain their emergence and temperature tolerance if life originated near hydrothermal vents. Transposed to the archaeal bilayer, this membrane architecture could explain the tolerance to high temperature in hyperthermophiles which grow at temperatures over 100 °C while having a membrane bilayer. The induction of a negative curvature to the membrane could also facilitate crucial cell functions that require high bending membranes.

Partitioning of Aβ Peptide Fragments into Blood-Brain Barrier Mimetic Bilayer.

We used all-atom replica-exchange umbrella sampling molecular dynamics simulations to investigate the partitioning of the charged tetrapeptide KLVF and its neutral apolar counterpart VVIA into the blood-brain barrier (BBB)-mimetic bilayer. Our findings allowed us to reconstruct the partitioning mechanism for these two Aβ peptide fragments. Despite dissimilar sequences, their permeation shares significant common features. Computations of free energies and permeabilities show that partitioning of both peptides is highly unfavorable, ruling out passive transport. The peptides experience multiple rotational transitions within the bilayer and typically cause considerable lipid disorder and bilayer thinning. Near the bilayer midplane, they lose almost entirely their solvation shell and the interactions with the lipid headgroups. The peptides cause complex reorganization within the proximal bilayer region. Upon insertion, they induce striking cholesterol influx reversed by its depletion and the influx of DMPC when the peptides reach the midplane. The differences in partitioning mechanisms are due to the much higher polarity of KLVF peptide, the permeation of which is more unfavorable and which exclusively assumes vertical orientations within the bilayer. In contrast, VVIA positions itself flat between the leaflets, causing minor disorder and even thickening of the BBB-mimetic bilayer. Due to the high density of the cholesterol-rich BBB bilayer, the unfavorable work associated with the peptide insertion provides a significant, but not dominant, contribution to the partition free energy, which is still governed by dehydration and loss of peptide-headgroup interactions. Comparison with experiments indicates that KLVF and VVIA permeation is similar to that of proline tetrapeptide, mannitol, or cimetidine, all of which exhibit no passive transport.

Partitioning of Benzoic Acid into 1,2-Dimyristoyl-sn-glycero-3-phosphocholine and Blood-Brain Barrier Mimetic Bilayers.

Using an all-atom explicit water model and replica exchange umbrella sampling simulations, we investigated the molecular mechanisms of benzoic acid partitioning into two model lipid bilayers. The first was formed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids, whereas the second was composed of an equimolar mixture of DMPC, 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine, palmitoylsphingomyelin, and cholesterol to constitute a blood-brain barrier (BBB) mimetic bilayer. Comparative analysis of benzoic acid partitioning into the two bilayers has revealed qualitative similarities. Partitioning into the DMPC and BBB bilayers is thermodynamically favorable although insertion into the former lowers the free energy of benzoic acid by approximately an additional 1 kcal mol-1. The partitioning energetics for the two bilayers is also largely similar based on the balance of benzoic acid interactions with apolar fatty acid tails, polar lipid headgroups, and water. In both bilayers, benzoic acid retains a considerable number of residual water molecules until reaching the bilayer midplane where it experiences nearly complete dehydration. Upon insertion into the bilayers, benzoic acid undergoes several rotations primarily determined by the interactions with the lipid headgroups. Nonetheless, in addition to the depth of the free energy minimum, the BBB bilayer differs from the DMPC counterpart by a much deeper location of the free energy minimum and the appearance of a high free energy barrier and positioning of benzoic acid near the midplane. Furthermore, DMPC and BBB bilayers exhibit different structural responses to benzoic acid insertion. Taken together, the BBB mimetic bilayer is preferable for an accurate description of benzoic acid partitioning.

Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations

The permeation of small-molecule drugs across a phospholipid membrane bears much interest both in the pharmaceutical sciences and in physical chemistry. Connecting the chemistry of the drug and the lipids to the resulting thermodynamic properties remains of immediate importance. Here we report molecular dynamics (MD) simulation trajectories using the coarse-grained (CG) Martini force field. A wide, representative coverage of chemistry is provided: across solutes—exhaustively enumerating all 105 CG dimers—and across six phospholipids. For each combination, umbrella-sampling simulations provide detailed structural information of the solute at all depths from the bilayer midplane to bulk water, allowing a precise reconstruction of the potential of mean force. Overall, the present database contains trajectories from 15,120 MD simulations. This database may serve the further identification of structure-property relationships between compound chemistry and drug permeability.

Permeability of membranes in the liquid ordered and liquid disordered phases

The functional significance of ordered nanodomains (or rafts) in cholesterol rich eukaryotic cell membranes has only begun to be explored. This study exploits the correspondence of cellular rafts and liquid ordered (Lo) phases of three-component lipid bilayers to examine permeability. Molecular dynamics simulations of Lo phase dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), and cholesterol show that oxygen and water transit a leaflet through the DOPC and cholesterol rich boundaries of hexagonally packed DPPC microdomains, freely diffuse along the bilayer midplane, and escape the membrane along the boundary regions. Electron paramagnetic resonance experiments provide critical validation: the measured ratio of oxygen concentrations near the midplanes of liquid disordered (Ld) and Lo bilayers of DPPC/DOPC/cholesterol is 1.75 ± 0.35, in very good agreement with 1.3 ± 0.3 obtained from simulation. The results show how cellular rafts can be structurally rigid signaling platforms while remaining nearly as permeable to small molecules as the Ld phase.

Hydrophobic Characteristic Is Energetically Preferred for Cysteine in a Model Membrane Protein

The naturally occurring amino acid cysteine has often been implicated with a crucial role in maintaining protein structure and stability. An intriguing duality in the intrinsic hydrophobicity of the cysteine side chain is that it exhibits both polar as well as hydrophobic characteristics. Here, we have utilized a cysteine-scanning mutational strategy on the transmembrane β-barrel PagP to examine the membrane depth-dependent energetic contribution of the free cysteine side chain (thiolate) versus the parent residue at an experimental pH of 9.5 in phosphatidylcholine vesicles. We find that introduction of cysteine causes destabilization at several of the 26 lipid-facing sites of PagP that we mutated in this study. The destabilization is minimal (0.5–1.5 kcal/mol) when the mutation is toward the bilayer midplane, whereas it is higher in magnitude (3.0–5.0 kcal/mol) near the bilayer interface. These observations suggest that cysteine forms more favorable interactions with the hydrophobic lipid core as compared to the amphiphilic water-lipid interface. The destabilizing effect is more pronounced when cysteine replaces the interfacial aromatics, which are known to participate in tertiary interaction networks in transmembrane β-barrels. Our observations from experiments involving the introduction of cysteine at the bilayer midplane further strengthen previous views that the free cysteine side chain does possess strongly apolar characteristics. Additionally, the free energy changes observed upon cysteine incorporation show a depth-dependent correlation with the estimated energetic cost of partitioning derived from reported hydrophobicity scales. Our results and observations from the thermodynamic analysis of the PagP barrel may explain why cysteine, despite possessing a polar sulfhydryl group, tends to behave as a hydrophobic (rather than polar) residue in folded protein structures.

Energy landscape for the insertion of amphiphilic nanoparticles into lipid membranes: A computational study.

Amphiphilic, monolayer-protected gold nanoparticles (NPs) have been shown to enter cells via a non-endocytic, non-disruptive pathway that could be valuable for biomedical applications. The same NPs were also found to insert into a series of model cell membranes as a precursor to cellular uptake, but the insertion mechanism remains unclear. Previous simulations have demonstrated that an amphiphilic NP can insert into a single leaflet of a planar lipid bilayer, but in this configuration all charged end groups are localized to one side of the bilayer and it is unknown if further insertion is thermodynamically favorable. Here, we use atomistic molecular dynamics simulations to show that an amphiphilic NP can reach the bilayer midplane non-disruptively if charged ligands iteratively “flip” across the bilayer. Ligand flipping is a favorable process that relaxes bilayer curvature, decreases the nonpolar solvent-accessible surface area of the NP monolayer, and increases attractive ligand-lipid electrostatic interactions. Analysis of end group hydration further indicates that iterative ligand flipping can occur on experimentally relevant timescales. Supported by these results, we present a complete energy landscape for the non-disruptive insertion of amphiphilic NPs into lipid bilayers. These findings will help guide the design of NPs to enhance bilayer insertion and non-endocytic cellular uptake, and also provide physical insight into a possible pathway for the translocation of charged biomacromolecules.

Presence and Role of Midplane Cholesterol in Lipid Bilayers Containing Registered or Antiregistered Phase Domains

Three-component lipid mixtures can produce coexisting liquid ordered and liquid disordered phases, a model for eukaryotic plasma membrane rafts. In compositionally symmetric bilayers with twophase-separated leaflets, phase domains of the two leaflets may align through registration, where domains are found across from domains of the same phase, or else antiregistration, where domains are found across from domains of the opposite phase. This alignment could serve as a method of information communication across the plasma membrane. We used coarse-grained molecular dynamics simulations to study ternary mixtures of a high-melting-temperature phospholipid, a low-melting-temperature phospholipid, and cholesterol. We found a significant presence of cholesterol molecules at the bilayer midplane rather than in a leaflet in some systems, corresponding to a lack of registration. Increasing the length of the acyl chains from 16 to 24 carbons in high-melting-temperature phospholipids or increasing the concentration of cholesterol from 20 to 35 mol % in the bilayer produced a transition from registration to antiregistration and gave rise to significant populations of midplane cholesterol.

Phase behavior of cholesterol-containing binary membrane of an ether-linked phospholipid, dihexadecylphosphatidylcholine

The thermotropic phase behavior of the cholesterol (Chol)-containing binary membrane of dihexadecylphosphatidylcholine (DHPC) was investigated as a function of the mole fraction of Chol Xch by DSC and fluorescence spectroscopy using 6-propionyl-2-(N,N-dimethylamino)naphthalene (Prodan). The main-transition enthalpy ΔHm was almost constant at Xch < ca. 0.05, but it decreased almost linearly with increasing Xch above 0.05 until it reached 0 at Xch = ca. 0.50, suggesting that the interaction between DHPC and Chol is relatively weaker than that between dipalmitoylphosphatidylcholine (DPPC) and Chol. The Prodan fluorescence spectra changed depending on the phase state, which was characterized by the wavelength at the emission maximum. Particularly, the two-phase state of the interdigitated (LβI) and non-interdigitated (Lβ) gel was sensitively detected as the superposition of the two elementary spectra corresponding to each phase state, allowing us to explain the Xch dependent non-linear behavior of the Chol-induced Lβ phase by introducing a proportionality factor ξ(Xch) and by assuming a simple probabilistic process. By comparing the phase diagram constructed for the DHPC–Chol binary membrane with that for the DPPC–Chol binary bilayer, a difference was observed in the minimum Xch value for the entire formation of the liquid ordered (Lo) phase. This difference could be explained in terms of the hydrophobic mismatch at the bilayer midplane by taking into account the difference in the capability of hydrogen bonding with the 3β-OH group of Chol due to the presence or absence of the carbonyl oxygens at the glycerol backbone.

Determining the Pivotal Plane of Fluid Lipid Membranes in Simulations

Each leaflet of a curved lipid membrane contains a surface at which the area strain vanishes, the so-called pivotal plane. Its distance z0 from the bilayer's mid-plane arises in numerous membrane structure related contexts, for instance the connection between monolayer and bilayer moduli, stress-profile moments, or area-difference elasticity theories. Experimentally, the pivotal plane is known to lie close to the glycerol backbone of a lipid, but only very few simulations have tried to locate it. Here we propose two precise methods for determining z0, both of which rely on monitoring the lipid imbalance across a curved bilayer. The first method considers the ratio of lipid number between the two leaflets of cylindrical or spherical vesicles and requires lipid flip-flop for equilibration. The second method looks at the leaflet difference across local sections cut out from a buckled membrane and is free of this limitation. Our simulations rely on two different coarse-grained lipid models. First, the generic three-bead solvent-free Cooke model, which is amenable to both methods and gives results for z0 that agree at the percent level. And second, a ten-bead representation of dimyristoylphosphocholine (DMPC) with the explicit solvent MARTINI model, which can only be analyzed with the buckling method. For the latter, the obtained value z0 = 0.850(11) nm lies about 0.4 nm inwards of the glycerol backbone, essentially in the middle of the leaflet, and is hence unexpectedly small. We attribute this to limitations of the coarse-grained description, suggesting that the location of the pivotal plane might be a novel indicator for how well lipid models capture the microscopic origins of curvature elasticity, especially the relative contributions of head and tail regions to the overall curvature modulus.

Lipid bilayer thickness determines cholesterol's location in model membranes.

Cholesterol is an essential biomolecule of animal cell membranes, and an important precursor for the biosynthesis of certain hormones and vitamins. It is also thought to play a key role in cell signaling processes associated with functional plasma membrane microdomains (domains enriched in cholesterol), commonly referred to as rafts. In all of these diverse biological phenomena, the transverse location of cholesterol in the membrane is almost certainly an important structural feature. Using a combination of neutron scattering and solid-state 2H NMR, we have determined the location and orientation of cholesterol in phosphatidylcholine (PC) model membranes having fatty acids of different lengths and degrees of unsaturation. The data establish that cholesterol reorients rapidly about the bilayer normal in all the membranes studied, but is tilted and forced to span the bilayer midplane in the very thin bilayers. The possibility that cholesterol lies flat in the middle of bilayers, including those made from PC lipids containing polyunsaturated fatty acids (PUFAs), is ruled out. These results support the notion that hydrophobic thickness is the primary determinant of cholesterol's location in membranes.

Interleaflet mixing and coupling in liquid-disordered phospholipid bilayers

Organized as bilayers, phospholipids are the fundamental building blocks of cellular membranes and determine many of their biological functions. Interactions between the two leaflets of the bilayer (interleaflet coupling) have been implicated in the passage of information through membranes. However, physically, the meaning of interleaflet coupling is ill defined and lacks a structural basis. Using all-atom molecular dynamics simulations of fluid phospholipid bilayers of five different lipids with differing degrees of acyl-chain asymmetry, we have examined interleaflet mixing to gain insights into coupling. Reasoning that the transbilayer distribution of terminal methyl groups is an appropriate measure of interleaflet mixing, we calculated the transbilayer distributions of the acyl chain terminal methyl groups for five lipids: dioleoylphosphatidylcholine (DOPC), palmitoyloleoylphosphatidylcholine (POPC), stearoyloleoylphosphatidylcholine (SOPC), oleoylmyristoylphosphatidylcholine (OMPC), and dimyristoylphosphatidylcholine (DMPC). We observed in all cases very strong mixing across the bilayer midplane that diminished somewhat with increasing acyl-chain ordering defined by methylene order parameters. A hallmark of the interleaflet coupling idea is complementarity, which postulates that lipids with short alkyl chains in one leaflet will preferentially associate with lipids with long alkyl chains in the other leaflet. Our results suggest a much more complicated picture for thermally disordered bilayers that we call distributed complementarity, as measured by the difference in the peak positions of the sn-1 and sn-2 methyl distributions in the same leaflet.

Determining the pivotal plane of fluid lipid membranes in simulations.

Each leaflet of a curved lipid membrane contains a surface at which the area strain vanishes, the so-called pivotal plane. Its distance z0 from the bilayer's midplane arises in numerous contexts, for instance the connection between monolayer and bilayer moduli, stress-profile moments, or area-difference elasticity theories. Here, we propose two precise methods for determining the location of the pivotal plane in computer simulations, both of which rely on monitoring the lipid imbalance across a curved bilayer. The first method considers the ratio of lipid number between the two leaflets of cylindrical or spherical vesicles; it hence requires lipid flip-flop for equilibration. The second method looks at the leaflet difference across local sections cut out from a buckled membrane; this observable equilibrates even in the absence of flip-flop. We apply our methods to two different coarse-grained lipid models, the generic three-bead solvent-free Cooke model and a ten-bead representation of dimyristoylphosphocholine with the explicit solvent MARTINI model. The Cooke model is amenable to both methods and gives results that agree at the percent level. Using it, we also show that the pivotal plane moves outward as lipid curvature becomes more positive. The MARTINI model can only be analyzed with the buckling method; the obtained value z0 = 0.850(11) nm lies about 0.4 nm inwards of the glycerol backbone and is hence unexpectedly small. We attribute this to limitations of the coarse-grained description, suggesting that the location of the pivotal plane might be a good indicator for how well lipid models capture the microscopic origins of curvature elasticity. Finally, we also show that the pivotal plane position itself moves as the membrane is bent. The leading correction is linear in curvature, dependent on the Poisson ratio, and can matter when analyzing experimental results obtained from highly curved inverse hexagonal phases.

The N-Terminal Domain Acts as an Anchor during the Gating Cycle of MscL

This study utilizes a finite element (FE) model to probe the gating mechanism of the mechanosensitive channel of large conductance (MscL). When compared to molecular dynamics simulations, FE computations are generally more applicable due to their much longer simulation times as well as larger size scales. Herein we use an FE model of MscL, which has been developed as an initial template to provide not only information about the gating cycle of this channel but also to provide a structural framework for a mechanistic understanding of the gating of other MS channels at the continuum level. The FE model, unlike molecular dynamics simulations, utilized membrane tension corresponding to midpoint activation of MscL close to that seen in patch-clamp experiments (<12 mN/m). For MscL in the open state, our model indicates that the N-terminus and TM1 of each subunit become aligned to form a single helix. Previous mutagenic work suggests that the N-terminus of MscL, which connects the TM1 helix to the lipid bilayer at an angle of ∼95° in the closed state, is imperative for mechanosensation of the channel. In agreement with experimental data, deletion of the N-terminal domain from our model increases the tensional force required for the full opening of MscL. Moreover, we observed that during gating, the channel gate moves from the inner leaflet region towards the bilayer midplane as the membrane thins. Since we do not see this upward movement of the gate when the N-terminal is removed from our model this further implies that N-terminal region acts as an anchor in the gating process of MscL.Supported by the University International Postgraduate Award (UIPA) to N.B. and APP1079398 grant from NHMRC to B.M.

Hydrocarbon Thickness Dictates Cholesterol's Location, Orientation and Motion in a Phospholipid Bilayer

The lateral sequestration of lipids with polyunsaturated fatty acid (PUFA) chains into membrane domains depleted of cholesterol has been hypothesized to have an important role in neurological function. This effect has long been attributed to a strong aversion of the disordered polyunsaturated fatty acid (PUFA) chains to the rigid smooth alpha face of cholesterol. Previously, we have performed neutron diffraction studies of deuterated cholesterol incorporated into bilayers composed of diarachidonoyl phosphatidylcholine (di-20:4 PC, DAPC), a lipid with two omega-6 PUFA chains. It was found that cholesterol sequestered at the bilayer midplane, in contrast to its usual upright orientation with the hydroxyl group located near the lipid/water interface. To date it remains unclear whether or not cholesterol's aversion to PUFA chains is a universal property of PUFAs, a behavior unique to omega-6 PUFAs, or the product of membrane disorder.Using different physical characterization techniques (i.e., neutron diffraction, NMR) and MD simulations, we obtained detailed structural data that rationalize much of the previously inexplicable data regarding cholesterol's behaviour in PUFA bilayers. We are able to demonstrate that cholesterol's mass distribution in the center of a PUFA bilayer is the same for both omega-6 and omega-3 PUFAs. In addition, neutron, 2H NMR and MD data suggest cholesterol's sequestration into the bilayer center may in fact be driven by hydrophobic thickness mismatch, and not necessarily membrane disorder.

The Curvature Induction of Surface-Bound Antimicrobial Peptides Piscidin 1 and Piscidin 3 Varies with Lipid Chain Length.

The initial steps of membrane disruption by antimicrobial peptides (AMPs) involve binding to bacterial membranes in a surface-bound (S) orientation. To evaluate the effects of lipid composition on the S state, molecular dynamics simulations of the AMPs piscidin 1 (p1) and piscidin 3 (p3) were carried out in four different bilayers: 3:1 DMPC/DMPG, 3:1 POPC/POPG, 1:1 POPE/POPG, and 4:1 POPC/cholesterol. In all cases, the addition of 1:40 piscidin caused thinning of the bilayer, though thinning was least for DMPC/DMPG. The peptides also insert most deeply into DMPC/DMPG, spanning the region from the bilayer midplane to the headgroups, and thereby only mildly disrupting the acyl chains. In contrast, the peptides insert less deeply in the palmitoyl-oleoyl containing membranes, do not reach the midplane, and substantially disrupt the chains, i.e., the neighboring acyl chains bend under the peptide, forming a basket-like conformation. Curvature free energy derivatives calculated from the simulation pressure profiles reveal that the peptides generate positive curvature in membranes with palmitoyl and oleoyl chains but negative curvature in those with myristoyl chains. Curvature inductions predicted with a continuum elastic model follow the same trends, though the effect is weaker, and a small negative curvature induction is obtained in POPC/POPG. These results do not directly speak to the relative stability of the inserted (I) states or ease of pore formation, which requires the free energy pathway between the S and I states. Nevertheless, they do highlight the importance of lipid composition and acyl chain packing.

Determining Structural and Mechanical Properties from Molecular Dynamics Simulations of Lipid Vesicles.

We have developed an algorithm to determine membrane structure, area per lipid, and bending rigidity from molecular dynamics simulations of lipid vesicles. Current methods to extract structure from vesicle simulations define densities relative to the global center of mass of the vesicle. This approach ignores the long-wavelength fluctuations (undulations) that develop across the sphere and broaden the underlying structure. Our method establishes a local reference frame by defining a radially undulating reference surface (URS) and thereby removes the broadening effect of the undulations. Using an arc-length low-pass filter, we render the URS by defining the bilayer midplane on an equi-angular θ, ϕ-grid (colatitude, longitude). This surface is then expanded onto a truncated series of spherical harmonics. The spherical harmonic coefficients characterize the long-wavelength fluctuations that define both the local reference frame—used to determine the bilayer’s structure—and the area per lipid (AL) along the undulating surface. Additionally, the resulting power spectrum of spherical harmonic coefficients can be fit to a Helfrich continuum model for membrane bending in spherical geometry to extract bending rigidity (kc). kc values determined for both DMPC and DMPC + cholesterol (30 mol %) vesicles are consistent with values from corresponding flat-patch systems determined using an independent, previously published spectral method. These new tools to accurately extract structure, AL, and kc should prove invaluable in evaluating the construction and equilibration of lipid vesicle simulations.