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.     

Validating affinities for ion-lipid association from simulation against experiment

Understanding biological membranes at physiological conditions requires comprehension of the interaction of lipid bilayers with sodium and potassium ions. These cations are adsorbed at palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayers as indicated from previous studies. Here we compare the affinity of Na(+) and K(+) for POPC in molecular dynamics (MD) simulations with recent data from electrophoresis experiments and isothermal calorimetry (ITC) at neutral pH. NaCl and KCl were described using GROMOS or parameters matching solution activities on the basis of Kirkwood-Buff theory (KBFF), and K(+) was also described using parameters by Dang et al., all in conjunction with the Berger parameters for the lipids and the SPC water model. Apparent binding constants of GROMOS-Na(+) and KBFF-K(+) are the same within error and in good agreement with values from ITC. Although these force fields yield the same number of bound ions per number of lipids for Na(+) and K(+), they give a larger number of Na(+) ions per surface area compared to K(+), in agreement with the electrophoresis experiments, because Na(+) causes a stronger reduction in the area per lipid than K(+). The intrinsic binding constants, on the other hand, are reproduced by Dang-K(+) but overestimated by GROMOS-Na(+) and KBFF-K(+). That no ion force field reproduces the intrinsic and the apparent binding constant simultaneously arises from the fact that in MD simulations, implicitly meant to mimic neutral pH, pure PC is usually modeled with zero surface charge. In contrast, POPC at neutral conditions in experiment carries a low but significant negative surface charge and is uncharged only at acidic pH as indicated from electrophoretic mobilities. Implications for future simulation and experimental studies are discussed.     

Asymmetry of lipid bilayers induced by monovalent salt: atomistic molecular-dynamics study

Interactions between salt ions and lipid components of biological membranes are essential for the structure, stability, and functions of the membranes. The specific ionic composition of aqueous buffers inside and outside of the cell is known to differ considerably. To model such a situation we perform atomistic molecular-dynamics (MD) simulations of a single-component phosphatidylcholine lipid bilayer which separates two aqueous reservoirs with and without NaCl salt. To implement the difference in electrolyte composition near two membrane sides, a double bilayer setup (i.e., two bilayers in a simulation box) is employed. It turns out that monovalent salt, being in contact with one leaflet only, induces a pronounced asymmetry in the structural, electrostatic, and dynamical properties of bilayer leaflets after 50 ns of MD simulations. Binding of sodium ions to the carbonyl region of the leaflet which is in contact with salt results in the formation of "Na-lipids" complexes and, correspondingly, reduces mobility of lipids of this leaflet. In turn, attractive interactions of chloride ions (mainly located in the aqueous phase close to the water-lipid interface) with choline lipid groups lead to a substantial (more vertical) reorientation of postphatidylcholine headgroups of the leaflet adjoined to salt. The difference in headgroup orientation on two sides of a bilayer, being coupled with salt-induced reorientation of water dipoles, leads to a notable asymmetry in the charge-density profiles and electrostatic potentials of bilayer constitutes of the two leaflets. Although the overall charge density of the bilayer is found to be almost insensitive to the presence of salt, a slight asymmetry in the charge distribution between the two bilayer leaflets results in a nonzero potential difference of about 85 mV between the two water phases. Thus, a transmembrane potential of the order of the membrane potential in a cell can arise without ionic charge imbalance between two aqueous compartments.     

Phase dependent electrochemical properties of polar self-assembled monolayers (SAMs) modified via the fusion of mixed phospholipid vesicles

Unilamellar vesicles of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and varying quantities of either 1,2-dimyristoyl-sn-glycero-3-[phospho-rac-(1-glycerol) (sodium salt) (DMPG) or 1,2-dimyristoyl-3-trimethylammonium-propane (chloride salt) (DMTAP) were used to deposit lipid bilayer assemblies on self-assembled monolayers (SAMs) on gold. The supporting SAMs in turn were composed of ferrocene-functionalized hexadecanethiol chains (FcC16SH) diluted to low coverage in 1-hydroxylhexadecanethiol (HOC16SH) or a single-component monolayer phase of the latter. The mass coverages of the DMPC/DMPG layers deposited in this way were measured using surface plasmon resonance (SPR) and found to decrease with an increasing content of DMPG in the vesicles. The SPR data show that the lipid assembly, while stable with respect to gentle rinsing in aqueous buffer, is reversible and the lipid adlayer is removable by immersion in a solvent such as ethanol. The effects of the adsorbed lipid layer on the electrochemical interactions of the hybrid lipid/SAM with several redox probes [e.g., K4Fe(CN)6, Ru(NH3)6Cl3, and CsHsFe-[(C5H4CH2N+H(CH3)2] were characterized using cyclic voltammetry (CV). At a composition of 5% DMPG in DMPC, the permeabilities of the probes through the lipid layer were affected significantly relative to that observed with a pure DMPC layer. These effects include a striking observation of an enhanced, ionic-charge-specific molecular discrimination of the electrochemical probes. At higher concentrations of the DMPG, significant permeation of the lipid adlayer was seen for all the probes. These latter changes are also attended by a significant increase in the capacitive currents measured in CV experiments as compared to those observed for either a pure SAM or one modified by only DMPC. This effect likely results from the influence of the charged lipid on the diffuse Gouy-Chapman electrolyte layer at the SAM interface. In contrast to the behaviors seen with DMPG, the incorporation of DMTAP into the adsorbed DMPC had no impact on the permeation of the adlayer by soluble redox probes as judged by the observed electrochemistry, a result that appears to correlate with a less ideal mixing of lipids in the DMPC/DMTAP system relative to that of a DMPC/DMPG mixture.     

Study of PEGylated lipid layers as a model for PEGylated liposome surfaces: molecular dynamics simulation and Langmuir monolayer studies

We have combined Langmuir monolayer film experiments and all-atom molecular dynamics (MD) simulation of a bilayer to study the surface structure of a PEGylated liposome and its interaction with the ionic environment present under physiological conditions. Lipids that form both gel and liquid-crystalline membranes have been used in our study. By varying the salt concentration in the Langmuir film experiment and including salt at the physiological level in the simulation, we have studied the effect of salt ions present in the blood plasma on the structure of the poly(ethylene glycol) (PEG) layer. We have also studied the interaction between the PEG layer and the lipid bilayer in both the liquid-crystalline and gel states. The MD simulation shows two clear results: (a) The Na(+) ions form close interactions with the PEG oxygens, with the PEG chains forming loops around them and (b) PEG penetrates the lipid core of the membrane for the case of a liquid-crystalline membrane but is excluded from the tighter structure of the gel membrane. The Langmuir monolayer results indicate that the salt concentration affects the PEGylated lipid system, and these results can be interpreted in a fashion that is in agreement with the results of our MD simulation. We conclude that the currently accepted picture of the PEG surface layer acting as a generic neutral hydrophilic polymer entirely outside the membrane, with its effect explained through steric interactions, is not sufficient. The phenomena we have observed may affect both the interaction between the liposome and bloodstream proteins and the liquid-crystalline-gel transition and is thus relevant to nanotechnological drug delivery device design.     

Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics

Accelerated molecular dynamics (aMD) is an enhanced sampling technique that expedites conformational space sampling by reducing the barriers separating various low-energy states of a system. Here, we present the first application of the aMD method on lipid membranes. Altogether, ～1.5 μs simulations were performed on three systems: a pure POPC bilayer, a pure DMPC bilayer, and a mixed POPC:DMPC bilayer. Overall, the aMD simulations are found to produce significant speedup in trans-gauche isomerization and lipid lateral diffusion versus those in conventional MD (cMD) simulations. Further comparison of a 70-ns aMD run and a 300-ns cMD run of the mixed POPC:DMPC bilayer shows that the two simulations yield similar lipid mixing behaviors, with aMD generating a 2-3-fold speedup compared to cMD. Our results demonstrate that the aMD method is an efficient approach for the study of bilayer structural and dynamic properties. On the basis of simulations of the three bilayer systems, we also discuss the impact of aMD parameters on various lipid properties, which can be used as a guideline for future aMD simulations of membrane systems.     

Rectification of the current in alpha-hemolysin pore depends on the cation type: the alkali series probed by MD simulations and experiments

A striking feature of the alpha-hemolysin channel-a prime candidate for biotechnological applications-is the dependence of its ionic conductance on the magnitude and direction of the applied bias. Through a combination of lipid bilayer single-channel recording and molecular dynamics (MD) simulations, we characterized the current-voltage relationship of alpha-hemolysin for all alkali chloride salts at neutral pH. The rectification of the ionic current was found to depend on the type of cations and increase from Li(+) to Cs(+). Analysis of the MD trajectories yielded a simple quantitative model that related the ionic current to the electrostatic potential, the concentration and effective mobility of ions in the channel. MD simulations reveal that the major contribution to the current asymmetry and rectification properties originates from the cationic contribution to the current that is significantly reduced in a cationic dependent way when the membrane polarity is reversed. The variation of chloride current was found to be less important. We report that the differential affinity of cations for the charged residues positioned at the channel's end modulates the number of ions inside the channel stem thus affecting the current properties. Through direct comparison of simulation and experiment, this study evaluates the accuracy of the MD method for prediction of the asymmetric, voltage dependent conductances of a membrane channel.     

Counterion-mediated pattern formation in membranes containing anionic lipids

Most lipid components of cell membranes are either neutral, like cholesterol, or zwitterionic, like phosphatidylcholine and sphingomyelin. Very few lipids, such as sphingosine, are cationic at physiological pH. These generally interact only transiently with the lipid bilayer, and their synthetic analogs are often designed to destabilize the membrane for drug or DNA delivery. However, anionic lipids are common in both eukaryotic and prokaryotic cell membranes. The net charge per anionic phospholipid ranges from − 1 for the most abundant anionic lipids such as phosphatidylserine, to near − 7 for phosphatidylinositol 3,4,5 trisphosphate, although the effective charge depends on many environmental factors. Anionic phospholipids and other negatively charged lipids such as lipopolysaccharides are not randomly distributed in the lipid bilayer, but are highly restricted to specific leaflets of the bilayer and to regions near transmembrane proteins or other organized structures within the plane of the membrane. This review highlights some recent evidence that counterions, in the form of monovalent or divalent metal ions, polyamines, or cationic protein domains, have a large influence on the lateral distribution of anionic lipids within the membrane, and that lateral demixing of anionic lipids has effects on membrane curvature and protein function that are important for biological control.     

Analysis of lipid surface area in protein-membrane systems combining Voronoi tessellation and Monte Carlo integration methods

All-atom molecular dynamics (MD) simulation has become a powerful research tool to investigate structural and dynamical properties of biological membranes and membrane proteins. The lipid structures of simple membrane systems in recent MD simulations are in good agreement with those obtained by experiments. However, for protein-membrane systems, the complexity of protein-lipid interactions makes investigation of lipid structure difficult. Although the area per lipid is one of the essential structural properties in membrane systems, the area in protein-membrane systems cannot be computed easily by conventional approaches like the Voronoi tessellation method. To overcome this limitation, we propose a new method combining the two-dimensional Voronoi tessellation and Monte Carlo integration methods. This approach computes individual surface areas of lipid molecules not only in bulk lipids but also in proximity to membrane proteins. We apply the method to all-atom MD trajectories of the sarcoplasmic reticulum Ca(2+)-pump and the SecY protein-conducting channel. The calculated lipid surface area is in agreement with experimental values and consistent with other structural parameters of lipid bilayers. We also observe changes in the average area per lipid induced by the conformational transition of the SecY channel. Our method is particularly useful for examining equilibration of lipids around membrane proteins and for analyzing the time course of protein-lipid interactions.     

Ion condensation behavior and dynamics of water molecules surrounding the sodium poly(methacrylic acid) chain in water: a molecular dynamics study

All-atom molecular dynamics simulations are used to study the condensation behavior of monovalent (Na(+)) and multivalent (Ca(2+)) salt counterions associated with the co-ions (Cl(-)) surrounding the charged poly(methacrylic acid) (PMAA) chain in water. The study is extended to the influences on chain conformation, local arrangement, and dynamics of water in the highly diluted aqueous solutions. We find that even when the salt ions are monovalent, they attract more than one charged monomer and act as a bridging agent within the chain, as the multivalent salt ions. In principle, the salt ions bridge between not only the "non-adjacent" but also the "adjacent" charged monomers, leading to a more coil-like and a locally stretched conformation, respectively. With an increase in the salt concentration, the amount of coiled-type condensed ions increase and reach a maximum when the chain conformation becomes the most collapsed; whereas, the stretched-type shows an opposite trend. Our results show that the attractive interactions through the condensed salt ions between the non-adjacent monomers are responsible for the conformational collapse. When the salt concentration increases high enough, a significant increase for the stretched-type condensed ions makes an expansion effect on the chain. These stretched-type salt ions, followed by the adsorption of the co-ions and water molecules, tend to form a multilayer organization outside surrounding the PMAA chain. Thus, the expansion degree of the chain conformation is greatly limited. When only the monovalent Na(+) ions are present in the solutions, water molecules are primarily adsorbed into either the condensed Na(+) ions or the COO(-) groups. These adsorbed water molecules form hydrogen bonds with each other and enhance the local bridging behavior associated with the Na(+) condensation on the resultant chain conformation. With an increase in the amount of multivalent Ca(2+) salt ions, more water molecules are bonded directly with the condensed Ca(2+) ions. In this case, only the condensed Ca(2+) ions provide a strong bridging effect within the polymer chain. We observe a significant shift towards a higher frequency of the oxygen vibration spectrum and only a slight shift towards a higher frequency of the hydrogen spectrum for the water molecules associated with the ion condensation.     

Thermodynamic study of small hydrophobic ions at the water-lipid interface

The thermodynamics of binding of two small hydrophobic ions such as norharman and tryptophan to neutral and negatively charged small unilamellar vesicles was investigated at pH 7.4 using fluorescence spectroscopy. Vesicles were formed at room temperature from dimyristoyl phosphatidylcholine (DMPC) or DMPC/dimyristoylphosphatidic acid and DMPC/dimyristoylphosphatidylglycerol. The changes in fluorescence properties were used to obtain association isotherms at variable membrane surface negative charge and at different ionic strengths. The binding of both ions was found to be quantitatively enhanced as the percentage of negative phospholipid increases in the membrane. Also, a decrease in ion binding was found to occur as the concentration of monovalent salt was increased (0.045-0.345 M). If electrostatic effects were ignored, the experimental data showed biphasic behavior in Scatchard plots. When electrostatic effects were taken into account by means of the Gouy-Chapman theory, the same data yielded linear Scatchard plots that were described by a simple partition equilibrium of the hydrophobic ion into the lipid-water interface. We demonstrate that the effective interfacial charge, nu, of the ion is a determinant factor to obtain a unique value of the intrinsic (hydrophobic) binding constant independently of the surface charge density of the lipid membrane.     

The structure of ions and zwitterionic lipids regulates the charge of dipolar membranes

In pure water, zwitterionic lipids form lamellar phases with an equilibrium water gap on the order of 2 to 3 nm as a result of the dominating van der Waals attraction between dipolar bilayers. Monovalent ions can swell those neutral lamellae by a small amount. Divalent ions can adsorb onto dipolar membranes and charge them. Using solution X-ray scattering, we studied how the structure of ions and zwitterionic lipids regulates the charge of dipolar membranes. We found that unlike monovalent ions that weakly interact with all of the examined dipolar membranes, divalent and trivalent ions adsorb onto membranes containing lipids with saturated tails, with an association constant on the order of ～10 M(-1). One double bond in the lipid tail is sufficient to prevent divalent ion adsorption. We suggest that this behavior is due to the relatively loose packing of lipids with unsaturated tails that increases the area per lipid headgroup, enabling their free rotation. Divalent ion adsorption links two lipids and limits their free rotation. The ion-dipole interaction gained by the adsorption of the ions onto unsaturated membranes is insufficient to compensate for the loss of headgroup free-rotational entropy. The ion-dipole interaction is stronger for cations with a higher valence. Nevertheless, polyamines behave as monovalent ions near dipolar interfaces in the sense that they interact weakly with the membrane surface, whereas in the bulk their behavior is similar to that of multivalent cations. Advanced data analysis and comparison with theory provide insight into the structure and interactions between ion-induced regulated charged interfaces. This study models biologically relevant interactions between cell membranes and various ions and the manner in which the lipid structure governs those interactions. The ability to monitor these interactions creates a tool for probing systems that are more complex and forms the basis for controlling the interactions between dipolar membranes and charged proteins or biopolymers for encapsulation and delivery applications.     

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

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

The influence of zwitterionic lipids on the electrostatic adsorption of macroions onto mixed lipid membranes

Charged lipid membranes commonly consist of a mixture of charged and zwitterionic lipids. We suggest a model that characterizes the influence of the dipolar nature of the zwitterionic lipid species on the electrostatic adsorption of macroions onto mixed membranes in the fluid state. The model is based on Poisson-Boltzmann theory which we have modified so as to account for the dipolar character of the zwitterionic lipids. In addition the membrane lipids are allowed to adjust their lateral distribution upon macroion adsorption. We consider and compare two experimentally relevant scenarios: cationic macroions adsorbed onto anionic membranes and anionic macroions adsorbed onto cationic membranes. We show that in the former case the adsorption strength is slightly weakened by the presence of the headgroup dipoles of the zwitterionic lipids. Here, macroion-induced lipid demixing is more pronounced and the lipid headgroups tilt away from a cationic macroion upon adsorption. In contrast, for the adsorption of anionic macroions onto a cationic membrane the zwitterionic lipids strongly participate in the electrostatic interaction between membrane and macroion, thus enhancing the adsorption strength significantly (we predict up to 20%). Consistent with that we find less lateral demixing of the charged lipids and a reorientation of the dipoles of the zwitterionic headgroups towards the anionic macroions. Our results may be of importance to understand the differences in the electrostatic adsorption of proteins/peptides onto cellular membranes versus complex formation between cationic membranes and DNA.     

Electrostatic, steric, and hydration interactions favor Na(+) condensation around DNA compared with K(+)

Condensation of monovalent counterions around DNA influences polymer properties of the DNA chain. For example, the Na(+) ions show markedly stronger propensity to induce multiple DNA chains to assemble into compact structures compared with the K(+) ions. To investigate the similarities and differences in the sodium and potassium ion condensation around DNA, we carried out a number of extensive all-atom molecular dynamics simulations of a DNA oligomer consisting of 16 base pairs, [d(CGAGGTTTAAACCTCG)](2), in explicit water. We found that the Na(+) ions penetrate the DNA interior and condense around the DNA exterior to a significantly larger degree compared with the K(+) ions. We have provided a microscopic explanation for the larger Na(+) affinity toward DNA that is based on a combination of steric, electrostatic, and hydration effects. Unexpectedly, we found that the Cl(-) co-ions provide more efficient electrostatic screening for the K(+) ions than for the Na(+) ions, contributing to the larger Na(+) condensation around DNA. To examine the importance of the discrete nature of water and ions, we also computed the counterion distributions from the mean-field electrostatic theory, demonstrating significant disagreements with the all-atom simulations. Prior experimental results on the relative extent of the Na(+) and K(+) condensation around DNA were somewhat contradictory. Recent DNA compaction experiments may be interpreted to suggest stronger Na(+) condensation around DNA compared to K(+), which is consistent with our simulations. We also provide a simple interpretation for the experimentally observed increase in DNA electrophoretic mobility in the alkali metal series, Li(+) < Na(+) < K(+) < Rb(+). We compare the DNA segment conformational preferences in various buffers with the proposed NMR models.     

Polyionic charge density plays a key role in differential recognition of mobile ions by biopolymers

We address the question of what are the molecular mechanisms providing discrimination between seemingly similar counterions binding to various biomolecular surfaces. In the case of protein association with Na (+) and K (+) ions, recent works proposed that specificity of carboxylate functional groups interacting with these mobile ions rationalizes the observed ionic discrimination. We probe in this work whether similar arguments may be used to explain higher propensity of Na (+) ions to associate with DNA compared with K (+) ions, which was suggested by our simulations and some experiments. By comparing our extensive molecular dynamics simulations of Na (+) and K (+) distributions around a 16-base-pair DNA oligomer, [(CGAGGTTTAAACCTCG)] 2, with additional simulations where DNA is replaced by a "soup" of monomers (dimethylphosphate anion), we conclude that DNA specificity toward Na (+)/K (+) is not determined by the underlying functional group specificity. Instead, the collective effect of DNA charges drives larger Na (+) association. To gain additional microscopic insights into the mechanisms of specificity on ionic associations in these systems, we carried out energetic analysis of the association between Na (+) and K (+) with chloride and dimethylphosphate anions. The insights gained from our computational work shed light on a number of experiments on electrolyte solutions of monovalent salts and DNA.     

Effects of lysophospholipids on membrane order of phosphatidylcholine

Lysophospholipids are known to play a role in a wide range of cellular processes involving membrane–protein or membrane–membrane interactions; however lysolipids–lamellar lipids interactions remain unclear. The effects of lysolipids on membrane order and dynamics were examined using optical birefringence and fluorescence techniques. We found that lysophosphatidic acid (LPA) induces a considerable disorder in chain orientation for synthetic lipid of dimyristoyl-phosphatidylcholines (DMPC), whereas a slight order for natural lipid of egg yolk phosphatidylcholine (Egg-PC), e.g. the chain order decreases by 10% at 0.1 mole ratio for DMPC in comparison with the membranes without LPA and increases by 3.4% at 0.09 mole ratio for Egg-PC. Also, membrane fluidity corresponds with the change in the chain disorder, namely, the fluidity increases for DMPC membranes, while decreases for Egg-PC membranes by addition of LPA. The difference in the effects of LPA is interpreted by a difference in the chain packing between the synthetic and the natural lipid bilayers. LPA can be incorporated into natural lipid membranes without disturbance, and readjusts itself to a more favorable hydrophobic match with the bilayers. Lysophophatidylcholine (LPC) also induces a disorder in DMPC membranes, but the decrease in chain order is only half compared with that for LPA.     

Impact on lipid membrane organization by free branched-chain fatty acids

Here, we exploit the non-invasive techniques of solid-state NMR (nuclear magnetic resonance) and differential scanning calorimetry (DSC) to study the effect of free iso and ante-iso branched chain fatty acids (BCFAs) on the physicochemical properties of lipid membranes. Free fatty acids are present in biological membranes at low abundance, but can influence the cellular function by modulating the membrane organization. Solid state NMR spectra of dimyristoylphosphatidylcholine (DMPC) lipid membranes containing either free 12-methyltetradecanoic acid (a15:0) or free 13-methyltetradecanoic acid (i15:0), show significant differences in their impact on the lipid bilayer. Chain order profiles obtained by deuterium NMR on fully deuterated DMPC-d(67) bilayers revealed an ordering effect induced by both fatty acids on the hydrophobic membrane core. This behavior was also visible in the corresponding DSC thermograms where the main phase transition of DMPC bilayers-indicative of the hydrophobic membrane region-was shifted to higher temperatures, with the iso isomer triggering more pronounced changes as compared to the ante-iso isomer. This is probably due to a higher packing density in the core of the lipid bilayer, which causes reduced diffusion across membranes. By utilizing the naturally occurring spin reporters nitrogen-14 and phosphorus-31 present in the hydrophilic DMPC headgroup region, even fatty acid induced changes at the membrane interface could be detected, an observation reflecting changes in the lipid headgroup dynamics.     

Molecular dynamics and brownian dynamics investigation of ion permeation and anesthetic halothane effects on a proton-gated ion channel

Bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) is activated to cation permeation upon lowering the solution pH. Its function can be modulated by anesthetic halothane. In the present work, we integrate molecular dynamics (MD) and Brownian dynamics (BD) simulations to elucidate the ion conduction, charge selectivity, and halothane modulation mechanisms in GLIC, based on recently resolved X-ray crystal structures of the open-channel GLIC. MD calculations of the potential of mean force (PMF) for a Na(+) revealed two energy barriers in the extracellular domain (R109 and K38) and at the hydrophobic gate of transmembrane domain (I233), respectively. An energy well for Na(+) was near the intracellular entrance: the depth of this energy well was modulated strongly by the protonation state of E222. The energy barrier for Cl(-) was found to be 3-4 times higher than that for Na(+). Ion permeation characteristics were determined through BD simulations using a hybrid MD/continuum electrostatics approach to evaluate the energy profiles governing the ion movement. The resultant channel conductance and a near-zero permeability ratio (P(Cl)/P(Na)) were comparable to experimental data. On the basis of these calculations, we suggest that a ring of five E222 residues may act as an electrostatic gate. In addition, the hydrophobic gate region may play a role in charge selectivity due to a higher dehydration energy barrier for Cl(-) ions. The effect of halothane on the Na(+) PMF was also evaluated. Halothane was found to perturb salt bridges in GLIC that may be crucial for channel gating and open-channel stability, but had no significant impact on the single ion PMF profiles.     

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.