Effects of phospholipid unsaturation on the bilayer nonpolar region: a molecular simulation study

Molecular dynamics simulations of two monounsaturated phosphatidylcholine (PC) bilayers made of 1-palmitoyl-2-oleoyl-PC (POPC; cis-unsaturated) and 1-palmitoyl-2-elaidoyl-PC (PEPC; trans-unsaturated) were carried out to investigate the effect of a double bond in the PC beta-chain and its conformation on the bilayer core. Four nanosecond trajectories were used for analyses. A fully saturated 1,2-dimyristoyl-PC (DMPC) bilayer was used as a reference system. In agreement with experimental data, this study shows that properties of the PEPC bilayer are more similar to those of the DMPC than to the POPC bilayer. The differences between POPC and PEPC bilayers may be attributed to the different ranges of angles covered by the torsion angles beta10 and beta12 of the single bonds next to the double bond in the oleoyl (O) and elaidoyl (E) chains. Broader distributions of beta10 and beta12 in the E chain than in the O chain make the E chain more flexible. In effect, the packing of chains in the PEPC bilayer is similar to that in the DMPC bilayer, whereas that in the POPC bilayer is looser than that in the DMPC bilayer. The effect of the cis-double bond on torsions at the beginning of the O chain (beta4 and beta5) is similar to that of cholesterol on these torsions in a myristoyl chain.     

Cyclo-hexa-peptides at the water/cyclohexane interface: a molecular dynamics simulation

Molecular dynamic (MD) simulations have been performed to study the behaviors of ten kinds of cyclo-hexa-peptides (CHPs) composed of amino acids with the diverse hydrophilic/hydrophobic side chains at the water/cyclohexane interface. All the CHPs take the “horse-saddle” conformations at the interface and the hydrophilicity/hydrophobicity of the side chains influences the backbones’ structural deformations. The orientations and distributions of the CHPs at the interface and the differences of interaction energies (ΔΔE) between the CHPs and the two liquid phases have been determined. RDF analysis shows that the H-bonds were formed between the O_C atoms of the CHPs’ backbones and H_w atoms of water molecules. N atoms of the CHPs’ backbones formed the H-bonds or van der Waals interactions with the water solvent. It was found that there is a parallel relationship between ΔΔE and the lateral diffusion coefficients (D _xy ) of the CHPs at the interface. The movements of water molecules close to the interface are confined to some extent, indicating that the dynamics of the CHPs and interfacial water molecules are strongly coupled.

Effects of oxygenated sterol on phospholipid bilayer properties: a molecular dynamics simulation

The properties of dipalmitoylphosphatidylcholine (DPPC):6-ketocholestanol bilayer at 50 mol% sterol were studied using the molecular dynamics simulation technique. Our simulations were performed at constant pressure and temperature on a nanosecond time scale. Data from this simulation were compared to the results of our previous simulations on DPPC and DPPC-cholesterol bilayers. We conclude that the differences in the properties of membranes with cholesterol and ketocholestanol are due to the difference in 6-ketocholestanol and cholesterol location in the bilayer. The presence of the keto group in ketocholestanol moves the sterol towards the polar region closer to interface with water. We predict that similar mechanisms would govern the properties of membranes with other oxygenated sterols, such as for example 7-ketocholesterol. Results of our simulations are in a good agreement with the data available from the experiment.     

Effects of cis and trans unsaturation on the structure of phospholipid bilayers: a high-pressure infrared spectroscopic study

In order to compare the effects of cis and trans unsaturation on the structure and packing of phospholipid bilayers, infrared spectra of aqueous dispersions of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dielaidoyl-sn-glycero-3-phosphocholine (DEPC) were measured in a diamond anvil cell at 28 degrees C as a function of pressure up to 36 kbar. The infrared spectra indicate that DEPC and DOPC undergo pressure-induced liquid-crystalline to gel phase transitions at critical pressures of 0.7 and 5.2 kbar, respectively. Below their respective critical pressures, the infrared spectra of DOPC and DEPC are essentially indistinguishable, whereas above these pressures, there are very pronounced differences in the barotropic behavior of these two lipids. Specifically, at the 5.2-kbar transition in DOPC, there are significant changes in the frequencies, intensities, and widths of bands associated with the interfacial C = O groups, the olefinic CH = CH groups, and the terminal CH3 groups, whereas the corresponding bands of DEPC are, by contrast, relatively insensitive to the pressure-induced phase transition. The unusual band shape changes in DOPC are attributed to a unique packing arrangement of the oleoyl acyl chains required to accommodate the bent geometries of adjacent cis double bonds. Moreover, above 5 kbar in DEPC, well-defined correlation field splittings of the CH2 scissoring and rocking modes are observed, with magnitudes very similar to those observed at comparable pressures in saturated lipid systems. The absence of correlation field splittings of the corresponding bands of DOPC up to 36 kbar suggests that the bent oleoyl acyl chains are closely packed with all chains oriented parallel to each other.     

Mean field stochastic boundary molecular dynamics simulation of a phospholipid in a membrane

Computer simulations of phospholipid membranes have been carried out by using a combined approach of molecular and stochastic dynamics and a mean field based on the Marcelja model. First, the single-chain mean field simulations of Pastor et al. [(1988) J. Chem. Phys. 89, 1112-1127] were extended to a complete dipalmitoylphosphatidylcholine molecule; a 102-ns Langevin dynamics simulation is presented and compared with experiment. Subsequently, a hexagonally packed seven-lipid array was simulated with Langevin dynamics and a mean field at the boundary and with molecular dynamics (and no mean field) in the center. This hybrid method, mean field stochastic boundary molecular dynamics, reduces bias introduced by the mean field and eliminates the need for periodic boundary conditions. As a result, simulations extending to tens of nanoseconds may be carried out by using a relatively small number of molecules to model the membrane environment. Preliminary results of a 20-ns simulation are reported here. A wide range of motions, including overall reorientation with a nanosecond decay time, is observed in both simulations, and good agreement with NMR, IR, and neutron diffraction data is found.     

Molecular dynamics study of a phospholipid monolayer at a water/triglyceride interface: towards lipid emulsion modelling

In order to mimic the surface of parenteral nutrition emulsion droplets, the first molecular dynamics simulation of a palmitoyloleoylphosphatidylcholine (POPC) monolayer at a water/triglyceride (trilinoleoylglycerol, LLL) interface was performed. Triglyceride influence was evaluated by comparing computed phospholipid properties to the ones in a similarly modelled hydrated POPC bilayer. As expected, polar head properties (molecular area, lipid hydration, headgroup orientation) were not affected by triglycerides. In contrast, slight differences were observed on phospholipid alkyl tail region (order parameter, diffusion, Van der Waals interactions). This first approach can reasonably be extended to a further more realistic multicomponent model of clinical nutrition emulsions.     

Cholesterol effects on the phospholipid condensation and packing in the bilayer: a molecular simulation study

A 15-ns molecular dynamics simulation of the fully hydrated liquid-crystalline dimyristoylphosphatidylcholine-cholesterol (DMPC-Chol) bilayer containing approximately 22 mol% Chol was carried out. The generated trajectory was analysed to investigate the mechanism of the Chol condensing effect on DMPC hydrocarbon chains and the influence of Chol on the chain packing in the membrane. Chol was found to induce stronger van der Waals interactions among the chains, whereas its interactions with the chains were weak. In the DMPC-Chol bilayer, as in the DMPC bilayer, DMPC chains were regularly packed around a chosen chain but around a Chol molecule they were not. DMPC gamma chains made closer contacts with Chol than the beta chains.     

Molecular dynamics simulation of a phospholipid membrane

We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in future simulations. This goal being reached it is then further possible to gain insight in to those properties that are experimentally more difficult to access. The system studied is dipalmitoylphosphatidylcholine/water, consisting of 5408 atoms. Using original force field parameters the membrane turned out to approach a gel-like state. With slight changes of the parameters, the system adopted a liquid-crystalline state. Separate 80 ps runs were performed on both the gel and liquid-crystalline systems. Comparison of MD results with reliable experimental data (bilayer repeat distance, surface area per lipid, tail order parameters, atom distributions) showed that our simulations, especially the one in the liquid-crystalline phase, can serve as a realistic model for a phospholipid membrane. Further analysis of the trajectories revealed valuable information on various properties. In the liquid-crystalline phase, the interface turns out to be quite diffuse, with water molecules penetrating into the bilayer to the position of the carbonyl groups. The 10–90% width of the interface turns out to be 1.3 nm and the width of the hydrocarbon interior 3.0 nm. The headgroup dipoles are oriented at a small angle with respect to the bilayer plane. The resulting charge distribution is almost completely cancelled by the water molecules. The electron density distribution shows a large dip in the middle of the membrane. In this part the tails are more flexible. The mean life time between dihedral transitions is 20 ps. The average number of gauche angles per tail is 3.5. The occurrence of kinks is not a significant feature.Abbreviations MD molecular dynamics - DPPC dipalmitoylphosphatidylcholine - SPC simple point charges - DPPE dipalmitoylphosphatidylethanolamine Correspondence to: H. J. C. Berendsen     

Selected biologically relevant ions at the air/water interface: a comparative molecular dynamics study

Interfacial behavior of selected biologically and technologically relevant ions is studied using molecular dynamics simulations employing polarizable potentials. Propensities of choline, tetraalkylammonium (TAA), and sodium cations, and sulfate and chloride anions for the air/water interface are analyzed by means of density profiles. Affinity of TAA ions for the interface increases with their increasing hydrophobicity. Tetramethylammonium favors bulk solvation, whereas cations with propyl and butyl chains behave as surfactants. The choice of counter-anions has only a weak effect on the behavior of these cations. For choline, sodium, chloride and sulfate, the behavior at the air/water interface was compared to the results of our recent study on the segregation of these ions at protein surfaces. No analogy between these two interfaces in terms of ion segregation is found.     

Effects of epicholesterol on the phosphatidylcholine bilayer: a molecular simulation study

Epicholesterol (Echol) is an epimeric form of cholesterol (Chol). A molecular dynamics simulation of the fully hydrated dimyristoylphosphatidylcholine-Echol (DMPC-Echol) bilayer membrane containing approximately 22 mol % of Echol was carried out for 5 ns. A 3-ns trajectory generated between 2 and 5 ns of molecular dynamics simulation was used for analyses to determine the effects of Echol on the membrane properties. As reference systems, pure DMPC and mixed DMPC-Chol bilayers were used. The study shows that Echol, like Chol, changes the organization of the bilayer/water interface and increases membrane order and condensation, but to a lesser degree. Effects of both sterols are based on the same atomic level mechanisms; their different strength arises from different vertical localizations of Echol and Chol hydroxyl groups in the membrane/water interface.     

Effects of electric field on alamethicin bound at the lipid-water interface: a molecular mechanics study.

A systematic molecular mechanics study of the alamethicin molecule was made to determine a set of low-energy conformers in vacuo and in aqueous environment. The behavior of these conformers was investigated at the phase boundary which was modeled as a plane dividing two compartments with solvation properties of water and octanol with a constant electric field applied normal to the boundary. The calculations were performed with a molecular mechanics program for calculation of stable conformations at the phase boundary utilizing the Empiric Conformational Energy Program for Peptides force field and the Hopfinger-Scheraga solvation model. 371 minimum energy conformers of alamethicin, determined in vacuo with the build-up procedure, were used as starting conformations for energy minimization in aqueous environment and at the phase boundary. Only 49 interphase-bound structures were within 12 kcal/mol of the minima which was found. No helical structures having values close to the canonical parameters for an alpha- or 3(10)-helix were found despite the presence of eight alpha-methylalanine residues which favor the formation of these helices; four helix-like structures were found, having all negative phi, psi values. All the helical conformers have very high energies in water (approximately 14 kcal/mol), but are quite stable at the phase boundary (3.7-6.8 kcal/mol above the lowest minima found). The implications of these results for proposed mechanisms for membrane-binding and voltage-dependent gating are considered.     

Interfacial water on crystalline silica: a comparative molecular dynamics simulation study

Understanding the properties of interfacial water at solid–liquid interfaces is important in a wide range of applications. Molecular dynamics is becoming a widespread tool for this purpose. Unfortunately, however, the results of such studies are known to strongly depend on the selection of force fields. It is, therefore, of interest to assess the extent by which the implemented force fields can affect the predicted properties of interfacial water. Two silica surfaces, with low and high surface hydroxyl density, respectively, were simulated implementing four force fields. These force fields yield different orientation and flexibility of surface hydrogen atoms, and also different interaction potentials with water molecules. The properties for interfacial water were quantified by calculating contact angles, atomic density profiles, surface density distributions, hydrogen bond density profiles and residence times for water near the solid substrates. We found that at low surface density of hydroxyl groups, the force field strongly affects the predicted contact angle, while at high density of hydroxyl groups, water wets all surfaces considered. From a molecular-level point of view, our results show that the position and intensity of peaks observed from oxygen and hydrogen atomic density profiles are quite different when different force fields are implemented, even when the simulated contact angles are similar. Particularly, the surfaces simulated by the CLAYFF force field appear to attract water more strongly than those simulated by the Bródka and Zerda force field. It was found that the surface density distributions for water strongly depend on the orientation of surface hydrogen atoms. In all cases, we found an elevated number of hydrogen bonds formed between interfacial water molecules. The hydrogen bond density profile does not depend strongly on the force field implemented to simulate the substrate, suggesting that interfacial water assumes the necessary orientation to maximise the number of water–water hydrogen bonds irrespectively of surface properties. Conversely, the residence time for water molecules near the interface strongly depends on the force field and on the flexibility of surface hydroxyl groups. Specifically, water molecules reside for longer times at contact with rigid substrates with high density of hydroxyl groups. These results should be considered when comparisons between simulated and experimental data are attempted.     

Influence of phospholipid unsaturation on the cholesterol distribution in membranes.

Over the last half decade, we have studied saturated and unsaturated phosphatidylcholine (PC)-cholesterol membranes, with special attention paid to fluid-phase immiscibility in cis-unsaturated PC-cholesterol membranes. The investigations were carried out with fatty acid and sterol analogue spin labels for which reorientational diffusion of the nitroxide was measured using conventional ESR technique. We also used saturation recovery ESR technique where dual probes were utilized. Bimolecular collision rates between a membrane-soluble square-planar copper complex,3-ethoxy-2-oxobutyraldehyde bis(N4,N4-dimethylthiosemicarbazonato)copper(II) (CuKTMS2) and one of several nitroxide radical lipid-type spin labels were determined by measuring the nitroxide spin-lattice relaxation time (T1). The results obtained in all these studies can be explained if the following model is assumed: 1) at physiological temperatures, fluid-phase micro-immiscibility takes place in cis-unsaturated PC-cholesterol membranes, which induces cholesterol-rich domains in the membrane due to the steric nonconformability between the rigid fused-ring structure of cholesterol and the 30 degrees bend at the cis double bond of the alkyl chains of unsaturated PC. 2) The cholesterol-rich domains are small and/or of short lifetime (10(-9) s to less than 10(-7) s). Our results also suggest that the extra space that is available for conformational disorder and accommodation of small molecules is created in the central part of the bilayer by intercalation of cholesterol in cis-unsaturated PC membrane due to the mismatch in the hydrophobic length and nonconformability between cis-unsaturated PC alkyl chains and the bulky tetracyclic ring of cholesterol.     

Incorporation of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane.

In this paper we report on the molecular dynamics simulation of a fluid phase hydrated dimyristoylphosphatidylcholine bilayer. The initial configuration of the lipid was the x-ray crystal structure. A distinctive feature of this simulation is that, upon heating the system, the fluid phase emerged from parameters, initial conditions, and boundary conditions determined independently of the collective properties of the fluid phase. The initial conditions did not include chain disorder characteristic of the fluid phase. The partial charges on the lipids were determined by ab initio self-consistent field calculations and required no adjustment to produce a fluid phase. The boundary conditions were constant pressure and temperature. Thus the membrane was not explicitly required to assume an area/phospholipid molecule thought to be characteristic of the fluid phase, as is the case in constant volume simulations. Normal to the membrane plane, the pressure was 1 atmosphere, corresponding to the normal laboratory situation. Parallel to the membrane plane a negative pressure of -100 atmospheres was applied, derived from the measured surface tension of a monolayer at an air-water interface. The measured features of the computed membrane are generally in close agreement with experiment. Our results confirm the concept that, for appropriately matched temperature and surface pressure, a monolayer is a close approximation to one-half of a bilayer. Our results suggest that the surface area per phospholipid molecule for fluid phosphatidylcholine bilayer membranes is smaller than has generally been assumed in computational studies at constant volume. Our results confirm that the basis of the measured dipole potential is primarily water orientations and also suggest the presence of potential barriers for the movement of positive charges across the water-headgroup interfacial region of the phospholipid.     

Effects of a carane derivative local anesthetic on a phospholipid bilayer studied by molecular dynamics simulation

Molecular dynamics (MD) simulations of two hydrated palmitoyloleoylphosphatidylcholine (POPC) bilayers each containing eight carane derivative (KP-23) local anesthetic (LA) molecules in neutral (POPC-LA) or protonated (POPC-LAH) forms were carried out to investigate the effect of KP-23 and its protonation on the bilayer. 3-ns trajectories were used for analyses. A pure POPC bilayer was employed as a reference system. In both POPC-LA and POPC-LAH systems a few KP-23 molecules intercalated into the bilayer and moved near the bilayer/water interface. They were located on the hydrophobic core side of the interface in the POPC-LA bilayer, but on the water phase side in the POPC-LAH bilayer. The order of the POPC chains was higher in the POPC-LA bilayer than in the pure POPC bilayer and was lower in the POPC-LAH bilayer. Interactions between polar groups of KP-23 and POPC or water were responsible for a lower hydration of POPC headgroups in POPC bilayers containing KP-23 than in the pure POPC bilayer. KP-23 molecules were found to form aggregates both in POPC-LA and POPC-LAH bilayers. Due to higher amphiphilicity of LAH, the LAH aggregate was more micelle-like and larger than the LA one. The results demonstrate the rapid timescales of the initial processes that take place at and near the bilayer interface as well as details of the atomic level interactions between local anesthetic and the lipid matrix of a cell membrane.     

GD1a in phospholipid bilayer: a molecular dynamics simulation

Molecular dynamics simulation of ganglioside GD1a attached to the upper layer of a fully hydrated lipid bilayer of dimyristoyl phosphatidyl choline (DMPC) at room temperature under periodic boundary conditions was performed. The time average conformation of GD1a reveals that the terminal sialic acid is more exposed into the solvent than the internal branched one. Many interresidual contacts between N-acetyl galactosamine-internal branched sialic acid; external Gal-external sialic acid; N-acetyl galactosamine-internal gal are also observed. The conformation of the GD1-hexasaccharide is stabilized by a number of intra molecular hydrogen bonds that were previously observed experimentally. The simulation results indicate that the presence of a single GD1a molecule has local effects on the bilayer. A local disorder in the arrangement of the acyl chains as well as the head groups is evident in the upper layer due to the presence of GD1a.     

Effect of phospholipid unsaturation on protein kinase C activation.

To examine the hypothesis that physical features of the membrane contribute to protein kinase C activation, phosphatidylcholine/phosphatidylserine/diolein (70:25:5) vesicles of defined acyl chain composition were tested for their ability to activate the enzyme. Maximal activation was found to correlate with the mole percent unsaturation in the system. Unsaturation could be provided by either the phosphatidylserine or the phosphatidylcholine component. Vesicles containing 5 mol% diolein but lacking any unsaturation in the phospholipid did not support activity, indicating that acidic head groups alone are not sufficient for activity. The saturated lipid vesicles could be rendered effective but only at very high (25 mol%) concentrations of diolein. The degree of acyl chain unsaturation and the positioning of the double bond had little effect on the activity, suggesting that the effect of the unsaturation is due to some physical property of the lipid rather than to a specific lipid-protein interaction. Addition of cholesterol to both saturated and unsaturated systems indicated that fluidity, as assessed by fluorescence anisotropy, did not correlate with activity. These results suggest that a physical property of the membrane other than fluidity is important for the activation of protein kinase C. A model for protein kinase C activation involving phase separation and/or head group spacing is discussed.     

Infrared reflection-absorption of melittin interaction with phospholipid monolayers at the air/water interface.

The interaction of melittin with monolayers of 1,2-dipalmitoylphosphatidylcholine and 1,2-dipalmitoylphosphatidylserine has been investigated with infrared external reflection-absorption spectroscopy. Improved instrumentation permits determination of acyl chain conformation and peptide secondary structure in situ at the air/water interface. The IR frequency of the 1,2-dipalmitoylphosphatidylcholine antisymmetric acyl chain CH2 stretching vibration decreases by 1.3 cm-1 upon melittin insertion, consistent with acyl chain ordering, whereas the same vibrational mode increases by 0.5 cm-1 upon peptide interaction with the 1,2-dipalmitoylphosphatidylserine monolayer, indicative of chain disordering. Thus the peptide interacts quite differently with zwitterionic compared with negatively charged monolayer surfaces. Melittin in the monolayer adopted a secondary structure with an amide l(l') frequency (1635 cm-1) dramatically different from the alpha-helical motif (amide l frequency 1656 cm-1 in a dry or H2O hydrated environment, amide l' frequency 1645 cm-1 in an H-->D exchanged alpha-helix) assumed in bilayer or multibilayer environments. This work represents the first direct in situ spectroscopic indication that peptide secondary structure in lipid monolayers may differ from that in bilayers.     

Adsorption and desorption studies of phospholipid at the air/water interface

The desorption and adsorption properties of phosphatidylserine (extracted from beef brain) at the air/water interface were studied through surface pressure measurements. The rate of dissolution of phosphatidylserine monolayer into the underlying water of natural pH is extremely slow at room temperature but increases rather suddenly around 40°C. This sudden increase of dissolution rate might be explained as the Kraft point phenomena analogous to the ionic surfactants.