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     

Molecular dynamics simulation of dipalmitoylphosphatidylcholine membrane with cholesterol sulfate

Using the molecular dynamics simulation technique, we studied the changes occurring in a dipalmitoylphosphatidylcholine (DPPC):cholesterol (CH) membrane at 50 mol% sterol when cholesterol is replaced with cholesterol sulfate (CS). Our simulations were performed at constant pressure and temperature on a nanosecond time scale. We found that 1) the area per DPPC:CS heterodimer is greater than the area of the DPPC:CH heterodimer; 2) CS increases ordering of DPPC acyl chains, but to a lesser extent than CH; 3) the number of hydrogen bonds between DPPC and water is decreased in a CS-containing membrane, but CS forms more water hydrogen bonds than CH; and 4) the membrane dipole potential reverses its sign for a DPPC-CS membrane compared to a DPPC-CH bilayer. We also studied the changes occurring in lipid headgroup conformations and determined the location of CS molecules in the membrane. Our results are in good agreement with the data available from experiments.     

Thermal effects on motion and orientation of the cholestane spin label in planar multibilayers of dimyristoylphosphatidylcholine and dipalmitoylphosphatidylcholine

A detailed picture of the orientation and restricted motion of the cholestane spin label (3-spiro-doxyl-5α-cholestane) in planar multibilayers of dipalmitoylphosphatidylcholine and dimyristoylphosphatidylcholine has been recorded by simultaneous simulation of ESR spectra obtained with the magnetic field parallel and perpendicular to the bilayers (Shimoyama, Y., Eriksson, L.E.G. and Ehrenberg, A. (1978) Biochim. Biophys. Acta 508, 213–235). The analysis has been made over the temperature range ?30°C to 60°C on samples containing 20 to 22% water. At low temperatures the cholestane spin label is tilted with respect to the lipid bilayer normal by an angle of approx. 30° which disappears at the pretransition. In this low temperature range the restricted twisting motion has an activation energy of 5.5 kJ·mol^?1. Above the main transition the twisting motion is unrestricted and has the activation energy 20 kJ·mol^?1. From below the pretransition to above the main transition the velocity of the twisting motion increases by an order of magnitude. The amplitude of the wobbling motion increases abruptly from 0° to 35° at the main transition.     

A spin label study of the urinary bladder luminal membrane

Spin label experiments have been carried out on the urinary bladder luminal membrane of the bovine transitional epithelium employing the 5-, 7-, 12-, and 16-doxyl substituted stearic acid methyl esters, and compared for reference to similarly labeled bovine erythrocytes. The bladder membranes are significantly different from the bovine red blood cell membranes and show a lower order and polarity near the membrane surface. This fact and the general similarity of results for the bladder and isolated plaque membranes suggests that the highly organized proteins of the bladder membrane may act as a coat on the lipid bilayer and, while intrinsic in nature, do not significantly perturb the hydrophobic core of the lipid bilayer.     

Molecular dynamics simulation of a dipalmitoylphosphatidylcholine bilayer with NaCl

Molecular dynamics simulations are performed on two hydrated dipalmitoylphosphatidylcholine bilayer systems: one with pure water and one with added NaCl. Due to the rugged nature of the membrane/electrolyte interface, ion binding to the membrane surface is characterized by the loss of ion hydration. Using this structural characterization, binding of Na(+) and Cl(-) ions to the membrane is observed, although the binding of Cl(-) is seen to be slightly weaker than that of Na(+). Dehydration is seen to occur to a different extent for each type of ion. In addition, the excess binding of Na(+) gives rise to a net positive surface charge density just outside the bilayer. The positive density produces a positive electrostatic potential in this region, whereas the system without salt shows an electrostatic potential of zero.     

Distinct states of lipid mobility in bovine rod outer segment membranes Resolution of spin label results

Freely diffusable lipid spin labels in bovine rod outer segment disc membranes display an apparent two-component ESR spectrum. One component is markedly more immobilized than that found in fluid lipid bilayers, and is attributed to lipid interacting directly with rhodopsin. For the 14-doxyl stearic acid spin label this more immobilized component has an outer splitting of 59 G at 0°C, with a considerable temperature dependence, the effective outer splitting decreasing to 54 G at 24°C. Spin label lipid chains covalently attached to rhodopsin can also display a two-component spectrum in rod outer segment membranes. In unbleached, non-delipidated membranes the 16-doxyl stearoyl maleimide label shows an immobilized component which has an outer splitting of 59 G at 0°C and a considerable temperature dependence. This component which is not resolved at high temperatures (24–35°C), is attributed to the lipid chains interacting directly with the monomeric protein, as with the diffusable labels. In contrast, in rod outer segment membranes which have been either delipidated or extensively bleached, a strongly immobilized component is observed with the 16-doxyl maleimide label at all temperatures. This immobilized component has an outer splitting of 62–64 G at 0°C, with very little temperature dependence (61–62 G at 35°C), and is attributed to protein aggregation.     

Molecular dynamics simulation of Bombolitin II in the dipalmitoylphosphatidylcholine membrane bilayer

The orientation behavior of Bombolitin II (BLT2) in the dipalmitoylphosphatidylcholine membrane bilayer was investigated by using molecular-dynamics simulation. During the 20-ns simulation, the BLT2 began to tilt and finally reached the angle of 51° from the membrane-normal. The structure of the peptide formed the amphipathic α-helical structure during the entire simulation time. The peptide tilts with its hydrophobic side faced to the hydrophobic core of the bilayer. We analyzed the mechanism of the tilting behavior of the peptide associated with the membrane in detail. The analysis showed that the hydrogen-bond interaction and the electrostatic interaction were found to exist between Lys¹² and a lipid molecule. These interactions are considered to work as an important factor in tilting the peptide to the membrane-normal.     

Monoclonal antibodies to a nitroxide lipid hapten

The isolation and characterization of a hybridoma cell line producing a monoclonal IgG₁ antibody against a spin-label nitroxide group is described. The antibody recognizes a synthetic hapten containing linked dinitrophenyl and 2,2,6,6-tetramethylpiperidinyl 1-oxy groups, having an affinity of 3.6±1.0·10⁶ M^?1 for the soluble hapten at 25°C. The antibody binds to phospholipid vesicles containing 2 mol% of spin label-derivitized lipid (lipid hapten) with an affinity of 1.5±0.2·10⁸ M^?1. This monoclonal IgG₁ mediates the binding of hapten-bearing lipid vesicles to mouse macrophage RAW264 cells bearing Fc receptors. The cellular responses to this binding are similar to those observed previously using polyclonal rabbit anti-hapten IgG. As with the heterogeneous antibodies, the monoclonal IgG₁ is more efficient in mediating cellular uptake when the vesicles are in the ‘fluid’ physical state (dimyristoylphosphatidylcholine at 37°C) compared to ‘solid’ (dipalmitoylphosphatidylcholine at 37°C). Despite the enhanced binding of ‘fluid’ phospholipid vesicles to cells, only the ‘solid’ vesicles triggered a significant respiratory burst in RAW264 macrophages.     

Conjugated double bonds in lipid bilayers: a molecular dynamics simulation study

Conjugated linoleic acids (CLA) are found naturally in dairy products. Two isomers of CLA, that differ only in the location of cis and trans double bonds, are found to have distinct and different biological effects. The cis 9 trans 11 (C9T11) isomer is attributed to have the anti-carcinogenic effects, while the trans 10 cis 12 (T10C12) isomer is believed to be responsible for the anti-obesity effects. Since dietary CLA are incorporated into membrane phospholipids, we have used Molecular Dynamics (MD) simulations to investigate the comparative effects of the two isomers on lipid bilayer structure. Specifically, simulations of phosphatidylcholine lipid bilayers in which the sn-2 chains contained one of the two isomers of CLA were performed. Force field parameters for the torsional potential of double bonds were obtained from ab initio calculations. From the MD trajectories we calculated and compared structural properties of the two lipid bilayers, including areas per molecule, density profiles, thickness of bilayers, tilt angle of tail chains, order parameters profiles, radial distribution function (RDF) and lateral pressure profiles. The main differences found between bilayers of the two CLA isomers, are (1) the order parameter profile for C9T11 has a dip in the middle of sn-2 chain while the profile for T10C12 has a deeper dip close to terminal of sn-2 chain, and (2) the lateral pressure profiles show differences between the two isomers. Our simulation results reveal localized physical structural differences between bilayers of the two CLA isomers that may contribute to different biological effects through differential interactions with membrane proteins or cholesterol.     

Molecular dynamics simulations of microstructure and mixing dynamics of cryoprotective solvents in water and in the presence of a lipid membrane

Molecular dynamics (MD) simulation is used to investigate the solubility behavior of cryoprotective (CP) solvents, such as DMSO, ethylene glycol (EG) and glycerol (GL), in pure water and in the presence of a lipid membrane. The MD study is focused on an equilibration timescale required for mixing large CP aggregates with aqueous and aqueous/lipid environments. The MD analysis demonstrates that DMSO mixes rapidly with water, so that all solute molecules are uniformly distributed in the equilibrium aqueous solution. Our investigation of the microstructure of binary EG/water and GL/water systems reveals that, despite the miscibility of both CP solvents with water, they are not ideally mixed in aqueous solutions at the molecular level. The MD simulations show that the mixing dynamics of the large CP cluster and surrounding water is found to be strongly dependent on nature of hydrophilic and hydrophobic interactions acting between cryoprotectant molecules. In particular, a spatial hydrogen-bond network formed between CP molecules plays an important role in the mixing dynamics between CP agents and water. A further analysis on the mixing behavior of the CP solvents with pure water and with aqueous solutions at a lipid membrane interface shows that, due to strong binding of the CP molecules to membrane surface, the equilibration process in the lipid environment becomes very slow, at least of the order of microseconds. The MD results are discussed in the context of the better understanding on the composition of the aqueous mixtures of the EG and GL solvents. Knowledge of the microstructure and the dynamics of these systems helps to develop better cryopreservation protocols and to propose more optimal cooling/warming regimes for cellular cryosolutions.     

Molecular dynamics simulation of a myosin subfragment-1 docking with an actin filament

Myosins are typical molecular motor proteins, which convert the chemical energy of ATP into mechanical work. The fundamental mechanism of this energy conversion is still unknown. To explain the experimental results observed in molecular motors, Masuda has proposed a theory called the “Driven by Detachment (DbD)” mechanism for the working principle of myosins. Based on this theory, the energy used during the power stroke of the myosins originates from the attractive force between a detached myosin head and an actin filament, and does not directly arise from the energy of ATP. According to this theory, every step in the myosin working process may be reproduced by molecular dynamics (MD) simulations, except for the ATP hydrolysis step. Therefore, MD simulations were conducted to reproduce the docking process of a myosin subfragment-1 (S1) against an actin filament. A myosin S1 directed toward the barbed end of an actin filament was placed at three different positions by shifting it away from the filament axis. After 30 ns of MD simulations, in three cases out of ten trials on average, the myosin made a close contact with two actin monomers by changing the positions and the orientation of both the myosin and the actin as predicted in previous studies. Once the docking was achieved, the distance between the myosin and the actin showed smaller fluctuations, indicating that the docking is stable over time. If the docking was not achieved, the myosin moved randomly around the initial position or moved away from the actin filament. MD simulations thus successfully reproduced the docking of a myosin S1 with an actin filament. By extending the similar MD simulations to the other steps of the myosin working process, the validity of the DbD theory may be computationally demonstrated.     

Molecular dynamics of lipid association at the hydrophobic interface of gramicidin S

Gramicidin S was incorporated into dimyristoylphosphatidylcholine dispersions and the observed two-component EPR spectra of spin-labelled lipids at 30 °C were analysed by a two-stage algorithm, including spectral subtractions and two-site exchange simulations. A limited range of temperatures around 30 °C was found suitable for such measurements. It has been found that negatively charged labelled lipids display a selectivity towards the intramembranous part of the peptide. The relative association constants for spin-labelled stearic acid (14-SASL) and phosphatidylserine (14-PSSL) were K _r = 2.08± 0.10 and 1.18±0.08, respectively, when compared with the zwitterionic phosphatidylcholine label (14-PCSL, K _r≡ 1). The lateral diffusion of spin-labelled lipids in peptide-free regions causes exchange between those labels in the bulk fluid lipid phase and motionally restricted boundary labelled lipids at the apolar interface of gramicidin S. Owing to exchange, the spectral anisotropy of labelled lipids giving rise to the slow-motion spectral component was gradually decreased, and there was an augmentation of spectral intensity in between the motionally restricted (slow motion) and the fast tumbling (motionally averaged) labelled lipid components. Two-component exchange simulations allowed the determination of off-rates of labelled phospholipids, showing an inverse proportionality with lipid-protein selectivity. Spin-labelled procaine exhibited limited selectivity and fast exchange similar to the on-coming non-specifically associated lipids. Received: 25 May 1998 / Revised version: 14 September 1998 / Accepted: 5 November 1998     

Proton involvement with the light-induced hindrance of spin label motion in the lumen of spinach thylakoids

The light-induced hindrance of spin label motion increases linearly with light intensity. However, it has not been possible to unambiguously demonstrate light saturation due to the very high rates of spin label reduction at high light intensity. The light-induced hindrance of spin label motion may be mimicked in the dark by subjecting thylakoids to appropriately low pH regimes. Uncouplers such as gramicidin-D and methylamine reduce the light-induced hindrance to dark levels as does ethylenedinitrilotetraacetate (EDTA) treatment. Valinomycin plus KCl which destroys the electric potential is only partially effective in reducing the light-induced hindrance. These results indicate that protons in the aqueous lumen of the thylakoids are closely involved with the observed light-induced hindrance of spin label motion.     

Molecular dynamics simulations of local anesthetic articaine in a lipid bilayer

In order to investigate structural and dynamical properties of local anesthetic articaine in a model lipid bilayer, a series of molecular dynamics simulations have been performed. Simulations were carried out for neutral and charged (protonated) forms of articaine inserted in fully hydrated dimyristoylphosphatidylcholine (DMPC) lipid bilayer. For comparison purpose, a fully hydrated DMPC bilayer without articaine was also simulated. The length of each simulation was 200 ns. Various properties of the lipid bilayer systems in the presence of both charged and uncharged forms of articaine taken at two different concentrations have been examined: membrane area per lipid, mass density distributions, order parameters, radial distribution functions, head group tilt, diffusion coefficients, electrostatic potential, etc, and compared with results of previous simulations of DMPC bilayer in the presence of lidocaine. It was shown that addition of both charged and neutral forms of articaine causes increase of the dipole electrostatic potential in the membrane interior.     

Molecular dynamics simulation of a phosphatidylglycerol membrane

Although molecular dynamics simulations are an important tool for studying membrane systems, relatively few simulations have used anionic lipids. This paper reports the first simulation of a pure phosphatidylglycerol (PG) bilayer. The properties of this equilibrated palmitoyloleoylphosphatidylglycerol membrane agree with experimental observations of PG membranes and with previous simulations of monolayers and mixed bilayers containing PG lipids. These simulations also provide interesting insights into hydrogen bonding interactions in PG membranes. This equilibrated membrane will be a useful starting point for simulations of membrane proteins interacting with PG lipids.     

Molecular dynamics simulations of membrane proteins

Membrane proteins control the traffic across cell membranes and thereby play an essential role in cell function from transport of various solutes to immune response via molecular recognition. Because it is very difficult to determine the structures of membrane proteins experimentally, computational methods have been increasingly used to study their structure and function. Here we focus on two classes of membrane proteins—ion channels and transporters—which are responsible for the generation of action potentials in nerves, muscles, and other excitable cells. We describe how computational methods have been used to construct models for these proteins and to study the transport mechanism. The main computational tool is the molecular dynamics (MD) simulation, which can be used for everything from refinement of protein structures to free energy calculations of transport processes. We illustrate with specific examples from gramicidin and potassium channels and aspartate transporters how the function of these membrane proteins can be investigated using MD simulations.     

Azethoxyl nitroxide spin labels. ESR studies involving thiourea crystals, model membrane systems and chromatophores, and chemical reduction with ascorbate and dithiothreitol

Trans- and cis-azethoxyl nitroxides , , and can be trapped in the cavities of thiourea crystals. The presence of a single gauche conformation on either side of the pyrrolidine ring within the crystals was indicated by the ESR spectra. Rotation about the long molecular axis then corresponds approximately to y-axis motion of the nitroxide moiety. Proxyl nitroxides in which the nitroxide group is located on the penultimate carbon of long chain lipids can also be trapped and were shown to adopt the azethoxyl conformation in the thiourea crystals.The measured ΔA values (A_| − A) of oriented egg lecithin multilayers containing trans- and cis-azethoxyl nitroxides and were quite small, consistent with the unique orientation of the nitroxide principal axes with respect to the long axis of the molecule. The ΔA values for a series of lipids bearing a label near the terminus of the chain were very similar to that of , showing that the azethoxyl conformation is likely the predominant one in these labels in orienting systems.Computer simulations of the ESR spectra of and in egg lecithin vesicles provided values for molecular orientation and motion parameters consistent with those expected from a consideration of molecular models in the extended (all trans) conformation.Azethoxyl nitroxides have also proven useful in the investigation of motion restricted (boundary) lipid in a lipid-protein system. Thus, the values (69 ± 10%) for the amount of boundary lipid in the chromatophore membranes from Rhodopseudomonas sphaeroides as determined using trans- and cis- are in good agreement with values using 16-doxylstearic acid (64 ± 3%). The fact that all three labels show about the same fraction of boundary lipid in this system indicates that the lipid binding sites are relatively insensitive to the geometry of the lipid chain. Also, both and appear to be able to detect a third lipid environment not seen with the doxyl fatty acid. The apparent fluidity of this component lies between that of boundary and bilayer lipid. The unique orientation of the nitroxide principal axes with respect to the long molecular axis in azethoxyl nitroxides and allows detection of hindrance to rotation about the long molecular axis, in contrast to the analogous doxyl and proxyl fatty acids.Comparative reduction studies using ascorbate and dithiothreitol indicate that azethoxyl nitroxides are slightly more resistant toward reduction than proxyl nitroxides and much more resistant than doxyl nitroxides.     

Molecular dynamics simulation of silicate glasses

Summary Although the structure of glasses is not really accessible by experimental methods, molecular dynamics is a very useful alternative, as we have tried to demonstrate in this chapter. The simulations reproduce the broad macroscopic features found in these glasses, both structural and transport-related, providing a basis for the more detailed atomic scale features found in the simulated structures. An understanding of important aspects of alkali ion transport, such as the mixed alkali effect and anomalous behaviour in some alumino-silicates, can thus be approached from the atomistic pictures of the glasses produced by the simulations. Although there is room for improvements to the potential models available, it should be clear that the further application of computer simulation methods, such as molecular dynamics, promises to provide much needed advances in glass science and engineering.     

Molecular dynamics simulation of polyelectrolyte with oppositely charged monomeric and dimeric surfactants

Interactions of anionic polyelectrolyte (PE) with cationic monomeric (MS) and dimeric surfactants (DS) have been investigated by coarse-grained molecular dynamics (MD) simulation. A PE/surfactant mixture is observed to evolve over time into micellar complex of increasing size. The critical aggregation concentration (CAC) is qualitatively found to be much lower than the critical micellization concentration (CMC) of the free surfactant. Compared to the monomeric analog, a DS interacts more strongly with the oppositely charged polyion chain. The equilibrium complex size becomes larger with increasing surfactant concentration. Simulation results are consistent with experimental observations and reveal that the electrostatic and hydrophobic interactions play an important role in the formation of micellar complex.