Hydrated Dimyristoylphosphatidylcholine Bilayer Research Articles

Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes

Microscopic structure and dynamics of water and lipids in a fully hydrated dimyristoylphosphatidylcholine phospholipid lipid bilayer membrane in the liquid-crystalline phase have been analyzed with all-atom molecular dynamics simulations based on the recently parameterized CHARMM36 force field. The diffusive dynamics of the membrane lipids and of its hydration water, their reorientational motions as well as their corresponding spectral densities, related to the absorption of radiation, have been considered for the first time using the present force field. In addition, structural properties such as density and pressure profiles, a deuterium-order parameter, surface tension, and the extent of water penetration in the membrane have been analyzed. Molecular self-diffusion, reorientational motions, and spectral densities of atomic species reveal a variety of time scales playing a role in membrane dynamics. The mechanisms of lipid motion strongly depend on the time scale considered, from fast ballistic translation at the scale of picoseconds (effective diffusion coefficients of the order of 10(-5) cm(2)/s) to diffusive flow of a few lipids forming nanodomains at the scale of hundreds of nanoseconds (diffusion coefficients of the order of 10(-8) cm(2)/s). In the intermediate regime of sub-diffusion, collisions with nearest neighbors prevent the lipids to achieve full diffusion. Lipid reorientations along selected directions agree well with reported nuclear magnetic resonance data and indicate two different time scales, one about 1 ns and a second one in the range of 2-8 ns. We associated the two time scales of reorientational motions with angular distributions of selected vectors. Calculated spectral densities corresponding to lipid and water reveal an overall good qualitative agreement with Fourier transform infrared spectroscopy experiments. Our simulations indicate a blue-shift of the low frequency spectral bands of hydration water as a result of its interaction with lipids. We have thoroughly analyzed the physical meaning of all spectral features from lipid atomic sites and correlated them with experimental data. Our findings include a "wagging of the tails" frequency around 30 cm(-1), which essentially corresponds to motions of the tail-group along the instantaneous plane formed by the two lipid tails, i.e., in-plane oscillations are clearly of bigger importance than those along the normal-to-the plane direction.

The effect of pressure on halothane binding to hydrated DMPC bilayers

Halothane binding to hydrated dimyristoylphosphatidylcholine (DMPC) bilayer membranes has been examined over a wide range of pressures from 105 to 4 × 108 Pa. We show that the solvation of halothane by the membrane and bulk water are both pressure dependent, with an increased pressure driving halothane into the membrane. Analysis of these results shows that this pressure dependence is not the cause of pressure reversal, the process whereby general anaesthetics lose their efficacy at pressures of about 8 × 106 to about 2.5 × 107 Pa.

The effects of 7-dehydrocholesterol on the structural properties of membranes

Smith-Lemli-Opitz syndrome, a congenital and developmental malformation disease, is typified by abnormal accumulation of 7-dehydrocholesterol (7DHC), the immediate precursor of cholesterol (CHOL), and depletion thereof. Knowledge of the effect of 7DHC on the biological membrane is, however, still fragmentary. In this study, large-scale atomistic molecular dynamics simulations, employing two distinct force fields, have been conducted to elucidate differences in the structural properties of a hydrated dimyristoylphosphatidylcholine bilayer due to CHOL and 7DHC. The present series of results indicate that CHOL and 7DHC possess virtually the same ability to condense and order membranes. Furthermore, the condensing and ordering effects are shown to be strengthened at increasing sterol concentrations.

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.

Free-energy change of inserting halothane into different depths of a hydrated DMPC bilayer

Using the method of energy representation, we have calculated the free-energy change of inserting a halothane molecule into different depths of a hydrated dimyristoylphosphatidylcholine (DMPC) bilayer at pressures of 10 5 Pa to 4 × 10 7 Pa . Our results show that the free-energy change is more negative within the membrane than in bulk water. The halothane distribution is diffuse, and the preferred location is near the headgroup. The pressure effect is found to be minimal within the pressure range examined, which corresponds to previous biological experimental conditions.

A possible mechanism for pressure reversal of general anaesthetics from molecular simulations

The effect of general anaesthetics is pressure-dependent. We have simulated a fully hydrated dimyristoylphosphatidylcholine bilayer with halothane (a general anaesthetic) embedded, at pressures of 1, 200 and 400 atm, respectively. We find that at higher pressures, halothane molecules tend to cluster together. Based on these results, we propose a possible mechanisms for pressure reversal of anaesthesia.

Molecular packing in 1-hexanol–DMPC bilayers studied by molecular dynamics simulation

The structure and molecular packing density of a “mismatched” solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data on comparable systems. The local density or molecular packing in DMPC–hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results suggested a positive volume change, Δ V m, of 4 cm 3 mol − 1 hexanol partitioned at 310 K in good accordance with experimental values. Analysis of the apparent volumes of each component in the pure and mixed states further showed that Δ V m reflects a balance between a substantial increase in the packing density of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C8) is stretched by about 4%. Concomitantly, the average lateral area per chain decreases and these two effects compensate so that the overall packing density in the outer region, where the hexanol molecules are located, remains practically constant. The core of the bilayer (C9–C13) is slightly thinned. The average lateral area per chain in this region expands, resulting in a looser packing density. The net effect in the core is a 2–3% decrease in density corresponding to a total volume increase of ∼ 14 cm 3 mol − 1 hexanol partitioned.

Comparative Molecular Dynamics Study of Lipid Membranes Containing Cholesterol and Ergosterol

Sterol molecules are essential for maintaining the proper structure and function of eukaryotic cell membranes. The influence of cholesterol (the principal sterol of higher animals) on the lipid bilayer properties was extensively studied by both experimental and simulation methods. In contrast, the effect of ergosterol (the principal fungal sterol) on the membrane structure and dynamics is much less recognized. This work presents the results of comparative molecular dynamics simulation of the hydrated dimyristoylphosphatidylcholine bilayer containing ∼25 mol % of cholesterol or ergosterol. A detailed analysis of the molecular properties (e.g., bilayer thickness, lipid order, diffusion, intermolecular interactions, etc.) of both sterol-induced liquid-ordered membrane phases is presented. Presence of sterols in the membrane significantly changes its property, especially fluidity and molecular packing. Moreover, in accordance with the experiments, our calculations show that, compared to cholesterol, ergosterol has higher ordering effect on the phospholipid acyl chains. This different influence on the properties of the lipid bilayer stems from differences in conformational freedom of sterol side chains. Additionally, obtained models of lipid membranes containing human and fungal sterols, constituting the result of our work, can be also utilized in other chemotherapeutic studies on interaction of selected ligands (e.g., antifungal compounds) with membranes.

Interaction of a peptide nanotube with a water–membrane interface

Inserting peptide nanotubes into lipid bilayers modulates the permeability properties of the cell wall, thus conferring potential bacteriocidal capability. Interaction of a peptide nanotube formed by eight cyclo[RRKWLWLW] subunits with the surface of a hydrated dimyristoylphosphatidylcholine bilayer is investigated using molecular dynamics simulations. The present sequence of alternated D–L-α-amino acids has been shown to yield remarkable antibacterial in vitro activity, and the chosen topoisomer corresponds to the optimum amphipathy of the tubular structure, whereby non-polar and charged side chains are segregated by the aqueous interface. The cohesion of the nanotube is ensured by a scaffold of intermolecular hydrogen bonds between adjacent cyclic peptides, supplemented by favorable like-charged contacts of arginine side chains. It is further reinforced by interactions of charged residues with the lipid head groups and of non-polar residues with the lipid acyl chains. The simulation reveals a partial breaking of the synthetic channel accompanying its early insertion into the lipid bilayer. The latter opens new questions about how peptide nanotubes permeate the membrane, in particular whether or not (i) self-assembly precedes partitioning and (ii) translocation occurs with the complete tubular structure.

Orientation and Conformational Preference of Leucine-Enkephalin at the Surface of a Hydrated Dimyristoylphosphatidylcholine Bilayer: NMR and MD Simulation

The morphogenic opiate pentapeptide leucine-enkephalin (lenk) in a hydrated dimyristoylphosphatidylcholine (DMPC) bilayer is studied using NMR spectroscopy and molecular dynamics simulation. Contrary to the frequent assumption that the peptide attains a single fixed conformation in the presence of membranes, we find that the lenk molecule is flexible, switching between specific bent conformations. The constraints to the orientation of the aromatic rings that are identified by the NMR experiment are found by the MD simulation to be related to the depth of the peptide in the bilayer. The motion of the N-H vectors of the peptide bonds with respect to the magnetic field direction as observed by MD largely explain the magnitude of the observed residual dipolar coupling (RDC), which are much reduced over the static (15)N-(1)H coupling. The measured RDCs are nevertheless significantly larger than the predicted ones, possibly due the absence of long-time motions in the simulations. The conformational behavior of lenk at the DMPC surface is compared to that in the aqueous solution, both in the neutral and in the zwitterionic forms.

Molecular Dynamics Investigation of an Oriented Cyclic Peptide Nanotube in DMPC Bilayers

Nanotubes resulting from the self-assembly of cyclic peptides formed by eight α-amino acids and inserted into lipid bilayers have been shown to function as synthetic, integral transmembrane channels. A nanotube consisting of eight cyclo[(l-Trp-d-Leu)3-l-Gln-d-Leu] subunits, organized in an antiparallel, β-sheetlike channel embedded in a hydrated dimyristoylphosphatidylcholine bilayer was investigated in an 8-ns molecular dynamics trajectory. This large-scale statistical simulation brings to light not only the atomic-level structural features of the synthetic channel, but also its dynamical properties. Overall, the nanotube conserves its hollow tubular structure. The calculation reproduces the tilt of the channel with respect to the normal of the bilayer, in reasonable agreement with experiment. The results show a dislocation of the nanotube indicative of a possible disassembly process that may influence the channel conduction. The dynamics of the water in the hollow tubular structure has been characterized, and the conductance of the channel has been estimated. Transport properties of the peptide nanotube are discussed in comparison with other transporters.

The closed state of a H+ channel helical bundle combining precise orientational and distance restraints from solid state NMR.

An interhelical distance has been precisely measured by REDOR solid-state NMR spectroscopy in the transmembrane tetrameric bundle of M2-TMP, from the M2 proton channel of the influenza A viral coat. The high-resolution structure of the helical backbone has been determined using orientational restraints from uniformly aligned peptide preparations in hydrated dimyristoylphosphatidylcholine bilayers. Here, the distance between (15)N(pi) labeled His37 and (13)C(gamma) labeled Trp41 is determined to be less than 3.9 A. Such a short distance, in combination with the known tilt and rotational orientation of the individual helices, permits not only a determination of which specific side chain pairings give rise to the interaction, but also the side chain torsion angles and restraints for the tetrameric bundle can also be characterized. The resulting proton channel structure is validated in a variety of ways. Both histidine and tryptophan side chains are oriented in toward the pore where they can play a significant functional role. The channel appears to be closed by the proximity of the four indoles consistent with electrophysiology and mutagenesis studies of the intact protein at pH 7.0 and above. The pore maintains its integrity to the N terminal side of the membrane, and at the same time, a cavity is generated that appears adequate for binding amantadine. Finally, the observation of a 2 kHz coupling in the PISEMA spectrum of (15)N(pi)His37 validates the orientation of the His37 side chain based on the observed REDOR distance.

Orientational Order of the Water Molecules Across a Fully Hydrated DMPC Bilayer: A Monte Carlo Simulation Study

The orientational order of water molecules located in different regions of a fully hydrated dimyristoylphosphatidylcholine (DMPC) membrane is analyzed and compared to that in pure water on the basis of an all-atom Monte Carlo simulation. The preferential orientation of the water molecules relative to the membrane as well as the relative orientation and hydrogen-bonding structure of neighboring molecules is discussed in detail. Due to the distribution of the charged groups of the lipid molecules, the water molecules in the interfacial region of the membrane are turning preferentially toward the membrane interior with their dipole moments, whereas in the hydrocarbon region the water dipoles are pointing toward the aqueous phase. The density of the water molecules in the hydrocarbon phase is found to be rather inhomogeneous; the few water molecules in this region are grouping together and form small hydrogen-bonded clusters. The long, mostly parallel lipid tails are forcing these water molecules to be aligned in planes parallel with them and also the hydrogen-bonded neighbors to be arranged around each other in a coplanar way. It is found that the relative importance of the interstitial molecules, which left the hydrogen-bonded network of the other molecules and are located in its cavities, increases considerably upon the approach of the molecules to the middle of the membrane. It is also found that the geometry of the hydrogen bond around the bonding H atom does not change noticeably across the bilayer, whereas when the molecules approach the membrane interior, the arrangement of the hydrogen-bonded neighbors around each other becomes less and less tetrahedral, until this preference for tetrahedral arrangement disappears completely.

G Protein-coupled receptor-bioligand interactions modeled in a phospholipid bilayer

The arginine vasopressin (AVP) V2 receptor (V2R), a member of the G protein-coupled receptor (GPCR) superfamily, mediates the regulation of renal water absorption whose disorders cause nephrogenic diabetes insipidus. A complete molecular model of V2R embedded in a fully hydrated dimyristoylphosphatidylcholine (DMPC) bilayer was developed. Both free and AVP-bound states of V2R were studied. An initial V2R was built using a rule-based automated method for GPCR modeling, implementing both the low-resolution structure of bovine rhodopsin and the multisequence analysis of the GPCR superfamily. The loops were added using homology modeling as implemented in SYBYL. The docking site of AVP was selected and justified upon consideration of ligand–receptor interactions versus structure–activity data. The model was initially relaxed using constrained simulated annealing in vacuo. Subsequently, it was placed in the relaxed fully hydrated DMPC bilayer and submitted to ∼1.5 ns molecular dynamics using the AMBER 4.1 package upon constant number–pressure–temperature (NPT) conditions on parallel computers: Cray T3E and/or IBM SP2. Physical properties of the system were evaluated and compared with a pure hydrated DMPC bilayer. The receptor–ligand interactions, solvation interactions, individual lipid–protein interactions, and fluctuations of the protein, the lipid, and water were analyzed in detail. Receptor residues likely to be involved in the ligand binding were selected. As expected, the membrane-spanning helices of the protein fluctuate less than do the peripheral loops. The protein locally disturbs the lipid structure. A contiguous network of polar residues, extending from the bottom of the docked ligand to the intracellular domain, is observed inside the receptor in the AVP-bound V2R, while a similar network is broken in the empty V2R. This observation may suggest possible active and resting states of V2R, respectively. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 73: 61–70, 1999

260 ps Molecular Dynamics Simulation of Substance P With Hydrated Dimyristoyl Phosphatidyl Choline Bilayer

We present here results on 260 pico seconds (ps) molecular dynamics (MD) simulation of substance P (SP) in hydrated bilayer of dimyristoyl phosphatidyl choline (DMPC) (39 molecules of DMPC with 776 water molecules). 260 ps MD simulation has been carried out in 0.001 ps time interval with united atom force field, using AMBER 4.0 package. Non bonded pair list was updated every 20 cycles using 12.5 Angstrom cut off distance. Analysis of MD data is done using our package ANALMD. The obtained models are presented using graphics package RASMOL. All simulations, analysis of MD data and graphics is done on INDIGO-2, R-4400 extreme graphics work station. Our results show no systematic change in order parameter, but reduction in transfraction of the chain torsional angles, compared to our earlier results on MD simulation on hydrated DMPC bilayer without SP. C-terminal and central peptide residues adopt partial helical conformation. Helix type as classified on the basis of H-bonds is between alpha and 3(10). The peptide backbone shows flexibility during heating runs. Later, it is stabilized and there was not much change in the spatial position of the backbone. Lipid matrix serves the role of immobilization of the peptide backbone in a preferred conformation.

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.

Study of the topography of cannabinoids in model membranes using X-ray diffraction

Small-angle X-ray diffraction was used to determine the topography of (−)- Δ 8-tetrahydrocannabinol in partially hydrated dimyristoylphosphatidylcholine bilayers. Electron density profiles of lipid bilayers in the presence and absence of the cannabinoid were calculated using Fourier transform. Step-function equivalent profiles were then constructed to obtain the absolute electron density scale. We have compared the electron density profiles of the above preparations to determine the location of the drug molecule in the bilayer. By using (−)-5′-iodo- Δ 8-tetrahydrocannabinol in parallel experiments, we were also able to locate the iodine atom in the bilayer and deduce the conformation of the cannabinoid side alkyl chain. All comparisons were made between different preparations having the same mesomorphic form and total period repeat distance. To achieve this, we have carried out X-ray diffraction experiments at various temperatures to cover the different mesomorphic phases and combined our data with the corresponding results from differential scanning calorimetry. Based on the results of this work and previous data on the orientation of the cannabinoid in model membranes, we concluded that the phenolic hydroxy group of the drug molecule exists near the carbonyl groups of DMPC and that the average position of the iodine atom is approx. 5.5 Å from the center (terminal methyl region) of the DMPC bilayer. This requires the cannabinoid side-chain to assume an orientation parallel to the bilayer chains.

Kinetics of the main phase transition in lipid bilayer membranes containing n-alkanols: A time-resolved X-ray diffraction study

The interaction of a series of n-alkanols with dimyristoylphosphatidylcholine (DMPC) bilayers was studied using time-resolved X-ray diffraction techniques and scanning calorimetry. The length of the alkanol chain was found to influence the d-spacings for the L β′ and L α phases for fully hydrated DMPC bilayers. The effect of n-alkanol on the kinetics of the L β′ to L α phase transformation was found to be a function of both the length of the alkanol chain and the size of the domain structures found laterally within a bilayer. In addition, the time required to induce the L β′ to L α phase transition as a function of a temperature jump was found to correlate with the degree of cooperativity in the transition.