Simulating the Physiological Phase of Hydrated DPPC Bilayers: The Ester Moiety

Abstract

The charge on the ester oxygen of the sn2 group of the dipalmitoylphosphatidylcholine (DPPC) has a remarkable effect on the square area per lipid in simulations of a hydrated bilayer. This is in contrast to simulations of nonpolar, neutral lipids, where it has been found to have little effect. The charges associated with the GROMOS96 45A3 and 45A4 biomolecular force fields have been previously shown to cause significant membrane shrinkage. We find that the use of larger charges at the ester groups alone (as opposed to on all the polar moieties in the head group) remedies the shrinkage. The source of this effect in DPPC lies in the fact that the charge distribution of this polar group profoundly influences its free energy of hydration and, correspondingly, the water distribution around it. In an attempt to rationally tune the ester parameters, the repulsive Lennard–Jones parameters that represent the van der Waals interaction have been refined to reproduce the experimental density and heat of vaporization, and the charges of the ester groups have been tuned to reproduce the experimental free energies of hydration of a series of alkane esters. The new parameters form part of the GROMOS96 53A5 and 53A6 force fields. However, with the new force‐field parameters, the area per lipid in simulations of hydrated DPPC bilayers lies below that of the physiological liquid‐crystalline phase, the implications of which are discussed.     

Tip penetration through lipid bilayers in atomic force microscopy

In studies of solid supported lipid bilayers with atomic force microscopes (AFM) the force between tip and bilayer is routinely measured. During the approach of the AFM tip in aqueous electrolyte first a short-range repulsive force is observed. For many solid-like and some liquid-like lipid bilayers a subsequent break-through is observed. We observe such a break-through also for dioleoyloxypropyl-trimethylammonium chloride (DOTAP) which is expected to be liquid-like. Here we describe a model which assumes that the jump reflects the penetration of the AFM tip through the lipid bilayer. The model predicts a logarithmical dependence of the break-through force on the approaching velocity of the AFM tip. Two parameters are introduced: The ratio A/αV, α being a geometric factor, A being the area over which pressure is exerted on the bilayer, V the activation volume, and k₀, the rate of spontaneous formation of a hole in the lipid bilayer that is big enough to allow the break-through of the tip. Experiments with bilayers consisting of DOTAP and dioleoylphosphatidylserine (DOPS) show that the break-through forces behave in the predicted way. For DOTAP we obtain ratios A/αV of about 58 nm⁻¹ and rates k₀ ranging from 1.9×10⁻⁸ to 2.5×10⁻⁴ s⁻¹. For DOPS the corresponding values are 162 nm⁻¹ and 2.0 s⁻¹.     

Elastic modulus of free-standing lipid bilayer

In the current study, molecular dynamics (MD), finite element (FE) method, and genetic algorithm are employed to compute Young’s modulus of free-standing DPPC lipid bilayer. MD method is utilized to simulate loading of a free-standing DPPC lipid bilayer under an indenter. Indentation experiment is also simulated with FE method where genetic algorithm controls value of Young’s modulus in FE simulation and finds the best value for it. The best value means the value results in a force–depth curve which agrees well with the curve obtained from MD simulation. While simulating indentation with MD method two distinct regimes are distinguished in force–depth curve before rupture of the bilayer. The first regime shows elastic response of the bilayer to indentation and it is shown that force–depth curve can be fitted with a cubic polynomial in this regime. The second regime starts at the point which the force–depth curve changes from convex to concave. This point is an inflection point and would be regarded as yield point of the bilayer. Slope of the curve decreases with indentation depth in this regime which shows changes in internal structure of the bilayer. Also we investigate effects of indenter’s shape and indentation speed on computed Young’s modulus and show rate-dependent behavior of free-standing lipid bilayer.     

Porphinato Zinc Complexes Incorporated into the Bilayer Membrane of Lipid Liposomes

3,8,13,17-Tetramethyl-7,12-divinyl-2,18-bis(18-hydroxyoctadecyl propionate) porphinato zinc (BHPZn) and a model compound, dimethyl ester of protoporphinato zinc (DMPZn), were synthesized and incorporated into the hydrophobic region of bilayer membrane of dipalmitoylphosphatidylcholine (DPPC) liposome. The introduction of long alkyl groups onto the porphyrin ring is effective for restriction of porphyrin aggregation in the bilayer membrane of DPPC liposome. When the molar ratio of DPPC lipid to porphyrin is above 100, the spectrum of BHPZn in the liposome suggests that it is in a typically monomeric state. Quenching of BHPZn fluorescence in the hydrophobic bilayer membrane by hydrophilic quenchers is slow and shows smaller Stern-Volmer constants, while the quenching by hydrophobic quenchers shows much larger Stern-Volmer constants than that of the model compound, DMPZn. These results suggest that the location of the porphyrin ring of BHPZn is fixed at a certain depth in the hydrophobic bilayer membrane of DPPC liposome, and that that of DMPZn is widely distributed in the whole hydrophobic region.     

Determining the Local Shear Viscosity of a Lipid Bilayer System by Reverse Non‐Equilibrium Molecular Dynamics Simulations

The parallel shear viscosity of a dipalmitoylphosphatidylcholine (DPPC) bilayer system is studied by reverse non‐equilibrium molecular dynamics simulations (RNEMD) with two different united‐atom force fields. The results are related to diffusion coefficients and structural distributions obtained by equilibrium molecular simulations. We investigate technical issues of the algorithm in the bilayer setup, namely, the dependence of the velocity profiles on the imposed flux and the influence of the thermostat on the calculated shear viscosity. We introduce the concept of local shear viscosity and investigate its dependence on the slip velocity of the monolayers and the particle density at the headgroup–water interface and the tail–tail interface. With this we demonstrate that the lipid bilayer is more viscous than the surrounding water phase, and that slip takes place near the headgroup region and in the centre of the bilayer where the alkyl tails meet. We also quantify the apparent increase in viscosity of the water molecules entangled at the water–headgroup interface.     

United atom force field for phospholipid membranes: Constant pressure molecular dynamics simulation of dipalmitoylphosphatidicholine/water system

We refined the united atom field for the simulations of phospholipid membranes. To validate this potential we performed 1000-ps constant pressure simulation of a dipalmitoylphosphatidicholine (DPPC) bilayer at T=50° C. The average area per head group (61.6±0.6) Ų obtained in our simulation agrees well with the measured one of (62.9±1.3) Ų. The calculated S_CD order parameters for the Sn-2 hydrocarbon tail also display a good agreement with the experiment. The conformations of head groups in our simulations of the liquid crystal phase are different than the ones observed in the crystal structure. ©1999 John Wiley & Sons, Inc. J Comput Chem 20, 531–545, 1999     

Comparison of the thermal behavior and conformational changes in partially and fully hydrated dipalmitoylphosphatidylcholine systems

The temperature dependence of conformational changes for partially and fully hydrated DPPC systems through two physicochemical techniques, namely DSC and Raman spectroscopy, is studied. DSC experiments have shown a different thermal behavior between the two considered systems, indicating the effective role of water in the thermal behavior. A temperature resolution of inter- and intramolecular interactions during the main melting phase transition was achieved by using three different Raman intensity ratios, which confirm that the main phase transition represents a two-stage transition. Van’t Hoff plots for the C–C, C–H, C=O and C₄N⁺ stretching modes, in a temperature range just below the main transition temperature, have been used to compare the thermodynamic parameters extracted by the two physicochemical techniques. The significance of these results can be summarized as follows: (a) DSC and Raman spectroscopy have shown complementary results indicating that DPPC exists in partially or fully hydrated states; (b) thermodynamic parameters ΔΗ and ΔS calculated in both techniques for the two different hydration states of DPPC were in harmony; (c) water more significantly affects the thermal and dynamic properties of fully hydrated DPPC bilayers than of the partially hydrated DPPC; and (d) water disturbs the head-group packing, the alkyl chains interactions and the mesophase region. It appears that the amount of water plays a vital role in the bilayer structure. As more and more extensive studies appear in the literature on biomolecules or drug membrane interactions, this information will be valuable in understanding the role of water in these interactions.     

Fusogenic tilted peptides induce nanoscale holes in supported phosphatidylcholine bilayers

Tilted peptides are known to insert in lipid bilayers with an oblique orientation, thereby destabilizing membranes and facilitating membrane fusion processes. Here, we report the first direct visualization of the interaction of tilted peptides with lipid membranes using in situ atomic force microscopy (AFM) imaging. Phase-separated supported dioleoylphosphatidylcholine/dipalmitoylphosphatidylcholine (DOPC/DPPC) bilayers were prepared by fusion of small unilamellar vesicles and imaged in buffer solution, in the absence and in the presence of the simian immunodeficiency virus (SIV) peptide. The SIV peptide was shown to induce the rapid appearance of nanometer scale bilayer holes within the DPPC gel domains, while keeping the domain shape unaltered. We attribute this behavior to a local weakening and destabilization of the DPPC domains due to the oblique insertion of the peptide molecules. These results were directly correlated with the fusogenic activity of the peptide as determined using fluorescently labeled DOPC/DPPC liposomes. By contrast, the nontilted ApoE peptide did not promote liposome fusion and did not induce bilayer holes but caused slight erosion of the DPPC domains. In conclusion, this work provides the first direct evidence for the production of stable, well-defined nanoholes in lipid bilayer domains by the SIV peptide, a behavior that we have shown to be specifically related to the tilted character of the peptide. A molecular mechanism underlying spontaneous insertion of the SIV peptide within lipid bilayers and the subsequent removal of bilayer patches is proposed, and its relevance to membrane fusion processes is discussed.     

Performance of the general amber force field in modeling aqueous POPC membrane bilayers

The aim of this work was to answer the question of whether the general amber force field (GAFF) is good enough to simulate fully hydrated POPC membrane bilayers. The test system contained 128 POPC and 2985 TIP3P water molecules. The equilibration was carried out in a nonarbitrary manner to reach the stable liquid-crystalline phase. The simulations were performed by using particle mesh Ewald electrostatics implemented in molecular dynamics packages Amber8 (NPT ensembles) and NAMD2 (NPgammaT ensembles). The computational results were assessed against the following experimental membrane properties: (i) area per lipid, (ii) area compressibility modulus, (iii) order parameter, (iv) gauche conformations per acyl chain, (v) lateral diffusion coefficients, (vi) electron density profile, and (vii) bound water at the lipid/water interface. The analyses revealed that the tested force field combination approximates the experimental values at an unexpectedly good level when the NPgammaT ensemble is applied with a surface tension of 60 mN m(-1) per bilayer. It is concluded that the GAFF/TIP3P combination can be utilized for aqueous membrane bilayer simulations, as it provides acceptable accuracy for biomolecular modeling.     

Methotrexate interaction with a lipid membrane model of DPPC

Dipalmitoylphosphatidylcholine (DPPC) liposomes were employed as membrane models for the investigation of the interaction occurring between methotrexate (MTX) and bilayer lipid matrix. Liposomes were obtained by hydrating a lipid film with 50 mM Tris buffer (pH 7.4). The differential scanning calorimetry (DSC) evaluation of the thermotropic parameters associated with the phase transitions of DPPC liposomes gave useful information about the kind of drug-membrane interaction. The results showed an electrostatic interaction taking place with the negatively charged molecules of MTX and the phosphorylcholine head groups, constituting the outer part of DPPC bilayers. No interaction with the hydrophobic phospholipid bilayer domains was detected, revealing a poor capability of MTX to cross through lipid membranes to reach the interior compartment of a lipid bounded structure. These findings correlate well within vitro biological experiments on MTX cell susceptibility.     

Effects of cholesterol component on molecular interactions between paclitaxel and phospholipid within the lipid monolayer at the air-water interface

Cholesterol is a main component of the cell membrane and could have significant effects on drug-cell membrane interactions and thus the therapeutic efficacy of the drug. It also plays an important role in liposomal formulation of drugs for controlled and targeted delivery. In this research, Langmuir film technique, atomic force microscopy (AFM) and Fourier transform infrared spectroscopy (FTIR) are employed for a systematic investigation on the effects of cholesterol component on the molecular interactions between a prototype antineoplastic drug (paclitaxel) and 1,2-dipalmitoyl-sn-glycerol-3-phosphocholine (DPPC) within the cell membrane by using the lipid monolayer at the air-water interface as a model of the lipid bilayer membrane and the biological cell membrane. Analysis of the measured surface pressure (pi) versus molecular area (a) isotherms of the mixed DPPC/paclitaxel/cholesterol monolayers at various molar ratios shows that DPPC, paclitaxel and cholesterol can form a non-ideal miscible system at the air-water interface. Cholesterol enhances the intermolecular forces between paclitaxel and DPPC, produces an area-condensing effect and thus makes the mixed monolayer more stable. Investigation of paclitaxel penetration into the mixed DPPC/cholesterol monolayer shows that the existence of cholesterol in the DPPC monolayer can considerably restrict the drug penetration into the monolayer, which may have clinical significance for diseases of high cholesterol. FTIR and AFM investigation on the mixed monolayer deposited on solid surface confirmed the obtained results.     

Vesicle—vesicle interaction and forces between bilayers in phospholipid systems incorporating phosphatidylinositol

Sonicated vesicles have been prepared from mixtures of dipalmitoylphosphatidylcholine (DPPC) and phosphatidylinositol (PI) covering a range of composition. The effect of temperature on the rates of aggregation of the vesicles on addition of calcium and magnesium ions has been investigated. Apart from pure PI vesicles the rates of aggregation decrease dramatically as the temperature approaches the gel-to-liquid crystalline phase transition temperature of DPPC. Low angle X-ray analysis of lamellar phases of DPPC-PI (75:25 wt%) in the presence of Ca²⁺ ions shows that between 35 and 45°C the repeat distance goes from 136 to 68 Å. It is suggested that below the chain-melting temperature of DPPC Ca²⁺ ions induce lateral phase separation of PI giving a lamellar repeat distance corresponding to the thickness of two bilayers.The net repulsive pressure between DPPC-PI bilayers has been measured by a vapour pressure technique as a function of temperature. At close apposition (<15 Å) the pressure is characteristic of hydration repulsion and increases with temperature. The repulsive force between the bilayers, lateral pressure and compressibility of the bilayers have also been determined. On progressively removing water from between the bilayers 5–14% of the work done goes into bilayer deformation, the remaining 86–95% being required to bring the bilayers together.     

Solubilization of supported lipid membranes by octyl glucoside observed by time-lapse atomic force microscopy

Detergents are very useful for the purification of membrane proteins. A good detergent for protein extraction has to prevent denaturation by unfolding, and to avoid aggregation. Therefore, gaining access to the mechanism of biomembranes’ solubilization by detergents is crucial in biochemical research. Among the wide range of detergents used to purify membrane proteins, n-octyl β-d-glucopyranoside (OG) is one of the most important as it can be easily removed from final protein extracts.

Here, we used real-time atomic force microscopy (AFM) imaging to visualize the behavior of a model supported lipid bilayer in the presence of OG. Two kinds of supported model membranes were prepared by fusion of unilamellar vesicles: with an equimolar mixing of dioleoylphosphatidylcholine/dipalmitoylphosphatidylcholine (DOPC/DPPC) or with DPPC alone. Time-lapse AFM experiments evidenced that below its critical micelle concentration (CMC), OG was not able to solubilize the bilayer but the gel DPPC domains were instantly dissolved into the DOPC matrix. This result was interpreted as a disorganization of the DPPC molecular packing induced by OG. When membranes were incubated with OG at concentrations higher than CMC, the detergent immediately provoked the complete and immediate desorption of the whole bilayer for both compositions: DPPC and DOPC/DPPC. After a while, some patches appeared onto the bare mica surface. This redeposition activity, together with fusion events, progressively led to the recovery of a continuous bilayer. These results provide a new insight on the unique properties of OG employed in membrane reconstitution protocols.     

Molecular dynamics simulations of DiI-C18(3) in a DPPC lipid bilayer

We performed a 40 ns simulation of 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI-C18(3)) in a 1,2-dipalmitoyl-sn-glycero-3-phosphatidyl choline (DPPC) bilayer in order to facilitate interpretation of lipid dynamics and membrane structure from fluorescence lifetime, anisotropy, and fluorescence correlations spectroscopy (FCS). Incorporation of DiI of 1.6 to 3.2 mol% induced negligible changes in area per lipid but detectable increases in bilayer thickness, each of which are indicators of membrane structural perturbation. The DiI chromophore angle was 77 +/- 17 degrees with respect to the bilayer normal, consistent with rotational diffusion inferred from polarization studies. The DiI headgroup was located 0.63 nm below the lipid head group-water interface, a novel result in contrast to some popular cartoon representations of DiI but consistent with DiI's increase in quantum yield when incorporated into lipid bilayers. Importantly, the fast component of rotational anisotropy matched published experimental results demonstrating that sufficient free volume exists at the sub-interfacial region to support fast rotations. Simulations with non-charged DiI head groups exhibited DiI flip-flop, demonstrating that the positively-charged chromophore stabilizes the orientation and location of DiI in a single monolayer. DiI induced detectable changes in interfacial properties of water ordering, electrostatic potential, and changes in P-N vector orientation of DPPC lipids. The diffusion coefficient of DiI (9.7 +/- 0.02 x 10(-8) cm2 s(-1)) was similar to the diffusion of DPPC molecules (10.7 +/- 0.04 x 10(-8) cm2 s(-1)), supporting the conclusion that DiI dynamics reflect lipid dynamics. These results provide the first atomistic level insight into DiI dynamics, results essential in elucidating lipid dynamics through single molecule fluorescence studies.     

Lateral Diffusion of Lipids and Diffusion of Water through Lipid Bilayers in the Presence of (1,1-Dimethyl-3-Oxobutyl)Phosphonates

The influence of some amphiphilic (diethyl, dipropyl, and dibutyl) esters of (1,1-dimethyl-3-oxobutyl)phosphonic acid with the regularly changing number of CH₂ groups in the hydrocarbon (hydrophobic) moiety on the lateral diffusion of dioleoyl phosphatidylcholine lipid and transmembrane diffusion of water in the oriented multibilayer system was studied by ¹H pulsed field gradient NMR at phosphonate concentrations up to 30 mol %. The shape of the ³¹P NMR spectra and the dependence of the shape of the ¹H NMR spectra on the bilayer orientation suggest that the presence of phosphonates does not affect the phase state of the system. The lamellar liquid crystalline phase remains unchanged, and phosphonate molecules become incorporated into the bilayer and have the same orientation as phospholipid molecules. The presence of phosphonates in the lipid bilayer increases the coefficients of lipid lateral diffusion and water diffusion through bilayers. This effect depends monotonically on the number of CH₂ groups in the phosphonate molecule. The most probable place for the incorporation of amphiphilic phosphonate molecules is the hydrophilic/hydrophobic interphase region of the bilayer. The molecules incorporated into the interphase disorder the bilayer and increase lateral diffusion of lipids and bilayer permeability compared with the ester-free bilayer. When the number of CH₂ groups in the ester molecule increases from diethyl to dibutyl phosphonate, the arrangement of lipid hydrocarbon tails becomes more ordered. This decreases the lipid lateral diffusion coefficient and bilayer permeability to water molecules.     

Phase separation of saturated and mono-unsaturated lipids as determined from a microscopic model

A molecular model is proposed of a bilayer consisting of fully saturated dipalmitoylphosphatidylcholine (DPPC) and mono-unsaturated dioleoylphosphatidylcholine (DOPC). The model not only encompasses the constant density within the hydrophobic core of the bilayer, but also the tendency of chain segments to align. It is solved within self-consistent field theory. A model bilayer of DPPC undergoes a main-chain transition to a gel phase, while a bilayer of DOPC does not do so above zero degrees centigrade because of the double bond which disrupts order. We examine structural and thermodynamic properties of these membranes and find our results in reasonable accord with experiment. In particular, order-parameter profiles are in good agreement with NMR experiments. A phase diagram is obtained for mixtures of these lipids in a membrane at zero tension. The system undergoes phase separation below the main-chain transition temperature of the saturated lipid. Extensions to the ternary DPPC, DOPC, and cholesterol system are outlined.     

Translocation of Ca2+ across lipid bilayer membrane due to defects induced by teleocidin

The effect of defects in a dipalmitoylphosphatidylcholine (DPPC) membrane on Ca²⁺ permeability across the membrane was studied. Addition of teleocidin to a suspension of DPPC vesicles encapsulating Quin 2 increased the fluorescence intensity of Quin 2. Change of fluorescence intensity was significant below the phase-transition temperature of the membrane, and increased according to the kind of divalent metal ions in the medium in the order of Mg²⁺2+2+. It was confirmed that DPPC vesicles did not change the vesicular structure upon binding teleocidin to the membrane. Therefore, the fluorescence increase below the phase-transition temperature was ascribed to the influx of divalent cations into DPPC vesicles through cracks formed in the membrane upon distribution of teleocidin. By contrast, 12-0-tetradecanoylphorbol-13-acetate (TPA) did not change the fluorescence intensity of Quin 2 significantly. It should be noted that teleocidin, which located at the membrane surface, yielded more significant defects across the lipid membrane than TPA, which was incorporated into the hydrophobic core of the membrane.     

Atomistic simulation of lipid and DiI dynamics in membrane bilayers under tension

Membrane tension modulates cellular processes by initiating changes in the dynamics of its molecular constituents. To quantify the precise relationship between tension, structural properties of the membrane, and the dynamics of lipids and a lipophilic reporter dye, we performed atomistic molecular dynamics (MD) simulations of DiI-labeled dipalmitoylphosphatidylcholine (DPPC) lipid bilayers under physiological lateral tensions ranging from -2.6 mN m(-1) to 15.9 mN m(-1). Simulations showed that the bilayer thickness decreased linearly with tension consistent with volume-incompressibility, and this thinning was facilitated by a significant increase in acyl chain interdigitation at the bilayer midplane and spreading of the acyl chains. Tension caused a significant drop in the bilayer's peak electrostatic potential, which correlated with the strong reordering of water and lipid dipoles. For the low tension regime, the DPPC lateral diffusion coefficient increased with increasing tension in accordance with free-area theory. For larger tensions, free area theory broke down due to tension-induced changes in molecular shape and friction. Simulated DiI rotational and lateral diffusion coefficients were lower than those of DPPC but increased with tension in a manner similar to DPPC. Direct correlation of membrane order and viscosity near the DiI chromophore, which was just under the DPPC headgroup, indicated that measured DiI fluorescence lifetime, which is reported to decrease with decreasing lipid order, is likely to be a good reporter of tension-induced decreases in lipid headgroup viscosity. Together, these results offer new molecular-level insights into membrane tension-related mechanotransduction and into the utility of DiI in characterizing tension-induced changes in lipid packing.     

Encapsulation of drugs by lyophilized empty dipalmitoylphosphatidylcholine liposomes: effect of calcium ion

The effects of divalent cation (Ca2+) on the characteristics of dipalmitoylphosphatidylcholine (DPPC) liposomes regenerated from lyophilized empty liposomes by rehydration and warming were investigated. The results showed that the volume (ml) of internal aqueous compartment per g lipid (captured volume; Vcap) has a maximum at a certain concentration range of calcium chloride and the maximal value is more than ten times the minimal value. This phenomenon can be explained by considering that binding of Ca2+ to phosphate groups in DPPC molecules induces an increase in the distance (r) between adjacent bilayer membranes in multilamellar liposomes through electrostatic force and causes an increase in Vcap. The dynamic properties of lyophilized liposomes in the rehydration process were examined using a multilamellar vesicle model. The results of simulation suggested that a repulsive force induced between the adjacent bilayer membranes causes rearrangement of the constituent lipid molecules in a liposome followed by an increase in the distance r, a decrease in the internal lamellar number, a smaller increase in liposome size and finally a significant increase in Vcap.