Effect of double bond position on lipid bilayer properties: insight through atomistic simulations

Phosphatidylcholines (PCs) are among the most common phospholipids in plasma membranes. Their structural and dynamic properties are known to be strongly affected by unsaturation of lipid hydrocarbon chains, yet the role of the exact positions of the double bonds is poorly understood. In this work, we shed light on this matter through atomic-scale molecular dynamics simulations of eight different one-component lipid bilayers comprised of PCs with 18 carbons in their acyl chains. By introducing a single double bond in each acyl chain and varying its position in a systematic manner, we elucidate the effects of a double bond on various membrane properties. Studies in the fluid phase show that a number of membrane properties depend on the double bond position. In particular, when the double bond in an acyl chain is located close to the membrane-water interface, the area per lipid is considerably larger than that found for a saturated lipid. Further, when the double bond is shifted from the interfacial region toward membrane center, the area per lipid is observed to increase and have a maximum when the double bond is in the middle of the chain. Beyond this point, the surface area decreases systematically as the double bond approaches membrane center. These changes in area per lipid are accompanied by corresponding changes in membrane thickness and ordering of the chains. Further changes are observed in the tilt angles of the chains, membrane hydration together with changes in the number of gauche conformations, and direct head group interactions. All of these effects can be associated with changes in acyl chain conformations and local effects of the double bond on the packing of the surrounding atoms.     

Correction of apparent finite size effects in the area per lipid of lipid membranes simulations

Molecular dynamics simulations of lipids bilayers have reported that the average area per lipid increases with the size of the simulated unit cell under constant temperature, pressure, and number of molecules. Here we show that the cause of this finite size effect are artifacts associated with the heat bath coupling. This can be corrected by coupling individually each degree of freedom to the heat bath, instead of coupling globally the system. We present the results of the investigation on three aspects of molecular dynamics simulations and their effect on the computed average area per lipid: (I) the accuracy in the computation of electrostatic interactions, the energy, and the virial, (II) long range Lennard-Jones interactions for systems with symmetry in one plane, and (III) thermodynamic baths. We show that the average area per lipid remains constant for simulations of systems containing 32, 64, and 256 lipids.     

Equilibrium distributions of dipalmitoyl phosphatidylcholine and dilauroyl phosphatidylcholine in a mixed lipid bilayer: atomistic semigrand canonical ensemble simulations

Conventional molecular dynamics (MD) simulations are seriously limited by the slow rate of diffusive mixing in their ability to predict lateral distributions of different lipid types within mixed-lipid bilayers using atomistic models. A method to overcome this limitation, using configuration-bias Monte Carlo (MC) "mutation" moves to transform lipids from one type to another in dynamic equilibrium, is demonstrated in binary fluid-phase mixtures of lipids whose tails differ in length by four carbons. The hybrid MC-MD method operates within a semigrand canonical ensemble, so that an equilibrium composition of the mixture is determined by a constant difference in chemical potential (Delta(mu)) chosen for the components. Within several nanoseconds, bilayer structures initiated as pure dipalmitoyl phosphatidylcholine (DPPC) or pure dilauroyl phosphatidylcholine (DLPC) converge to a common composition and structure in independent simulations conducted at the same Delta(mu). Trends in bilayer thickness, area per lipid, density distributions across the bilayer, and order parameters have been investigated at three mixture compositions and compared with results from the pure bilayers at 323 K. The mixtures showed a moderate increase in DPPC acyl tail sites crossing the bilayer midplane relative to pure DPPC. Correlations between lateral positions of the two lipid types within or across the bilayer were found to be weak or absent. While the lateral distribution is consistent with nearly ideal mixing, the dependence of composition on Delta(mu) indicates a positive excess free energy of mixing.     

Folding and self-association of atTic20 in lipid membranes: implications for understanding protein transport across the inner envelope membrane of chloroplasts

Background

We have previously shown that the P. gingivalis HmuY hemophore-like protein binds heme and scavenges heme from host hemoproteins to further deliver it to the cognate heme receptor HmuR. The aim of this study was to characterize structural features of HmuY variants in the presence and absence of heme with respect to roles of tryptophan residues in conformational stability.

Results

HmuY possesses tryptophan residues at positions 51 and 73, which are conserved in HmuY homologs present in a variety of bacteria, and a tryptophan residue at position 161, which has been found only in HmuY identified in P. gingivalis strains. We expressed and purified the wildtype HmuY and its protein variants with single tryptophan residues replaced by alanine or tyrosine residues. All HmuY variants were subjected to thermal denaturation and fluorescence spectroscopy analyses. Replacement of the most buried W161 only moderately affects protein stability. The most profound effect of the lack of a large hydrophobic side chain in respect to thermal stability is observed for W73. Also replacement of the W51 exposed on the surface results in the greatest loss of protein stability and even the large aromatic side chain of a tyrosine residue has little potential to substitute this tryptophan residue. Heme binding leads to different exposure of the tryptophan residue at position 51 to the surface of the protein. Differences in structural stability of HmuY variants suggest the change of the tertiary structure of the protein upon heme binding.

Conclusions

Here we demonstrate differential roles of tryptophan residues in the protein conformational stability. We also propose different conformations of apo- and holoHmuY caused by tertiary changes which allow heme binding to the protein.     

Effect of phloretin on the dipole potential of phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol monolayers

The effect of phloretin on the potential of phosphatidylcholine (PC), phosphatidylethanolamine (PE,) and phosphatidylglycerol (PG) monolayers below and above the phase transition in mixtures of different PC/PE ratios with and without cholesterol of ester and ether phospholipids have been determined. The effectiveness of phloretin to decrease the dipole potential of monolayers in the fluid state is lessened by the moieties esterified to the phosphate group in the sequence choline > ethanolamine > glycerol. These effects on the dipole potential of monolayers are independent of the presence of carbonyls. In addition, in the gel state phloretin does not affect the dipole potential on dimyristoylphosphatidylethanolamine, although it is very pronounced in dimyristoylphosphatidylcholine. The changes of the dipole potential induced by phloretin were correlated with the packing of the lipids and with the formation of intermolecular hydrogen bonds between adjacent phospholipid molecules. These results may be indicative of the different distribution of polarized water around the phosphate groups imposed by the surrounding environment.     

Effect of NaCl and KCl doping on the growth of sulphamic acid crystals

The nonlinear optical single crystals of doped sulphamic acid (SA) were grown from aqueous solution by doping with NaCl and KCl using slow evaporation method. Powder X-ray diffraction studies confirm that the grown crystals belong to orthorhombic system. The density and melting point measurements of the grown crystals were determined by floatation technique and capillary tube method, respectively. The range of optical transmittance was ascertained by recording the UV–Vis–NIR spectrum. Atomic absorption study reveals the presence of dopants in the doped crystals. The thermal analyses indicated that the doped SA crystals are more stable than pure crystals. The Vicker's microhardness studies revealed that the dopants increased the hardness of the crystals. SHG efficiency studies of the crystals are found to be increased in the presence of NaCl and KCl dopants.     

Electrochemical characterization of an asymmetric nanofiltration membrane with NaCl and KCl solutions: influence of membrane asymmetry on transport parameters

Electrochemical characterization of a nanofiltration asymmetric membrane was carried out by measuring membrane potential, salt diffusion, and electrical parameters (membrane electrical resistance and capacitance) with the membrane in contact with NaCl and KCl solutions at different concentrations (10(-3)< or =c(M)< or =5 x 10(-2)). From these experiments characteristic parameters such as the effective concentration of charge in the membrane, ionic transport numbers, and salt and ionic permeabilities across the membrane were determined. Membrane electrical resistance and capacitance were obtained from impedance spectroscopy (IS) measurements by using equivalent circuits as models. This technique allows the determination of the electrical contribution associated with each sublayer; then, assuming that the dense sublayer behaves as a plane capacitor, its thickness can be estimated from the capacitance value. The influence of membrane asymmetry on transport parameters have been studied by carrying out measurements for the two opposite external conditions. Results show that membrane asymmetry strongly affects membrane potential, which is attributed to the Donnan exclusion when the solutions in contact with the dense layer have concentrations lower than the membrane fixed charge (X(ef) approximately -0.004 M), but for the reversal experimental condition (high concentration in contact with the membrane dense sublayer) the membrane potential is practically similar to the solution diffusion potential. The comparison of results obtained for both electrolytes agrees with the higher conductivity of KCl solutions. On the other hand, the influence of diffusion layers at the membrane/solution interfaces in salt permeation was also studied by measuring salt diffusion at a given NaCl concentration gradient but at five different solutions stirring rates.     

Effect of acetone accumulation on structure and dynamics of lipid membranes studied by molecular dynamics simulations

The modulation of the properties and function of cell membranes by small volatile substances is important for many biomedical applications. Despite available experimental results, molecular mechanisms of action of inhalants and organic solvents, such as acetone, on lipid membranes remain not well understood. To gain a better understanding of how acetone interacts with membranes, we have performed a series of molecular dynamics (MD) simulations of a POPC bilayer in aqueous solution in the presence of acetone, whose concentration was varied from 2.8 to 11.2 mol%. The MD simulations of passive distribution of acetone between a bulk water phase and a lipid bilayer show that acetone favors partitioning into the water-free region of the bilayer, located near the carbonyl groups of the phospholipids and at the beginning of the hydrocarbon core of the lipid membrane. Using MD umbrella sampling, we found that the permeability barrier of ∼0.5 kcal/mol exists for acetone partitioning into the membrane. In addition, a Gibbs free energy profile of the acetone penetration across a bilayer demonstrates a favorable potential energy well of −3.6 kcal/mol, located at 15–16 Å from the bilayer center. The analysis of the structural and dynamics properties of the model membrane revealed that the POPC bilayer can tolerate the presence of acetone in the concentration range of 2.8–5.6 mol%. The accumulation of the higher acetone concentration of 11.2 mol% results, however, in drastic disordering of phospholipid packing and the increase in the membrane fluidity. The acetone molecules push the lipid heads apart and, hence, act as spacers in the headgroup region. This effect leads to the increase in the average headgroup area per molecule. In addition, the acyl tail region of the membrane also becomes less dense. We suggest, therefore, that the molecular mechanism of acetone action on the phospholipid bilayer has many common features with the effects of short chain alcohols, DMSO, and chloroform.     

Lipid-protein interactions in membranes: effect of lipid composition on mobility of spin-labeled cysteine residues in yeast plasma membrane.

In order to gain direct evidence for lipid-dependent protein conformation in membrane, effects of modification of lipid composition on mobility of spin-labeled cysteine residues were investigated in the plasma membrane of the yeast Saccharomyces cerevisiae. Conversion of the bulk of phospholipids to diglycerides by treatment of the membrane with phospholipase C substantially enhanced spectral anisotropy. However, alterations of the viscosity of the lipid-bilayer by enriching the membrane with palmitelaidic or oleic acid had no effect on mobility of spin-labeled cysteine residues. These observations indicate that while the spin-labeled residues are not in direct contact with the lipid core of the membrane, there are lipid-protein interactions to the extent that removal of the polar portion of the bulk of phospholipids induces conformational changes in proteins, which in turn restrict mobility of these residues. It is concluded that conformation of membrane proteins on lipid structure and that phospholipids have a role in preserving the native conformation of proteins.     

Molecular dynamics simulations of ternary membrane mixture: phosphatidylcholine, phosphatidic acid, and cholesterol

A ternary mixture of 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC), 1-palmitoyl-2-oleoyl phosphatidic acid (POPA), and cholesterol (CHOL) works effectively for a functional conformation of nicotinic acetylcholine receptor (nAChR) that can undergo agonist-induced conformation changes, but POPC alone can stabilize only a desensitized state of nAChR. To gain insights into the lipid mixture that has strong impact to nAChR functions, we performed more than 50 ns all atom molecular dynamic (MD) simulations at 303 K on a fully hydrated bilayer consisting of 240 POPC, 80 POPA, and 80 CHOL (3:1:1). The MD simulation revealed various interactions between different types of molecular pairs that ultimately regulated lipid organization. The heterogeneous interactions among three different constituents resulted in a broad spectrum of lipid properties, including extensive distributions of average area per lipid and varied lipid ordering as a function of lipid closeness to CHOL. Higher percentage of POPA than POPC had close association with CHOL, which coincided with relatively higher ordering of POPA molecules in their acyl chains near lipid head groups. Lower fraction of gauche dihedrals was also found in the same region of POPA. Although the CHOL molecules had the effects on the enhancement of surrounding lipid order, relatively low lipid order parameters and high fraction of gauche bonds were observed in the ternary mixture. Collectively, these results suggest that the dynamical structure of the ternary system could be determinant for a functional nAChR.     

From simple surface models to lipid membranes: Universal aspects of the hydration interaction from solvent-explicit simulations

A review of atomistic simulation approaches including explicit water for the study of hydration forces between polar surfaces is presented. In particular, we discuss different methods for keeping the chemical potential of water constant and compare advantages and limitations of each method. It turns out that modifications of hydration forces due to surface softness can be accounted for by a convolution over the surface shape profile. Universal aspects of the hydration interaction observed in simulations of different surface chemistries are highlighted, while special attention is given to hydration forces between self-assembled phospholipid membranes.     

Effects of block copolymer's architecture on its association with lipid membranes: experiments and simulations

Triblock copolymers of the form poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) have been shown to effectively interact with and restore activity of damaged cell membranes. To better understand the interaction between these polymers and cell membranes, we have modeled the outer leaflet of a cell membrane with a lipid monolayer spread at the air-water interface and injected poloxamers of varying architectures into the subphase beneath the monolayer. Subsequent interactions of the polymer with the monolayer upon compression were monitored with concurrent Langmuir isotherm and fluorescence microscopy measurements. Monte Carlo simulations were run in parallel using a coarse-grained model to capture interactions between lipids and poloxamers. Changing the ratio of the PEO to PPO block lengths (NPEO:NPPO) affects the equilibrium spreading pressure of the polymer. Poloxamers with a relatively longer central hydrophobic block are less soluble, resulting in more polymer adsorbed to the interface and therefore a higher equilibrium spreading pressure. Simulation results show that changing the poloxamer structure effectively affects its solubility. This is also reflected in the degree of lipid corralling as poloxamers with a higher chemical potential (and resulting higher equilibrium spreading pressure) cause the neighboring lipid domains to be more ordered. Upon lateral compression of the monolayers, the polymer is expelled from the film beyond a certain squeeze-out pressure. A poloxamer with a higher NPEO:NPPO ratio (with either NPEO or NPPO held constant in each series) has a lower squeeze-out pressure. Likewise when the total size of the polymer is varied with a constant hydrophilic:hydrophobic ratio, smaller poloxamers are squeezed out at a lower pressure. Our simulation results capture the trends of our experimental observations, both indicating how the interactions between lipids and poloxamers can be tuned by the polymer architecture.     

Recognition of multiblock copolymers on nanopatterned surfaces: insight from molecular simulations

The recognition of multiblock copolymers on nanopatterned surfaces has been investigated by molecular simulations. All the copolymers (AnB12-n)5 are composed of 60 square-well segments, but with various architectures by changing n. Segment density profiles, radii of gyration, pattern transfer parameters, and three adsorption conformations (tail, loop, and train) are examined quantitatively. It is found that the copolymer can recognize the adsorbing stripes on surface and the surface vicinity. The recognition affinity becomes stronger with increasing the stripe width, the adsorption strength, and the number of adsorbing segments in copolymer chain. From surface to bulk phase, the shape of copolymer changes from elongated to elliptical, and finally to globular. Among the three adsorption conformations, tail has the greatest average size while train has the smallest. With the increased number of nonadsorbing segments, the average size shows an increase in tail but a decrease in train.     

Adamantyl ferrocene derivatives: Antioxidant abilities and effects on model lipid membranes

A series of homoannularly and heteroannularly substituted adamantyl ferrocene derivatives has been synthesized and their effects on membrane fluidity were investigated using liposomes as the membrane models. The liposome formulations of adamantyl ferrocene derivatives were characterized by using dynamic light scattering, differential scanning calorimetry and fluorescence anisotropy measurements. It was demonstrated that adamantyl ferrocene derivatives incorporated into the liposome significantly affect the structure of the lipid bilayer. The results of the study have revealed that adamantyl ferrocene derivatives, compounds 9 – 12, partition into the hydrophobic/hydrophilic interface of the membrane, causing a significant decrease in membrane fluidity. The antioxidant potential of synthesized compounds was assessed with DPPH method and it was shown that the examined compounds possess certain antioxidant activity.     

Glycolipid membranes through atomistic simulations: effect of glucose and galactose head groups on lipid bilayer properties

Though glycolipids are involved in a multitude of cellular functions, the understanding of their atom-scale properties in lipid membranes has remained very limited due to the lack of atomistic simulations. In this work, we employ extensive simulations to characterize one-component membranes comprised of glycoglycerolipids, focusing on two common glyco head groups, namely glucose and galactose. The properties of these two glycoglycerolipid bilayers are compared in a systematic manner with membranes consisting of phosphatidylcholine (PC) or phosphatidylethanolamine (PE) lipids, whose structures aside from the head group are identical with those of the two glycolipids. We find that the glycolipid systems are characterized by a substantial number of hydrogen bonds in the head group region, leading to membrane packing that is stronger than in a PC but less significant than that in a PE bilayer. The role played by the glyco head group is especially evident in the electrostatic membrane potential, which is particularly large in the glycolipid membranes. For the same reason, the interfacial forces near glycolipid bilayers are significantly different from those found in PC and PE bilayers, affecting, e.g., the ordering of water close to the membrane. These effects are particularly important for the case of galactose, an important component in thylacoids.     

Monomeric fullerenes in lipid membranes: effects of molecular shape and polarity

We report a combined theoretical and experimental study on the single-molecule interaction of fullerenes with phospholipid membranes. We studied pristine C(60) (1) and two N-substituted fulleropyrrolidines (2 and 3), one of which (3) bore a paramagnetic nitroxide group. Theoretical predictions of fullerene distribution and permeability across lipid bilayers were combined with electron paramagnetic resonance (EPR) experiments in aligned DMPC/DHPC bicelles containing the paramagnetic fulleropyrrolidine 3 or either one of the diamagnetic fullerenes together with spin-labeled lipids. We found that, at low concentrations, fullerenes are present in the bilayer as single molecules. Their preferred location in the membrane is only slightly influenced by the derivatization: all derivatives were confined just below the hydrophilic/hydrophobic interface, because of the key role played by dispersion interactions between the highly polarizable fullerene cage and the hydrocarbon chains, which are especially tight within this region. However, the deviation from spherical shape is sufficient to induce a preferential orientation of 2 and 3 in the membrane. We predict that monomeric fullerenes spontaneously penetrate the bilayer, in agreement with the results of molecular dynamics simulations, but we point out the limits of the currently used permeability model when applied to hydrophobic solutes.     

484—Photosensitive lipid membranes: Part II. The collodion-oleic acid,methylene blue sensitized membrane in aerated KCl solutions. Evidence for the intervention of singlet oxygen in the photoreaction mechanism

The photoresponse of lipid membranes of oleic acid, sensitized with methylene blue and immobilized by collodion, was examined in acrated, aqueous KCl solutions. Deposited on suitable metal electrodes, these membranes can reach considerable photovoltages, of the order of ?360 mV, depending mainly on the electrolyte concentration, the highest values being obtained with concentrated (2M) KCl solutions.In the presence of a typical singlet oxygen quencher, such as N₃Na, the photoresponse is diminished in a quantitative manner, whereas the presence of D₂O, as singlet oxygen lifetime promoter, increases the photoresponse in KCl 1 × 10^?1M solutions. Thus, the intervention of singlet oxygen in the photoreaction mechanism is indirectly proved.