Molecular dynamics simulations of cardiolipin bilayers

Cardiolipin is a key lipid component in the inner mitochondrial membrane, where the lipid is involved in energy production, cristae structure, and mechanisms in the apoptotic pathway. In this article we used molecular dynamics computer simulations to investigate cardiolipin and its effect on the structure of lipid bilayers. Three cardiolipin/POPC bilayers with different lipid compositions were simulated: 100, 9.2, and 0% cardiolipin. We found strong association of sodium counterions to the carbonyl groups of both lipid types, leaving in the case of 9.2% cardiolipin virtually no ions in the aqueous compartment. Although binding occurred primarily at the carbonyl position, there was a preference to bind to the carbonyl groups of cardiolipin. Ion binding and the small headgroup of cardiolipin gave a strong ordering of the hydrocarbon chains. We found significant effects in the water dipole orientation and water dipole potential which can compensate for the electrostatic repulsion that otherwise should force charged lipids apart. Several parameters relevant for the molecular structure of cardiolipin were calculated and compared with results from analyses of coarse-grained simulations and available X-ray structural data.     

Capillary electrophoresis of cardiolipin with on-line dye interaction and spectrophotometric detection

Cardiolipin is an important phospholipid present in the mitochondrial inner membrane. It plays a key function in mitochondrial respiration by interacting with many enzymes or cofactors related to oxidative phosphorylation complexes. We have determined the concentration of cardiolipin using on-line 10-N-nonyl acridine orange (NAO) dye interaction capillary electrophoresis (CE) and spectrophotometric detection with a sample throughput of 3 min. In addition to the presence of 0.1 mM NAO, the background electrolyte (BGE) composition has been set at 80% methanol-10% acetonitrile-10% H(2)O (all v/v) to provide both good solubility and the maximum absorbance enhancement at 497 nm for the NAO-cardiolipin complex as compared to NAO alone. Sample consumption for each injection is about 57 nL. A calibration curve is established from 0.5 microM to 0.1 mM with R (2) = 0.9912 with a detection limit of 0.05 microM for cardiolipin. In a blind study, actual mitochondrial cell membrane samples in the microL range before or after UV light exposure were analyzed using the CE method. Cardiolipin concentration decreased in the different parts of the membrane sample upon UV photolysis of the cells. Support for the theory that UV light can induce cardiolipin translocation from the inner membrane (IM) to the outer membrane (OM) was indicated by a significant percentage increase of cardiolipin (as measured by the cardiolipin in the OM as compared to the sum total in the OM and IM) from 30.7 +/- 2.4% before UV light photolysis to 38.3 +/- 2.2% after UV irradiation.     

Data-driven discovery of cardiolipin-selective small molecules by computational active learning

Subtle variations in the lipid composition of mitochondrial membranes can have a profound impact on mitochondrial function. The inner mitochondrial membrane contains the phospholipid cardiolipin, which has been demonstrated to act as a biomarker for a number of diverse pathologies. Small molecule dyes capable of selectively partitioning into cardiolipin membranes enable visualization and quantification of the cardiolipin content. Here we present a data-driven approach that combines a deep learning-enabled active learning workflow with coarse-grained molecular dynamics simulations and alchemical free energy calculations to discover small organic compounds able to selectively permeate cardiolipin-containing membranes. By employing transferable coarse-grained models we efficiently navigate the all-atom design space corresponding to small organic molecules with molecular weight less than ≈500 Da. After direct simulation of only 0.42% of our coarse-grained search space we identify molecules with considerably increased levels of cardiolipin selectivity compared to a widely used cardiolipin probe 10-N-nonyl acridine orange. Our accumulated simulation data enables us to derive interpretable design rules linking coarse-grained structure to cardiolipin selectivity. The findings are corroborated by fluorescence anisotropy measurements of two compounds conforming to our defined design rules. Our findings highlight the potential of coarse-grained representations and multiscale modelling for materials discovery and design.

We present a data-driven approach combining deep learning-enabled active learning with coarse-grained simulations and alchemical free energy calculations to discover small molecules to selectively permeate cardiolipin membranes.     

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.     

电解质浓度改变对心磷脂囊管结构稳定性的影响

心磷脂是构成线粒体内膜的特殊磷脂组分, 是线粒体内膜不同功能态下的拓扑结构变化的主要参与者. 本实验通过溶剂自然蒸发与微操注射两种途径, 原位研究了溶液中电解质浓度改变程度对心磷脂构成的囊管结构稳定性的影响, 以期对线粒体功能状态的变化机理有进一步的认识. 实验发现, 即使没有蛋白质对膜曲率的调制作用, 单纯由溶液浓度改变造成的刺激也可以引起心磷脂膜组装形态的改变. 皱缩的发生与膜表面的电势变化有关, 是可受浓度调控的可逆过程.     

Visualizing the solubilization of supported lipid bilayers by an amphiphilic peptide

The effect of the presequence peptide of cytochrome c oxidase subunit IV (p25) on supported phospholipid bilayers (SPBs) was visualized using atomic force microscopy (AFM). The presequence was found to cause the complete disruption of supported bilayers containing neutral lipids. At relatively low concentrations of presequence, the peptide was found to bind to the membrane, coalescing to form microdomains within the liquid-crystalline bilayer that were located predominantly at bilayer-mica boundaries. Further increases in peptide concentration resulted in the formation of holes within the SPB that were spanned by an interpenetrating network of narrower regions of the bilayer, which, at higher applied peptide concentrations, were observed to disappear through a budding process, ultimately leading to the formation of spherical structures at yet higher peptide concentrations. Within this paper, the impact the presequence has upon the structure and order of the membrane is discussed, as is the potential implication of this apparent solubilization process on the translocation of cytochrome c oxidase into the inner mitochondrial membrane.     

Determining the Zeta Potential of Porous Membranes Using Electrolyte Conductivity inside Pores

The zeta potential is an important and reliable indicator of the surface charge of membranes, and knowledge of it is essential for the design and operation of membrane processes. The zeta potential cannot be measured directly, but must be deduced from experiments by means of a model. The possibility of determining the zeta potential of porous membranes from measurements of the electrolyte conductivity inside pores (lambda(pore)) is investigated in the case of a ceramic microfiltration membrane. To this end, experimental measurements of the electrical resistance in pores are performed with the membrane filled with KCl solutions of various pHs and concentrations. lambda(pore) is deduced from these experiments. The farther the pH is from the isoelectric point and/or the lower the salt concentration is, the higher the ratio of the electrolyte conductivity inside pores to the bulk conductivity is, due to a more important contribution of the surface conduction. Zeta potentials are calculated from lambda(pore) values by means of a space charge model and compared to those calculated from streaming potential measurements. It is found that the isoelectric points are very close and that zeta potential values for both methods are in quite good agreement. The differences observed in zeta potentials could be due to the fact that the space charge model does not consider the surface conductivity in the inner part of the double layer. Measurements of the electrolyte conductivity within the membrane pores are proved to be a well-adapted procedure for the determination of the zeta potential in situations where the contribution of the surface conduction is significant, i.e., for small and charged pores. Copyright 2001 Academic Press.     

Bilayer-coated capsule membranes. IV. : Control of NaCl permeability by phase transition of synthetic bilayer coatings,depending on their hydrophilic head groups

Ultrathin nylon capsule membranes coated with synthetic bilayers, the hydrophilic head groups of which had cationic, anionic, zwitterionic and nonionic charges, were prepared. Permeation of NaCl trapped in the inner aqueous phase was reduced by a factor of 10-1000 relative to that of the uncoated, semipermeable capsules, and drastically changed at the phase transition temperature, T_c, of the coating bilayers, depending on the charge of their hydrophilic head group. In the case of capsules coated with positively or negatively charged bilayers, NaCl permeation was enhanced at temperatures above the T_c of the coating bilayers, as expected. On the other hand, NaCl release of capsules coated with neutral charged (nonionic and zwitterionic) bilayers was largely reduced at temperatures above the T_c. From activation energy data of Arrhenius plots, the permeation mechanism of NaCl, depending on the membrane surface charge, below and above the T_c was discussed.     

Impact of cholesterol on voids in phospholipid membranes

Free volume pockets or voids are important to many biological processes in cell membranes. Free volume fluctuations are a prerequisite for diffusion of lipids and other macromolecules in lipid bilayers. Permeation of small solutes across a membrane, as well as diffusion of solutes in the membrane interior are further examples of phenomena where voids and their properties play a central role. Cholesterol has been suggested to change the structure and function of membranes by altering their free volume properties. We study the effect of cholesterol on the properties of voids in dipalmitoylphosphatidylcholine (DPPC) bilayers by means of atomistic molecular dynamics simulations. We find that an increasing cholesterol concentration reduces the total amount of free volume in a bilayer. The effect of cholesterol on individual voids is most prominent in the region where the steroid ring structures of cholesterol molecules are located. Here a growing cholesterol content reduces the number of voids, completely removing voids of the size of a cholesterol molecule. The voids also become more elongated. The broad orientational distribution of voids observed in pure DPPC is, with a 30% molar concentration of cholesterol, replaced by a distribution where orientation along the bilayer normal is favored. Our results suggest that instead of being uniformly distributed to the whole bilayer, these effects are localized to the close vicinity of cholesterol molecules.     

DHA-induced changes of supported lipid membrane morphology

Docosahexaenoic acid (DHA) is a polyunsaturated long fatty acid known to have fundamental effects on cell membrane function. Here, the effect of DHA on phosphocholine-supported lipid bilayers was measured using the quartz crystal microbalance with dissipation monitoring (QCM-D) technique. Above a concentration of 60 muM (i.e., near the critical micelle concentration), DHA had drastic effects on the viscoelastic properties of the supported membranes, suggesting a more complex process and structure than simple insertion of molecules in the bilayer. Fluorescence microscopy revealed the spontaneous formation of elongated out-growths from the bilayers, which were remarkable for their length ( approximately 100 mum) and extensive coverage of the surface. These results demonstrate the applicability of QCM-D as a method to screen for conditions where membrane remodeling occurs but also that complementary techniques are required to describe in more detail the changes in viscoelastic properties of the membrane. These results are highly relevant for the present rapid development in the field of model lipid membranes aiming toward increased knowledge about processes occurring at biological surfaces.     

Effect of NaCl and KCl on phosphatidylcholine and phosphatidylethanolamine lipid membranes: insight from atomic-scale simulations for understanding salt-induced effects in the plasma membrane

To gain a better understanding of how monovalent salt under physiological conditions affects plasma membranes, we have performed 200 ns atomic-scale molecular dynamics simulations of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipid bilayers. These two systems provide representative models for the outer and inner leaflets of the plasma membrane, respectively. The implications of cation-lipid interactions in these lipid systems have been considered in two different aqueous salt solutions, namely NaCl and KCl, and the sensitivity of the results on the details of interactions used for ions is determined by repeating the simulations with two distinctly different force fields. We demonstrate that the main effect of monovalent salt on a phospholipid membrane is determined by cations binding to the carbonyl region of a membrane, while chloride anions mostly stay in the water phase. It turns out that the strength and character of the cation-lipid interactions are quite different for different types of lipids and cations. PC membranes and Na+ ions demonstrate strongest interactions, leading to notable membrane compression. This finding was confirmed by both force fields (Gromacs and Charmm) employed for the ions. The binding of potassium ions to PC membranes (and the overall effect of KCl), in turn, was found to be much weaker mainly due to the larger size of a K+ ion compared to Na+. Furthermore, the effect of KCl on PC membranes was found to be force-field sensitive: The binding of a potassium ion was not observed at all in simulations performed with the Gromacs force-field, which seems to exaggerate the size of a K+ ion. As far as PE lipid bilayers are concerned, they are found to be influenced by monovalent salt to a significantly lesser extent compared to PC bilayers, which is a direct consequence of the ability of PE lipids to form both intra- and intermolecular hydrogen bonds and hence to adopt a more densely packed bilayer structure. Whereas for NaCl we observed weak binding of Na+ cations to the PE lipid-water interface, in the case of KCl we witnessed almost complete lack of cation binding. Overall, our findings indicate that monovalent salt ions affect lipids in the inner and outer leaflets of plasma cell membranes in substantially different ways.     

PHOTOSENSITIVE BILAYER MEMBRANES AS MODEL SYSTEMS FOR PHOTOBIOLOGICAL PROCESSES

Abstract— Photobiological processes such as photosynthesis, photomorphogenesis, photomovement, and photoreception are all associated with the membranous portions of cells. The unique properties of membrane surfaces are apparently required to achieve biologically relevant energy transduction and photocontrol phenomena and consequently the use of model membrane systems is suggested as an advantageous approach to elucidation of the important physical and chemical processes involved. Black lipid membrane (BLM) and liposome techniques are critically reviewed as preferred techniques for constructing and manipulating lipid bilayers. The lipid bilayer is considered to be the basic foundation for biological membrane models, and specific physical phenomena observed with the bilayers and their biological ramifications are analyzed. Light-stimulated polarization of the membrane and electron transfer across the bilayer are viewed as appropriate analogs of vision and photosynthesis, respectively. Bilayer-adsorbed dye experiments are the simplest systems explored that exhibit polarization and charge transfer across the membrane. Chloroplast extract BLM experiments are cited as an example of the light-stimulated transfer of electrons across the membrane under the influence of a preexisting redox gradient. Biliprotein (phycocyanin or phycoerythrin) on one side of the chloroplast extract membrane permits the direction of electron flow across the membrane so that a redox gradient is created in a manner truly analogous to photosynthesis. The potential for solar energy conversion from such membranes is explicitly considered utilizing a schematic photoelectrochemical cell. Model membranes containing bacterial rhodopsin and phytochrome represent examples of ionic gradients that result in biological energy transduction. Studies of membranes that exhibit transient photoeffects are considered potentially relevant for the elucidation of phototaxis. The analysis of many properties of photosensitive membranes is greatly aided by the use of appropriate theoretical models. It is apparent that there is a great potential for the application of photosensitive model membranes in many research areas involving complex photobiological phenomena and novel methods for solar energy conversion.     

Phospholipid Bilayers as Molecular Models for Drug-Cell Membrana Interactions. The Case of the Antiinflamatory Drug Diclofenac

Phospholipids are amphipatic molecules with long hydrophobic acyl chains and zwitterionic polar heads which assemble into different types of molecular aggregates. The most relevant is the bilayer because of its relation with cell membranes, which are very complex entities. For this reason, simpler molecular models based on phospholipids bilayers are widely used. We have determined the bilayer structure of phospholipids located in the outer and inner monolayers of most cell membranes, and use them as molecular models to study the way different chemicals of biological interest interact with cell membranes. We present the results of our studies on the nonsteroidal anti-inflammatory drug diclofenac, from which little is known about its effects on human erythrocytes. This report presents the following evidence that diclofenac interacts with the human red cell membrane: a) X-ray diffraction and fluorescence spectroscopy of phospholipids bilayers show that diclofenac interacts with a class of lipids found in the outer moiety of the erythrocyte membrane; b) in isolated unsealed human erythrocyte membranes the drug induced a disordering effect on the acyl chains of the membrane lipid bilayer; c) in scanning electron microscopy studies on human erythrocytes it was observed that the drug induced morphological changes different from their normal biconcave shape.     

Role of lipid charge in organization of water/lipid bilayer interface: insights via computer simulations

Anionic unsaturated lipid bilayers represent suitable model systems that mimic real cell membranes: they are fluid and possess a negative surface charge. Understanding of detailed molecular organization of water-lipid interfaces in such systems may provide an important insight into the mechanisms of proteins' binding to membranes. Molecular dynamics (MD) of full-atom hydrated lipid bilayers is one of the most powerful tools to address this problem in silico. Unfortunately, wide application of computational methods for such systems is limited by serious technical problems. They are mainly related to correct treatment of long-range electrostatic effects. In this study a physically reliable model of an anionic unsaturated bilayer of 1,2-dioleoyl-sn-glycero-3-phosphoserine (DOPS) was elaborated and subjected to long-term MD simulations. Electrostatic interactions were treated with two different algorithms: spherical cutoff function and particle-mesh Ewald summation (PME). To understand the role of lipid charge in the system behavior, similar calculations were also carried out for zwitterionic bilayer composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). It was shown that, for the charged DOPS bilayer, the PME protocol performs much better than the cutoff scheme. In the last case a number of artifacts in the structural organization of the bilayer were observed. All of them were attributed to inadequate treatment of electrostatic interactions of lipid headgroups with counterions. Electrostatic properties, along with structural and dynamic parameters, of both lipid bilayers were investigated. Comparative analysis of the MD data reveals that the water-lipid interface of the DOPC bilayer is looser than that for DOPS. This makes possible deeper penetration of water molecules inside the zwitterionic (DOPC) bilayer, where they strongly interact with carbonyls of lipids. This can lead to thickening of the membrane interface in zwitterionic as compared to negatively charged bilayers.     

Comparison of N-alkyl acridine orange dyes as fluorescence probes for the determination of cardiolipin

The phospholipid (PL), cardiolipin (CL), is found almost exclusively in the inner membrane of mitochondria and loss of CL is considered as an important indication of cell apoptosis. Previously, 10-N-nonyl acridine orange (NAO) has been used as a fluorescent probe for the visualization of CL in mitochondrial cell membranes and in solution. In this work for the determination of CL, we have synthesized two new fluorescent probes, n-tetradecyl acridine orange (C14-AO), and n-octadecyl acridine orange (C18-AO) by reacting acridine orange with the corresponding n-alkyl bromide. Using excitation and emission wavelengths at about 500 and 525 nm and varying the percentage of methanol in water as the solvent, no interaction between CL and the fluorescent probes at 75% is noted but a proportional quenching of the fluorescence signal by CL is observed at 50% or less for C14-AO and 60% or less for C18-AO. Binding efficiency of these fluorescent probes to CL is compared using dye concentrations of 5, 10, and 20 μM. C18-AO shows a better sensitivity than C14-AO and NAO, respectively, but is less selective. For C14-AO, the detection limit and limit of quantitation are 0.07 and 0.21 μM, respectively, which are better than those previously reported for NAO. One anionic PL, phosphatidic acid, shows some quenching interference to both the C14 and C18 dyes but only at concentrations above the working range for sample analysis. The CL in mitochondrial membrane samples is determined by standard addition using C14-AO. The level of CL in the outer mitochondrial membrane compared to the inner membrane is significantly increased due to the addition of cadmium chloride into the cells causing cell apoptosis.     

The Effect of Bacterial Signal Indole on the Electrical Properties of Lipid Membranes

Indole is an important biological signalling molecule produced by many Gram positive and Gram negative bacterial species, including Escherichia coli. Here we study the effect of indole on the electrical properties of lipid membranes. Using electrophysiology, we show that two indole molecules act cooperatively to transport charge across the hydrophobic core of the lipid membrane. To enhance charge transport, induced by indole across the lipid membrane, we use an indole derivative, 4 fluoro‐indole. We demonstrate parallels between charge transport through artificial lipid membranes and the function of complex eukaryotic membrane systems by showing that physiological indole concentrations increase the rate of mitochondrial oxygen consumption. Our data provide a biophysical explanation for how indole may link the metabolism of bacterial and eukaryotic cells.     

Phosphate recovery by high flux low pressure multilayer membranes

This work illustrates the potential use of PEI/PSS bilayers assembled via layer by layer (lbl) method on a nylon microfiltration membrane for the recovery of phosphate from water in the presence of chloride under ultrafiltration conditions. A total of nine bilayers were used for the selective recovery of phosphate. Bilayers were constructed from polyelectrolyte solutions of varying ionic strength (0-1 M of NaCl). The selected pH for deposition of PEI (5.9) and the presence of supporting salt in the polyelectrolyte solution is expected to provide membranes with high permeability and high charge density. This particular combination of bilayers yielded high flux membranes that allowed selective removal of H(2)PO(4)(-) in the presence of Cl(-) at low pressure (0.28 bar). The magnitude of negative solute rejection of chloride showed increasing trend with the number of bilayer for a particular salt concentration. Whereas the increase in magnitude with ionic strength is so high (-6.18 to -269.17 at 0.5 M NaCl for 9 bl) that gave the best observed Cl(-)/H(2)PO(4)(-) selectivity (310.23, flux 13.53 m(3)/m(2)-day). To the best of our knowledge, this is the first time a multilayer polyelectrolyte system with such a high selectivity and rejection for H(2)PO(4)(-) is reported. The solution flux decreased with the number of bilayers and ionic strength. The rejection of phosphate was dependent on feed pH, concentration of deposited polyelectrolyte solution, and composition of membrane support.     

Zeta potential of ion-conductive membranes by streaming current measurements

Surface charge properties have a significant influence on membrane retention and fouling performance. As a key parameter describing the surface charge of membranes used in aqueous applications, zeta potential measurements on membranes of various types have attracted great attention. During the zeta potential characterization of a series of ion-conductive sulfonated poly(sulfone) membranes, it was found that the measured streaming current varied with the thickness of the sample, which is not predicted by the classical Smoluchowski equation. Moreover, for higher conductivity membranes with an increased concentration of sulfonate groups, the zeta potential tended toward zero. It was determined that the influence of membrane bulk conductance on the measured streaming current must be taken into account in order to correctly interpret the streaming current data for ion-conductive polymers and understand the relationship between membrane chemical composition and zeta potential. Extrapolating the measured streaming current to a membrane thickness of zero has proven to be a feasible method of eliminating the error associated with measuring the zeta potential on ion conductive polymer membranes. A linear resistance model is proposed to account for the observed streaming currents where the electrolyte channel is in parallel with the ion-conductive membranes.     

Nonintercalating nanosubstrates create asymmetry between bilayer leaflets

The physical properties of lipid bilayers can be remodeled by a variety of environmental factors. Here we investigate using molecular dynamics simulations the specific effects of nanoscopic substrates or external contact points on lipid membranes. We expose palmitoyl-oleoyl phosphatidylcholine bilayers unilaterally and separately to various model nanosized substrates differing in surface hydroxyl densities. We find that a surface hydroxyl density as low as 10% is sufficient to keep the bilayer juxtaposed to the substrate. The bilayer interacts with the substrate indirectly through multiple layers of water molecules; however, despite such buffered interaction, the bilayers exhibit certain properties different from unsupported bilayers. The substrates modify transverse lipid fluctuations, charge density profiles, and lipid diffusion rates, although differently in the two leaflets, which creates an asymmetry between bilayer leaflets. Other properties that include lipid cross-sectional areas, component volumes, and order parameters are minimally affected. The extent of asymmetry that we observe between bilayer leaflets is well beyond what has been reported for bilayers adsorbed on infinite solid supports. This is perhaps because the bilayers are much closer to our nanosized finite supports than to infinite solid supports, resulting in a stronger support-bilayer electrostatic coupling. The exposure of membranes to nanoscopic contact points, therefore, cannot be considered as a simple linear interpolation between unsupported membranes and membranes supported on infinite supports. In the biological context, this suggests that the exposure of membranes to nonintercalating proteins, such as those belonging to the cytoskeleton, should not always be considered as passive nonconsequential interactions.