Thermotropic and Barotropic Phase Behavior of Phosphatidylcholine Bilayers

Bilayers formed by phospholipids are frequently used as model biological membranes in various life science studies. A characteristic feature of phospholipid bilayers is to undergo a structural change called a phase transition in response to environmental changes of their surroundings. In this review, we focus our attention on phase transitions of some major phospholipids contained in biological membranes, phosphatidylcholines (PCs), depending on temperature and pressure. Bilayers of dipalmitoylphosphatidylcholine (DPPC), which is the most representative lipid in model membrane studies, will first be explained. Then, the bilayer phase behavior of various kinds of PCs with different molecular structures is revealed from the temperature–pressure phase diagrams, and the difference in phase stability among these PC bilayers is discussed in connection with the molecular structure of the PC molecules. Furthermore, the solvent effect on the phase behavior is also described briefly.     

Computer simulation studies of model biological membranes

This Account is focused on computer simulation studies of model biological membrane systems with potential applications in biomedical research. In the past decade, classical molecular dynamics has provided novel insights into the properties of model biomembrane systems, including the nature of the DNA-lipid interactions, the effect of pore-forming transmembrane peptides on the lipid environment, and the partitioning of volatile anesthetic molecules. Such simulations, employing full atomic detail, are typically restricted to systems of dimensions less than approximately 10 nm. Simplified models of the coarse-grain type have been intended to bridge the gap between full atomistic detail and the mesoscopic (micron) regime. The use of such models is illustrated with the example of anesthetics in a phospholipid bilayer.     

Molecular Dynamics Simulations of the Elusive Matrix-Open State of Mitochondrial ADP/ATP Carrier

We studied and compared in detail an elusive matrix open (m-state) and cytoplasmic open (c-state) state of ADP/ATP carrier (AAC) protein embedded in the DOPC bilayer by microsecond molecular dynamics (MD) simulations. We analyzed both states with and without cardiolipin (CDL) molecules, with a special emphasis on the recently obtained crystallographic structure of the AAC m-state. The obtained results show that both states of the protein are stable in the DOPC bilayer and impermeable to water. In comparison with the c-state of AAC, the m-state is more dynamic, but at the same time possesses a larger occluded area in the protein cavity. Both states of the protein are less flexible in simulations when CDL molecules are present, which is especially visible for the m-state. Finally, the analysis of the protein conformational changes during MD simulations shows that protein parts at the protein/lipid boundaries are prone to larger conformational changes in contrast to central region of the protein embedded in the bilayer core, thus further supporting the cycling mechanism suggested for ADP/ATP exchange by AAC.     

Preparation of DOPC and DPPC Supported Planar Lipid Bilayers for Atomic Force Microscopy and Atomic Force Spectroscopy

Cell membranes are typically very complex, consisting of a multitude of different lipids and proteins. Supported lipid bilayers are widely used as model systems to study biological membranes. Atomic force microscopy and force spectroscopy techniques are nanoscale methods that are successfully used to study supported lipid bilayers. These methods, especially force spectroscopy, require the reliable preparation of supported lipid bilayers with extended coverage. The unreliability and a lack of a complete understanding of the vesicle fusion process though have held back progress in this promising field. We document here robust protocols for the formation of fluid phase DOPC and gel phase DPPC bilayers on mica. Insights into the most crucial experimental parameters and a comparison between DOPC and DPPC preparation are presented. Finally, we demonstrate force spectroscopy measurements on DOPC surfaces and measure rupture forces and bilayer depths that agree well with X-ray diffraction data. We also believe our approach to decomposing the force-distance curves into depth sub-components provides a more reliable method for characterising the depth of fluid phase lipid bilayers, particularly in comparison with typical image analysis approaches.     

Destabilizing effects of fructose-1,6-bisphosphate on membrane bilayers

Fructose-1,6-bisphosphate (FBP) is a high-energy glycolytic intermediate that decreases the effects of ischemia; it has been used successfully in organ perfusion and preservation. How the cells utilize external FBP to increase energy production and the mechanism by which the molecule crosses the membrane bilayer are unclear. This study examined the effects of FBP on membrane bilayer permeability, membrane fluidity, phospholipid packing, and membrane potential to determine how FBP crosses the membrane bilayer. Large unilamellar vesicles composed of egg phosphatidylcholine (Egg PC) were made and incubated with 50 mM FBP spiked with ¹⁴C-FBP at 30°C. Uptake of FBP was significant (P<0.05) and dependent on the lipid concentration, suggesting that FBP affects membrane, bilayer permeability. With added calcium (10 mM), FBP uptake by lipid vesicles decreased significantly (P<0.05). Addition of either 5 or 50 mM FBP led to a significant increase (P<0.05) in Egg PC carboxyfluorescein leakage. We hypothesized that the membrane-permeabilizing effects of FBP may be due to a destabilization of the membrane bilayer. Small unilamellar vesicles composed of dipalmitoyl pC (DPPC) were made containing either diphenyl-1,3,5-hexatriene (DPH) or trimethylammmonia-DPH (TMA-DPH) and the effects of FBP on the fluorescence anisotropy (FA) of the fluorescent labels examined. FBP caused a significant decrease in the FA of DPH in the liquid crystalline state of DPPC (P<0.05), had no effect on FA of TMA-DPH in the liquid crystalline state of DPPC, but increased the FA of TMA-DPH in the gel state of DPPC. From phase transition measurements with DPPC/DPH or TMA-DPH, we calculated the slope of the phase transition as an indicator of the cooperativity of the DPPC molecules. FBP significantly decreased the slope, suggesting a decrease in fatty acyl chain interaction (P<0.05). The addition of 50 mM FBP caused a significant decrease (P<0.05) in the liquid crystalline/gel state fluorescence ratio of merocyanine 540, indicating increased head-group packing. To determine what effects these changes would have on cellular membranes, we labeled human endothelial cells with the membrane potential probe 3,3′-dipropylthiacarbocyanine iodide (DiSC₃) and then added FBP. FBP caused a significant, dose-dependent decrease in DiSC₃ fluorescence, indicating membrane depolarization. We suggest that FBP destabilizes membrane bilayers by decreasing fatty acyl chain interaction, leading to significant increases in membrane permeability that allow FBP to diffuse into the cell where it can be used as a glycolytic intermediate.     

Homology modeling and molecular dynamics simulations of the mu opioid receptor in a membrane-aqueous system

Three types of opioid receptors-mu, delta, and kappa-belong to the rhodopsin subfamily in the G protein-coupled receptor superfamily. With the recent characterization of the high-resolution X-ray crystal structure of bovine rhodopsin, considerable attention has been focused on molecular modeling of these transmembrane proteins. In this study, a homology model of the mu opioid receptor was constructed based on the X-ray crystal structure of bovine rhodopsin. A phospholipid bilayer was built around the receptor, and two water layers were placed on both surfaces of the lipid bilayer. Molecular-dynamics simulations were carried out by using CHARMM for the entire system, which consisted of 316 amino acid residues, 92 phospholipid molecules, 8327 water molecules, and 11 chloride counter ions-40 931 atoms altogether. The whole system was equilibrated for 250 ps followed by another 2 ns dynamic simulation. The opioid ligand naltrexone was docked into the optimized model, and the critical amino acid residues for binding were identified. The mu opioid receptor homology model optimized in a complete membrane-aqueous system should provide a good starting point for further characterization of the binding modes for opioid ligands. Furthermore, the method developed herein will be applicable to molecular model building to other opioid receptors as well as other GPCRs.     

Makromolekulare schalter für doppelschichtmembranen

Controlled polyelectrolyte adsorption can be used to render phospholipid bilayer membranes sensitive to physical and chemical signals. We describe in this paper the design and construction of macromolecular switches for bilayer membranes, which can be used to create lipid vesicles that release their contents rapidly and quantitatively in response to changes in pH, temperature, light intensity or glucose concentration. The kinetics and mechanisms of the molecular switching processes observed in such systems are also discussed.     

A molecular dynamics study of an archaeal tetraether lipid membrane: Comparison with a dipalmitoylphosphatidylcholine lipid bilayer

Molecular dynamics simulations of an archaeal membrane made up of bipolar tetraether lipids and a dipalmitoylphosphatidylcholine (DPPC) lipid membrane were performed and compared for the first time. The simulated archaeal membrane consists of a pure monolayer of asymmetrical lipids, analogous to the main polar lipid [MPL; Swain, M., Brisson, J.-R., Sprott, G.D., Cooper, F.P., and Patel, G.B., (1997) Identification of β-1-Gulose as the Sugar moiety of the Main Polar Lipid of Thermoplasma acidophilum, Biochim. Biophys. Acta 1345, 56–64] found in T. acidophilum, an extremophile archaeal organism. This simulated membrane lipid contains two cyclopentane rings located on one of the two aliphatic chains of the lipid. The archaeal membrane is simulated at 62°C, slightly above the optimal growth temperature of T. acidophilum. We compared the organization of this tetraether lipid monolayer with a DPPC bilayer simulated at 50°C, both of them being modeled in a partially hydrated state. Our results assess the singularity of the tetrather lipid organization, in particular the influence of the spanning structure on the molecular ordering within the archaeal membrane.     

Supramolecular Chemistry in the Biomembrane

The combination of supramolecular functional systems with biomolecular chemistry has been a fruitful exercise for decades, leading to a greater understanding of biomolecules and to a great variety of applications, for example, in drug delivery and sensing. Within these developments, the phospholipid bilayer membrane, surrounding live cells, with all its functions has also intrigued supramolecular chemists. Herein, recent efforts from the supramolecular chemistry community to mimic natural functions of lipid membranes, such as sensing, molecular recognition, membrane fusion, signal transduction, and gated transport, are reviewed.     

Engineering Lipid Bilayer Membranes for Protein Studies

Lipid membranes regulate the flow of nutrients and communication signaling between cells and protect the sub-cellular structures. Recent attempts to fabricate artificial systems using nanostructures that mimic the physiological properties of natural lipid bilayer membranes (LBM) fused with transmembrane proteins have helped demonstrate the importance of temperature, pH, ionic strength, adsorption behavior, conformational reorientation and surface density in cellular membranes which all affect the incorporation of proteins on solid surfaces. Much of this work is performed on artificial templates made of polymer sponges or porous materials based on alumina, mica, and porous silicon (PSi) surfaces. For example, porous silicon materials have high biocompatibility, biodegradability, and photoluminescence, which allow them to be used both as a support structure for lipid bilayers or a template to measure the electrochemical functionality of living cells grown over the surface as in vivo. The variety of these media, coupled with the complex physiological conditions present in living systems, warrant a summary and prospectus detailing which artificial systems provide the most promise for different biological conditions. This study summarizes the use of electrochemical impedance spectroscopy (EIS) data on artificial biological membranes that are closely matched with previously published biological systems using both black lipid membrane and patch clamp techniques.     

Interactions of Borneol with DPPC Phospholipid Membranes: A Molecular Dynamics Simulation Study

Borneol, known as a “guide” drug in traditional Chinese medicine, is widely used as a natural penetration enhancer in modern clinical applications. Despite a large number of experimental studies on borneol’s penetration enhancing effect, the molecular basis of its action on bio-membranes is still unclear. We carried out a series of coarse-grained molecular dynamics simulations with the borneol concentration ranging from 3.31% to 54.59% (v/v, lipid-free basis) to study the interactions of borneol with aDPPC(1,2-dipalmitoylsn-glycero-3-phosphatidylcholine) bilayer membrane, and the temperature effects were also considered. At concentrations below 21.89%, borneol’s presence only caused DPPC bilayer thinning and an increase in fluidity; A rise in temperature could promote the diffusing progress of borneol. When the concentration was 21.89% or above, inverted micelle-like structures were formed within the bilayer interior, which led to increased bilayer thickness, and an optimum temperature was found for the interaction of borneol with the DPPC bilayer membrane. These findings revealed that the choice of optimal concentration and temperature is critical for a given application in which borneol is used as a penetration enhancer. Our results not only clarify some molecular basis for borneol’s penetration enhancing effects, but also provide some guidance for the development and applications of new preparations containing borneol.     

Bilayer-mediated assembly of cationic nanoparticles adsorbed to lipid bilayers: Insights from molecular simulations

Understanding interactions between functionalized gold nanoparticles (NPs) and lipid bilayers is essential for biomedical applications. Experiments have shown that NPs that are stable in solution can assemble into clusters when adsorbed to a lipid bilayer, suggesting that bilayer-mediated interactions facilitate assembly. In this work, we use coarse-grained molecular dynamics simulations to study bilayer-mediated interactions between NPs adsorbed to single- and multicomponent lipid bilayers. We perform unbiased simulations and umbrella sampling calculations using an implicit solvent force field to determine the thermodynamic contributions to assembly. We show that bilayer-mediated interactions drive the assembly of NPs into linear aggregates on liquid-disordered bilayers, which we attribute to a reduction in bilayer curvature. Similar bilayer-mediated interactions induce the alignment of NP clusters with phase boundaries in phase-separated bilayers. Together, these simulation results provide new physical insight into the balance of forces that dictate the assembly of charged NPs at multicomponent lipid bilayer interfaces.     

Experimental evidence for the interaction of C-60 fullerene with lipid vesicle membranes

There are some molecular dynamic simulations but a paucity of experimental evidence of the effects of C-60 fullerene on lipid bilayers. The aim of this study is to assess the potential for disruption of the lipid bilayer by C-60 suspended in water. We selected a C-60 suspension that has previously been shown to provoke cell membrane destabilisation in vivo. Electromobility measurements show significant negative surface charge on the C-60 nanoparticles suspended in a glucose solution and a zeta potential of ?26 mV. The prevalent C-60 clusters have hydrodynamic radii of approximately 2 nm. Phase contrast microscopy and computer aided image analysis results show that C-60 causes shape transformations and rupture of unilamellar phospholipid vesicles, indicative of changes in their average mean curvature. Small-angle X-ray scattering reveals that C-60 provokes disruptions of external membranes of multilamellar vesicles only after freeze and thaw cycles. Here, the liposomes undergo breakage and annealing steps which increase the probability for fullerenes to insert into the MLVs. Our experimental findings confirm the potential of C-60 to reconstruct lipids in biological membranes. This research enhances our understanding of the impact of engineered nanoparticles on cell membranes.     

Dimerization of protegrin-1 in different environments

The dimerization of the cationic β-hairpin antimicrobial peptide protegrin-1 (PG1) is investigated in three different environments: water, the surface of a lipid bilayer membrane, and the core of the membrane. PG1 is known to kill bacteria by forming oligomeric membrane pores, which permeabilize the cells. PG1 dimers are found in two distinct, parallel and antiparallel, conformations, known as important intermediate structural units of the active pore oligomers. What is not clear is the sequence of events from PG1 monomers in solution to pores inside membranes. The step we focus on in this work is the dimerization of PG1. In particular, we are interested in determining where PG1 dimerization is most favorable. We use extensive molecular dynamics simulations to determine the potential of mean force as a function of distance between two PG1 monomers in the aqueous subphase, the surface of model lipid bilayers and the interior of these bilayers. We investigate the two known distinct modes of dimerization that result in either a parallel or an antiparallel β-sheet orientation. The model bilayer membranes are composed of anionic palmitoyl-oleoyl-phosphatidylglycerol (POPG) and palmitoyl-oleoyl-phosphatidylethanolamine (POPE) in a 1:3 ratio (POPG:POPE). We find the parallel PG1 dimer association to be more favorable than the antiparallel one in water and inside the membrane. However, we observe that the antiparallel PG1 β-sheet dimer conformation is somewhat more stable than the parallel dimer association at the surface of the membrane. We explore the role of hydrogen bonds and ionic bridges in peptide dimerization in the three environments. Detailed knowledge of how networks of ionic bridges and hydrogen bonds contribute to peptide stability is essential for the purpose of understanding the mechanism of action for membrane-active peptides as well as for designing peptides which can modulate membrane properties. The findings are suggestive of the dominant pathways leading from individual PG1 molecules in solution to functional pores in bacterial membranes.     

纯磷脂单分子膜压缩过程中磷脂分子的构象和取向(英文)

On the basis of energy conservation law and surface pressure isotherm, the conformation energy changes of dipalmitoylphosphatidylcholine (DPPC) and dipalmitoylphosphatidylglycerol (DPPG) in pure phospholipid monolayer at the air/water interface during compression are derived. The optimized conformations of phospholipids at absolute freedom state are simulated by Gaussian 98 software. Based on following assumptions: (1)the conformation energy change is mainly caused by the rotation of one special bond; (2)the atoms of glycerol near the water surface are active; (3)the rotation is motivated by hydrogen-bond action; (4)the rotation of bond is inertial, one simplified track of conformational change is suggested and the conformations of DPPC and DPPG at different states are determined by the plots of conformation energy change vs. dihedral angle. The thickness of the simulated phospholipid monolayer is consistent with published experimental result. According to molecular areas at different states, the molecular orientations in the compressing process are also developed.     

动态表面张力破裂磷脂膜的分子动力学模拟

磷脂双层膜在生物传感器、仿生膜和生物膜反应器等领域具有广阔的应用前景。揭示磷脂膜破裂过程规律对于磷脂膜器件设计和应用具有重要的基础意义。以二棕榈酰磷脂酰胆碱(dipalmitoyl phosphatidylcholine, DPPC)和二棕榈酰磷脂酰甘油(dipalmitoyl phosphoglycerol, DPPG)作为磷脂膜组分,采用粗粒化分子动力学模拟研究了磷脂膜组成对其破裂过程的影响规律。首先建立了磷脂膜破裂动力学的临界破裂时间及临界破裂表面张力的识别方法;进而考察了磷脂膜组成对其破裂动力学的影响规律。模拟结果表明随着带负电组分DPPG 含量增加,磷脂膜平均临界破裂时间延迟且分布变宽,即磷脂膜强度提高,磷脂膜破裂呈现非均匀特性。提出了描述动态表面张力作用下磷脂膜破裂过程的"动态"微观对抗理论,由该理论可预期磷脂膜的线张力随着DPPG 含量提高而增强,与分子动力学模拟结果相符。为基于磷脂膜的分子器件的设计提供了数值模拟及理论依据。     

Solid-state NMR studies of the structure, dynamics, and assembly of beta-sheet membrane peptides and alpha-helical membrane proteins with antibiotic activities

beta-Sheet antimicrobial peptides and alpha-helical channel-forming colicins are bactericidal molecules that target the lipid membranes of sensitive cells. Understanding the mechanisms of action of these proteins requires knowledge of their three-dimensional structure in the lipid bilayer. Solid-state NMR has been used to determine the conformation, orientation, depth of insertion, oligomerization, mobility, and lipid interaction of these membrane peptides and proteins. We review the NMR methods developed and applied to study the structure and dynamics of these antibiotic membrane proteins. These studies shed light on how these peptides disrupt lipid membranes and provide fundamental insights into the folding of beta-sheet and alpha-helical membrane proteins.     

Dynamic “Molecular Portraits” of Biomembranes Drawn by Their Lateral Nanoscale Inhomogeneities

To date, it has been reliably shown that the lipid bilayer/water interface can be thoroughly characterized by a sophisticated so-called “dynamic molecular portrait”. The latter reflects a combination of time-dependent surface distributions of various physicochemical properties, inherent in both model lipid bilayers and natural multi-component cell membranes. One of the most important features of biomembranes is their mosaicity, which is expressed in the constant presence of lateral inhomogeneities, the sizes and lifetimes of which vary in a wide range—from 1 to 10³ nm and from 0.1 ns to milliseconds. In addition to the relatively well-studied macroscopic domains (so-called “rafts”), the analysis of micro- and nanoclusters (or domains) that form an instantaneous picture of the distribution of structural, dynamic, hydrophobic, electrical, etc., properties at the membrane-water interface is attracting increasing interest. This is because such nanodomains (NDs) have been proven to be crucial for the proper membrane functioning in cells. Therefore, an understanding with atomistic details the phenomena associated with NDs is required. The present mini-review describes the recent results of experimental and in silico studies of spontaneously formed NDs in lipid membranes. The main attention is paid to the methods of ND detection, characterization of their spatiotemporal parameters, the elucidation of the molecular mechanisms of their formation. Biological role of NDs in cell membranes is briefly discussed. Understanding such effects creates the basis for rational design of new prospective drugs, therapeutic approaches, and artificial membrane materials with specified properties.     

Molecular dynamics simulations of enantiomeric separations as an interfacial process in HPLC

Since chromatographic separation is a dynamic process, with the interactions between the drug and the chiral stationary phase mediated by the solvent, no single interacting structure, such as could be found by minimizing the energy, could possibly describe and account for the ratio of residence times in the chromatographic column for the enantiomeric pair. We describe the use of explicit-solvent fully atomistic molecular dynamics simulations, permitting all the interactions between the atoms constituting the chiral stationary phase, solvent molecules and the drug molecule. This allows us to better understand the molecular dynamic chiral recognition that provides the discrimination, which results in the separation of enantiomers by high performance liquid chromatography. It also provides a means of predicting, for a given set of conditions, which enantiomer elutes first and an estimate of the expected separation factor. In this review, we consider the use of molecular dynamics toward this understanding and prediction.     

Kinetically Stable Bicelles with Dilution Tolerance,Size Tunability,and Thermoresponsiveness for Drug Delivery Applications

Mixtures of a phospholipid (1,2‐dipalmitoyl‐sn‐glycero‐3‐phosphatidylcholine, DPPC) and a sodium‐cholate‐derived surfactant (SC‐C₅) at room temperature formed phospholipid bilayer fragments that were edge‐stabilized by SC‐C₅: so‐called “bicelles”. Because the bilayer melting point of DPPC (41 °C) is above room temperature and because SC‐C₅ has an exceptionally low critical micelle concentration (<0.5 mm ), the bicelles are kinetically frozen at room temperature. Consequently, they exist even when the mixture is diluted to a concentration of 0.04 wt %. In addition, the lateral size of the bicelles can be fine‐tuned by altering the molar ratio of DPPC to SC‐C₅. On heating to ≈37 °C, the bicelles transformed into micelles composed of DPPC and SC‐C₅. By taking advantage of the dilution tolerance, size tunability, and thermoresponsiveness, we demonstrated in vitro drug delivery based on use of the bicelles as carriers, which suggests their potential utility in transdermal drug delivery.