Simple Lipid Research Articles

The membranes of Gram-negative bacteria: progress in molecular modelling and simulation.

Molecular modelling and simulations have been employed to study the membranes of Gram-negative bacteria for over 20 years. Proteins native to these membranes, as well as antimicrobial peptides and drug molecules have been studied using molecular dynamics simulations in simple models of membranes, usually only comprising one lipid species. Thus, traditionally, the simulations have reflected the majority of in vitro membrane experimental setups, enabling observations from the latter to be rationalized at the molecular level. In the last few years, the sophistication and complexity of membrane models have improved considerably, such that the heterogeneity of the lipid and protein composition of the membranes can now be considered both at the atomistic and coarse-grain levels of granularity. Importantly this means relevant biology is now being retained in the models, thereby linking the in silico and in vivo scenarios. We discuss recent progress in simulations of proteins in simple lipid bilayers, more complex membrane models and finally describe some efforts to overcome timescale limitations of atomistic molecular dynamics simulations of bacterial membranes.

Lipid domains in model membranes: a brief historical perspective.

All biological membranes consist of a complex composite of macromolecules and macromolecular assemblies, of which the fluid lipid-bilayer component is a core element with regard to cell encapsulation and barrier properties. The fluid lipid bilayer also supports the functional machinery of receptors, channels and pumps that are associated with the membrane. This bilayer is stabilized by weak physical and colloidal forces, and its nature is that of a self-assembled system of amphiphiles in water. Being only approximately 5 nm in thickness and still encapsulating a cell that is three orders of magnitude larger in diameter, the lipid bilayer as a material has very unusual physical properties, both in terms of structure and dynamics. Although the lipid bilayer is a fluid, it has a distinct and structured trans-bilayer profile, and in the plane of the bilayer the various molecular components, viz different lipid species and membrane proteins, have the capacity to organize laterally in terms of differentiated domains on different length and time scales. These elements of small-scale structure and order are crucial for the functioning of the membrane. It has turned out to be difficult to quantitatively study the small-scale structure of biological membranes. A major part of the insight into membrane micro- and nano-domains and the concepts used to describe them have hence come from studies of simple lipid bilayers as models of membranes, by use of a wide range of theoretical, experimental and simulational approaches. Many questions remain to be answered as to which extent the result from model studies can carry over to real biological membranes.

Bioproduction of Docosahexaenoic Acid by the Marine protist Schizochytrium

The heterotrophic protist Schizochytrium sp. was batch cultivated in media containing glucose, yeast extract, peptone, dihydrogen potassium phosphate and sea salt prepared in distilled water. The increasing amounts of yeast ex-tract stimulated growth however, influenced lipid accumulation negatively. It has been observed that the sea salt concentrations above half the average seawater salinity were required for good growth and lipid accumulation. Schizochytrium sp. was able to grow on a glucose concentration as high as 60 g/l, which resulted in reduced biomass and lipid yield. Although, the culture in study, effectively utilized certain simple and complex nitrogen sources lipid yield was more in complex nitrogen source, i.e. yeast extract and pep-tone, than in simple nitrogen source. Comparison of growth at 20 and 28 ºC showed that the higher incubation temperature was more favorable for the growth. The optimum pH was optimized as 7 with a rotation speed of 220 rpm. Incubation for 120 h was required for the maximum production of bio-mass, lipid and DHA. In this period, the percentage of docosahexaenoic acid (20.0 %) was produced in the lipid (4.0 g/l).

The evaluation of obesity through blood parametres

The purpose of this study was to determine the association between some simple anthropometric measurements and lipid parameters. In all patients, age, gender, weight, and height were recorded. Body mass index (BMI) calculated. Plasma leptin, total cholesterol (TC), triglyceride (TG), high density lipoprotein (HDL), low density lipoprotein (LDL), very low density lipoprotein (VLDL), impairment fasting glucose and CRP ( C-Reactive Protein Test) were recorded and compared. There was a significant correlation in adult obese patient group between BMI, TC, VLDL (p

Mechanical and molecular basis for the symmetrical division of the fission yeast nuclear envelope.

In fission yeast Schizosaccharomyces pombe, the nuclear envelope remains intact throughout mitosis and undergoes a series of symmetrical morphological changes when the spindle pole bodies (SPBs), embedded in the nuclear envelope, are pushed apart by elongating spindle microtubules. These symmetrical membrane shape transformations do not correspond to the shape behavior of an analogous system based on lipid vesicles. Here we report that the symmetry of the dividing fission yeast nucleus is ensured by SPB-chromosome attachments, as loss of kinetochore clustering in the vicinity of SPBs results in the formation of abnormal asymmetric shapes with long membrane tethers. We integrated these findings in a biophysical model, which explains the symmetry of the nuclear shapes on the basis of forces exerted by chromosomes clustered at SPBs on the extending nuclear envelope. Based on this analysis we conclude that the fission yeast nuclear envelope exhibits the same mechanical properties as simple lipid vesicles, but interactions with other cellular components, such as chromosomes, influence the nuclear shape during mitosis, allowing the formation of otherwise energetically unfavorable symmetrical dumbbell structures upon spindle elongation. The model allows us to explain the appearance of abnormal asymmetric shapes in fission yeast mutants with mis-segregated chromosomes as well as with altered nuclear membrane composition.

Human plasma lipidome is pleiotropically associated with cardiovascular risk factors and death.

Cardiovascular disease (CVD) is the most common cause of death in the United States and is associated with a high economic burden. Prevention of CVD focuses on controlling or improving the lipid profile of patients at risk. The human lipidome is made up of thousands of ubiquitous lipid species. By studying biologically simple canonical lipid species, we investigated whether the lipidome is genetically redundant and whether its genetic influences can provide clinically relevant clues of CVD risk. We performed a genetic study of the human lipidome in 1212 individuals from 42 extended Mexican American families. High-throughput mass spectrometry enabled rapid capture of precise lipidomic profiles, providing 319 unique species. Using variance component-based heritability analyses and bivariate trait analyses, we detected significant genetic influences on each lipid assayed. Median heritability of the plasma lipid species was 0.37. Hierarchical clustering based on complex genetic correlation patterns identified 12 genetic clusters that characterized the plasma lipidome. These genetic clusters were differentially but consistently associated with risk factors of CVD, including central obesity, obesity, type 2 diabetes mellitus, raised serum triglycerides, and metabolic syndrome. Also, these clusters consistently predicted occurrence of cardiovascular deaths during follow-up. The human plasma lipidome is heritable. Shared genetic influences reduce the dimensionality of the human lipidome into clusters that are associated with risk factors of CVD.

Lipid clustering correlates with membrane curvature as revealed by molecular simulations of complex lipid bilayers.

Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2), in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side) regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins.

Oscillatory phase separation in giant lipid vesicles induced by transmembrane osmotic differentials.

Giant lipid vesicles are closed compartments consisting of semi-permeable shells, which isolate femto- to pico-liter quantities of aqueous core from the bulk. Although water permeates readily across vesicular walls, passive permeation of solutes is hindered. In this study, we show that, when subject to a hypotonic bath, giant vesicles consisting of phase separating lipid mixtures undergo osmotic relaxation exhibiting damped oscillations in phase behavior, which is synchronized with swell-burst lytic cycles: in the swelled state, osmotic pressure and elevated membrane tension due to the influx of water promote domain formation. During bursting, solute leakage through transient pores relaxes the pressure and tension, replacing the domain texture by a uniform one. This isothermal phase transition--resulting from a well-coordinated sequence of mechanochemical events--suggests a complex emergent behavior allowing synthetic vesicles produced from simple components, namely, water, osmolytes, and lipids to sense and regulate their micro-environment.

Influence of lipid coatings on surface wettability characteristics of silicone hydrogels.

Insoluble lipids serve vital functions in our bodies and interact with biomedical devices, e.g., the tear film on a contact lens. Over a period of time, these naturally occurring lipids form interfacial coatings that modify the wettability characteristics of these foreign synthetic surfaces. In this study, we examine the deposition and consequences of tear film lipids on silicone hydrogel (SiHy) contact lenses. We use bovine meibum, which is a complex mixture of waxy esters, cholesterol esters, and lipids that is secreted from the meibomian glands located on the upper and lower eyelids of mammals. For comparison, we study two commercially available model materials: dipalmitoylphosphatidylcholine (DPPC) and cholesterol. Upon deposition, we find that DPPC and meibum remain closer to the SiHy surface than cholesterol, which diffuses further into the porous SiHy matrix. In addition, we also monitor the fate of unstable thin liquid films that consequently rupture and dewet on these lipid-decorated surfaces. This dewetting provides valuable qualitative and quantitative information about the wetting characteristics of these SiHy substrates. We observe that decorating the SiHy surface with simple model lipids such as DPPC and cholesterol increases the hydrophilicity, which consequently inhibits dewetting, whereas meibum behaves conversely.

Advanced CLARITY for rapid and high-resolution imaging of intact tissues.

CLARITY is a method for chemical transformation of intact biological tissues into a hydrogel-tissue hybrid, which becomes amenable to interrogation with light and macromolecular labels while retaining fine structure and native biological molecules. This emerging accessibility of information from large intact samples has created both new opportunities and new challenges. Here we describe protocols spanning multiple dimensions of the CLARITY workflow, ranging from simple, reliable and efficient lipid removal without electrophoretic instrumentation (passive CLARITY) to optimized objectives and integration with light-sheet optics (CLARITY-optimized light-sheet microscopy (COLM)) for accelerating data collection from clarified samples by several orders of magnitude while maintaining or increasing quality and resolution. The entire protocol takes from 7-28 d to complete for an adult mouse brain, including hydrogel embedding, full lipid removal, whole-brain antibody staining (which, if needed, accounts for 7-10 of the days), and whole-brain high-resolution imaging; timing within this window depends on the choice of lipid removal options, on the size of the tissue, and on the number and type of immunostaining rounds performed. This protocol has been successfully applied to the study of adult mouse, adult zebrafish and adult human brains, and it may find many other applications in the structural and molecular analysis of large assembled biological systems.

A novel assay of DGAT activity based on high temperature GC/MS of triacylglycerol.

Diacylglycerol acyltransferase (DGAT) catalyzes the final step in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG), a high-energy compound composed of three fatty acids esterified to a glycerol backbone. In vitro DGAT assays, which are usually conducted with radiolabeled substrate using microsomal fractions, have been useful in identifying compounds and genetic modifications that affect DGAT activity. Here, we describe a high-temperature gas chromatography (GC)/mass spectrometry (MS)-based method for monitoring molecular species of TAG produced by the catalytic action of microsomal DGAT. This method circumvents the need for radiolabeled or modified substrates, and only requires a simple lipid extraction prior to GC. The utility of the method is demonstrated using a recombinant type-1 Brassica napus DGAT produced in a strain of Saccharomyces cerevisae that is deficient in TAG synthesis. The GC/MS-based assay of DGAT activity was strongly correlated with the typical in vitro assay of the enzyme using [1-(14)C] acyl-CoA as an acyl donor. In addition to determining DGAT activity, the method is also useful for determining substrate specificity and selectivity properties of the enzyme.

Direct Visualization of the Action of Triton X-100 on Giant Vesicles of Erythrocyte Membrane Lipids

The raft hypothesis proposes that microdomains enriched in sphingolipids, cholesterol, and specific proteins are transiently formed to accomplish important cellular tasks. Equivocally, detergent-resistant membranes were initially assumed to be identical to membrane rafts, because of similarities between their compositions. In fact, the impact of detergents in membrane organization is still controversial. Here, we use phase contrast and fluorescence microscopy to observe giant unilamellar vesicles (GUVs) made of erythrocyte membrane lipids (erythro-GUVs) when exposed to the detergent Triton X-100 (TX-100). We clearly show that TX-100 has a restructuring action on biomembranes. Contact with TX-100 readily induces domain formation on the previously homogeneous membrane of erythro-GUVs at physiological and room temperatures. The shape and dynamics of the formed domains point to liquid-ordered/liquid-disordered (Lo/Ld) phase separation, typically found in raft-like ternary lipid mixtures. The Ld domains are then separated from the original vesicle and completely solubilized by TX-100. The insoluble vesicle left, in the Lo phase, represents around 2/3 of the original vesicle surface at room temperature and decreases to almost 1/2 at physiological temperature. This chain of events could be entirely reproduced with biomimetic GUVs of a simple ternary lipid mixture, 2:1:2 POPC/SM/chol (phosphatidylcholine/sphyngomyelin/cholesterol), showing that this behavior will arise because of fundamental physicochemical properties of simple lipid mixtures. This work provides direct visualization of TX-100-induced domain formation followed by selective (Ld phase) solubilization in a model system with a complex biological lipid composition.

Direct and remote constriction of membrane necks.

The physical properties of membrane necks are relevant in vesiculation, a process that plays an essential role in cellular physiology. Because the neck's radius is, in general, finite, membrane scission and the consequent pinching off of the vesicle can only occur if it is narrowed to permit the necessary membrane topological reformation. Here we examine, in a simple single phase lipid vesicle, how external forces can promote neck constriction not only by direct compression at the neck but also, counterintuitively, by dilation at remote locations. These results provide a new perspective on the role played by actin polymerization in the process of endocytosis.

Nasopharyngeal cancer-specific therapy based on fusion peptide-functionalized lipid nanoparticles.

Current treatment of advanced-stage nasopharyngeal carcinoma (NPC) is not satisfactory. Targeted therapies offer hope for extending survival. Here, we developed simple, robust, and NPC-specific therapeutic lipid nanoparticles based on a fusion peptide, α-NTP, made up of an amphipathic α-helical peptide (α-peptide) linked to an NPC-specific therapeutic peptide (NTP). We found that α-NTP not only retained the sub-30 nm nanostructure-controlling ability of the α-peptide but also displayed the enhanced NPC-targeting ability of the NTP, in which the α-peptide accelerated the uptake of the NTP by NPC cells, with a 4.8-fold increase. Following uptake, α-NTP-based lipid nanoparticles (α-NTP-LNs) exerted coordinated cytotoxicity by inducing cell death via apoptosis and autophagy. In vivo and ex vivo optical imaging data showed that systemically administered α-NTP-LNs efficiently accumulated in the NPC xenograft tumor and displayed high contrast between tumor and normal tissues, which was further confirmed by flow cytometry that there had been a 13-fold uptake difference between tumor cells and hepatocytes. More importantly, the therapeutic efficacy of α-NTP-LNs was specific to NPC xenograft formed with 5-8F cells but not to fibrosarcoma xenograft formed with HT1080 cells in vivo. The growth of 5-8F tumors was significantly inhibited by α-NTP-LNs, with more than 85% inhibition relative to control groups (e.g., α-NTP and PBS treatment). In a lung metastasis model of NPC, survival was significantly improved by α-NTP-LN treatment. In a word, these excellent properties of α-NTP-LNs worked in sync and synergistically, maximizing the therapeutic efficacy of α-NTP-LNs against NPC and its metastasis.

Toward the assembly of a minimal divisome.

The construction of an irreducible minimal cell having all essential attributes of a living system is one of the biggest challenges facing synthetic biology. One ubiquitous task accomplished by any living systems is the division of the cell envelope. Hence, the assembly of an elementary, albeit sufficient, molecular machinery that supports compartment division, is a crucial step towards the realization of self-reproducing artificial cells. Looking backward to the molecular nature of possible ancestral, supposedly more rudimentary, cell division systems may help to identify a minimal divisome. In light of a possible evolutionary pathway of division mechanisms from simple lipid vesicles toward modern life, we define two approaches for recapitulating division in primitive cells: the membrane deforming protein route and the lipid biosynthesis route. Having identified possible proteins and working mechanisms participating in membrane shape alteration, we then discuss how they could be integrated into the construction framework of a programmable minimal cell relying on gene expression inside liposomes. The protein synthesis using recombinant elements (PURE)system, a reconstituted minimal gene expression system, is conceivably the most versatile synthesis platform. As a first step towards the de novo synthesis of a divisome, we showed that the N-BAR domain protein produced from its gene could assemble onto the outer surface of liposomes and sculpt the membrane into tubular structures. We finally discuss the remaining challenges for building up a self-reproducing minimal cell, in particular the coupling of the division machinery with volume expansion and genome replication.

Biophysical Implications of Sphingosine Accumulation in Membrane Properties at Neutral and Acidic pH

Sphingosine (Sph) is a simple lipid involved in the regulation of several biological processes. When accumulated in the late endosomal/lysosomal compartments, Sph causes changes in ion signaling and membrane trafficking, leading to the development of Niemann-Pick disease type C. Little is known about Sph interaction with other lipids in biological membranes; however, understanding the effect of Sph in the physical state of membranes might provide insights into its mode of action. Using complementary established fluorescence approaches, we show that Sph accumulation leads to the formation of Sph-enriched gel domains in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/sphingomyelin (SM)/cholesterol (Chol) model membranes. These domains are more easily formed in membrane models mimicking the neutral pH plasma membrane environment (PM) as compared to the acidic lysosomal membrane environment (LM), where higher Sph concentrations (or lower temperatures) are required. Electrophoretic light scattering measurements further revealed that in PM-raft models (POPC/SM/Chol), Sph is mainly neutral, whereas in LM models, the positive charge of Sph leads to electrostatic repulsion, reducing the Sph ability to form gel domains. Thus, formation of Sph-enriched domains in cellular membranes might be strongly regulated by Sph charge.

What are the true values of the bending modulus of simple lipid bilayers?

Values of the bending modulus KC are reviewed, and possible causes for the considerable differences are discussed. One possible cause is the use of glucose and sucrose in the classical micromechanical manipulation and shape analysis methods. New data, using the more recent low angle X-ray method, are presented that do not support an effect of glucose or sucrose on KC. Another possible cause is using an incomplete theory to interpret the data. Adding a tilt term to the theory clearly does not affect the value obtained from the shape analysis method. It is shown that a tilt term, using a value of the modulus Kθ indicated by simulations, theory, and estimated from order parameters obtained from NMR and from the wide angle X-ray method, should also not affect the value obtained using the micromechanical manipulation method, although it does require a small correction when determining the value of the area compressibility modulus KA. It is still being studied whether including a tilt term will significantly affect the values of KC obtained using low angle X-ray data. It remains unclear what causes the differences in the experimental values of KC for simple lipid bilayers.

Dynamics of coarsening in multicomponent lipid vesicles with non-uniform mechanical properties.

Multicomponent lipid vesicles are commonly used as a model system for the complex plasma membrane. One phenomenon that is studied using such model systems is phase separation. Vesicles composed of simple lipid mixtures can phase-separate into liquid-ordered and liquid-disordered phases, and since these phases can have different mechanical properties, this separation can lead to changes in the shape of the vesicle. In this work, we investigate the dynamics of phase separation in multicomponent lipid vesicles, using a model that couples composition to mechanical properties such as bending rigidity and spontaneous curvature. The model allows the vesicle surface to deform while conserving surface area and composition. For vesicles initialized as spheres, we study the effects of phase fraction and spontaneous curvature. We additionally initialize two systems with elongated, spheroidal shapes. Dynamic behavior is contrasted in systems where only one phase has a spontaneous curvature similar to the overall vesicle surface curvature and systems where the spontaneous curvatures of both phases are similar to the overall curvature. The bending energy contribution is typically found to slow the dynamics by stabilizing configurations with multiple domains. Such multiple-domain configurations are found more often in vesicles with spheroidal shapes than in nearly spherical vesicles.

Application of lipid extracts from Solidago canadensis to phytomonitoring of PCB126 in transgenic Arabidopsis plants

The aim of this study is to elucidate the effect of lipid extracts from Solidago canadensis for phytomonitoring of polychlorinated biphenyl (PCB) 126 in the transgenic Arabidopsis plant XgD2V11-6 carrying the recombinant guinea pig (g) aryl hydrocarbon receptor (AhR)-mediated β-glucuronidase (GUS) reporter gene expression system. A lipid extract was prepared from S. canadensis and separated into simple lipid, glycolipid, and phospholipid fractions by silica gel column chromatography. Sterylglucoside (SG), monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG), and glucosyl ceramide were found in the glycolipid fraction. When the transgenic Arabidopsis plants were treated with the glycolipid fraction together with PCB126, PCB126-induced GUS activity significantly increased in the whole plant. Moreover, S. canadensis-derived SG, MGDG, and DGDG also significantly increased PCB126-induced GUS activity. These results indicated that glycolipids in S. canadensis enhanced the sensitivity of this monitoring assay.

Rapid and simple extraction of lipids from blood plasma and urine for liquid chromatography-tandem mass spectrometry

A simple and fast lipid extraction method from human blood plasma and urine is introduced in this study. The effective lipid extraction from biological systems with a minimization of the matrix effect is important for the successful qualitative and quantitative analysis of lipids in liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). The method described here is based on the modification of the quick, easy, cheap, effective, rugged and safe (QuEChERS) extraction method, which was originally developed for pesticide residue analysis in food, for the purpose of isolating lipids from biological fluids. Applicability of QuEChERS method for lipids was evaluated by varying organic solvents for the extraction/partitioning of lipids in MgSO4/CH3COONa for the removal of water and by varying sorbents (primary secondary amines, graphitized carbon black, silica, strong anion exchange resins and C18 particles) for the dispersive solid-phase extraction (dSPE) step. This study shows that 2:1 (v/v) CHCl3/CH3OH is effective in the extraction/partitioning step and that 50mg of C18 particles (for 0.1mL plasma and 1mL of urine) are more suitable for sample cleanup for the dSPE step of the QuEChERS method. Matrix effects were calculated by comparing the recovery values of lipid standards spiked to both plasma and urine samples after extraction with those of the same standards in a neat solution using nanoflow LC-ESI-MS/MS, resulting in improved MS signals due to the decrease of the ion suppression compared to the conventional Folch method. The modified QuEChERS method was applied to lipid extracts from both human urine and plasma samples, demonstrating that it can be powerfully utilized for high-speed (<15min) preparation of lipids compared to the Folch method, with equivalent or slightly improved results in lipid identification using nLC-ESI-MS/MS.