Transbilayer Lipid Movement Research Articles

In or out of the groove? Mechanisms of lipid scrambling by TMEM16 proteins

Phospholipid scramblases mediate the rapid movement of lipids between membrane leaflets, a key step in establishing and maintaining membrane homeostasis of the membranes of all eukaryotic cells and their organelles. Thus, impairment of lipid scrambling can lead to a variety of pathologies. How scramblases catalyzed the transbilayer movement of lipids remains poorly understood. Despite the availability of direct structural information on three unrelated families of scramblases, the TMEM16s, the Xkrs, and ATG-9, a unifying mechanism has failed to emerge thus far. Among these, the most extensively studied and best understood are the Ca2+ activated TMEM16s, which comprise ion channels and/or scramblases. Early work supported the view that these proteins provided a hydrophilic, membrane-exposed groove through which the lipid headgroups could permeate. However, structural, and functional experiments have since challenged this mechanism, leading to the proposal that the TMEM16s distort and thin the membrane near the groove to facilitate lipid scrambling. Here, we review our understanding of the structural and mechanistic underpinnings of lipid scrambling by the TMEM16s and discuss how the different proposals account for the various experimental observations.

Quantifying single-cell diacylglycerol signaling kinetics after uncaging

Studying the role of molecularly distinct lipid species in cell signaling remains challenging due to a scarcity of methods for performing quantitative lipid biochemistry in living cells. We have recently used lipid uncaging to quantify lipid-protein affinities and rates of lipid trans-bilayer movement and turnover in the diacylglycerol signaling pathway. This approach is based on acquiring live-cell dose-response curves requiring light dose titrations and experimental determination of uncaging photoreaction efficiency. We here aimed to develop a methodological approach that allows us to retrieve quantitative kinetic data from uncaging experiments that 1) require only typically available datasets without the need for specialized additional constraints and 2) should in principle be applicable to other types of photoactivation experiments. Our new analysis framework allows us to identify model parameters such as diacylglycerol-protein affinities and trans-bilayer movement rates, together with initial uncaged diacylglycerol levels, using noisy single-cell data for a broad variety of structurally different diacylglycerol species. We find that lipid unsaturation degree and side-chain length generally correlate with faster lipid trans-bilayer movement and turnover and also affect lipid-protein affinities. In summary, our work demonstrates how rate parameters and lipid-protein affinities can be quantified from single-cell signaling trajectories with sufficient sensitivity to resolve the subtle kinetic differences caused by the chemical diversity of cellular signaling lipid pools.

Cardiolipin for Enhanced Cellular Uptake and Cytotoxicity of Thermosensitive Liposome-Encapsulated Daunorubicin toward Breast Cancer Cell Lines.

Daunorubicin (DNR) and cardiolipin (CL) were co-delivered using thermosensitive liposomes (TSLs). 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1-myristoyl-2-stearoyl-sn-glycero-3-phosphocholine (MSPC), cholesterol, 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000] or DSPE-mPEG (2000) and CL were used in the formulation of liposomes at a molar ratio of 57:40:30:3:20, respectively. CL forms raft-like microdomains that may relocate and change lipid organization of the outer and inner mitochondrial membranes. Such transbilayer lipid movement eventually leads to membrane permeabilization. TSLs were prepared by thin-film hydration (drug:lipid ratio 1:5) where DNR was encapsulated within the aqueous core of the liposomes and CL acted as a component of the lipid bilayer. The liposomes exhibited high drug encapsulation efficiency (>90%), small size (~115 nm), narrow size distribution (polydispersity index ~0.12), and a rapid release profile under the influence of mild hyperthermia. The liposomes also exhibited ~4-fold higher cytotoxicity against MDA-MB-231 cells compared to DNR or liposomes similar to DaunoXome® (p < 0.001). This study provides a basis for developing a co-delivery system of DNR and CL encapsulated in liposomes for treatment of breast cancer.

Flip-Flop Promotion Mechanisms by Model Transmembrane Peptides.

Lipid transbilayer movement (flip-flop) is regulated by membrane proteins that are involved in homeostasis and signaling in eukaryotic cells. In the plasma membrane, an asymmetric lipid composition is maintained by energy-dependent unidirectional transport. Energy-independent flip-flop promotion by phospholipid scramblases disrupts the asymmetry in several physiological processes, such as apoptosis and blood coagulation. In the endoplasmic reticulum, rapid flip-flop is essential for bilayer integrity because phospholipids are synthesized only in the cytoplasmic leaflet. Phospholipid scramblases are also involved in lipoprotein biogenesis, autophagosome formation, and viral infection. Although several scramblases have been identified and investigated, the precise flip-flop promotion mechanisms are not fully understood. Model transmembrane peptides are valuable tools for investigating the general effects of lipid-peptide interactions. We focus on the development of model transmembrane peptides with flip-flop promotion abilities and their mechanisms.

TMEM16 scramblases thin the membrane to enable lipid scrambling

TMEM16 scramblases dissipate the plasma membrane lipid asymmetry to activate multiple eukaryotic cellular pathways. Scrambling was proposed to occur with lipid headgroups moving between leaflets through a membrane-spanning hydrophilic groove. Direct information on lipid-groove interactions is lacking. We report the 2.3 Å resolution cryogenic electron microscopy structure of the nanodisc-reconstituted Ca2+-bound afTMEM16 scramblase showing how rearrangement of individual lipids at the open pathway results in pronounced membrane thinning. Only the groove’s intracellular vestibule contacts lipids, and mutagenesis suggests scrambling does not require specific protein-lipid interactions with the extracellular vestibule. We find scrambling can occur outside a closed groove in thinner membranes and is inhibited in thicker membranes, despite an open pathway. Our results show afTMEM16 thins the membrane to enable scrambling and that an open hydrophilic pathway is not a structural requirement to allow rapid transbilayer movement of lipids. This mechanism could be extended to other scramblases lacking a hydrophilic groove.

Phospholipid Scrambling by G Protein-Coupled Receptors.

Rapid flip-flop of phospholipids across the two leaflets of biological membranes is crucial for many aspects of cellular life. The transport proteins that facilitate this process are classified as pump-like flippases and floppases and channel-like scramblases. Unexpectedly, Class A G protein-coupled receptors (GPCRs), a large class of signaling proteins exemplified by the visual receptor rhodopsin and its apoprotein opsin, are constitutively active as scramblases in vitro. In liposomes, opsin scrambles lipids at a unitary rate of >100,000 per second. Atomistic molecular dynamics simulations of opsin in a lipid membrane reveal conformational transitions that expose a polar groove between transmembrane helices 6 and 7. This groove enables transbilayer lipid movement, conceptualized as the swiping of a credit card (lipid) through a card reader (GPCR). Conformational changes that facilitate scrambling are distinct from those associated with GPCR signaling. In this review, we discuss the physiological significance of GPCR scramblase activity and the modes of its regulation in cells.

PMP2/FABP8 induces PI(4,5)P2-dependent transbilayer reorganization of sphingomyelin in the plasma membrane.

Sphingomyelin (SM) is a mammalian lipid mainly distributed in the outer leaflet of the plasma membrane (PM). We show that peripheral myelin protein 2 (PMP2), a member of the fatty-acid-binding protein (FABP) family, can localize at the PM and controls the transbilayer distribution of SM. Genetic screening with genome-wide small hairpin RNA libraries identifies PMP2 as a protein involved in the transbilayer movement of SM. A biochemical assay demonstrates that PMP2 is a phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2)-binding protein. PMP2 induces the tubulation of model membranes in a PI(4,5)P2-dependent manner, accompanied by the modification of the transbilayer membrane distribution of lipids. In the PM of PMP2-overexpressing cells, inner-leaflet SM is increased whereas outer-leaflet SM is reduced. PMP2 is a causative protein of Charcot-Marie-Tooth disease (CMT). A mutation in PMP2 associated with CMT increases its affinity for PI(4,5)P2, inducing membrane tubulation and the subsequent transbilayer movement of lipids.

Detection of Transport Intermediates in the Peptidoglycan Flippase MurJ Identifies Residues Essential for Conformational Cycling.

Bacterial cell wall synthesis is an essential process in bacteria and one of the best targets for antibiotics. A critical step on this pathway is the export of the lipid-linked cell wall monomer, Lipid II, by its transporter MurJ. The mechanism by which MurJ mediates the transbilayer movement of Lipid II is not understood because intermediate states of this process have not been observed. Here we demonstrate a method to capture and detect interactions between MurJ and its substrate Lipid II by photo-cross-linking and subsequent biotin-tagging. We show that this method can be used to covalently capture intermediate transport states of Lipid II on MurJ in living cells. Using this strategy we probed several lethal arginine mutants and found that they retain appreciable substrate-binding ability despite being defective in Lipid II transport. We propose that Lipid II binding to these residues during transport induces a conformational change in MurJ required to proceed through the Lipid II transport cycle. The methods described to detect intermediate transport states of MurJ will be useful for characterizing mechanisms of inhibitors.

Structural Feature of Lipid Scrambling Model Transmembrane Peptides: Same-Side Positioning of Hydrophilic Residues and Their Deeper Position.

Phospholipid scramblases that catalyze lipid transbilayer movement are associated with intercellular signaling and lipid homeostasis. Although several studies have shown that the hydrophilic residue-rich groove of the proteins mediates lipid scrambling, the interactions between the groove and the lipid bilayers remain poorly understood. Here we have revealed the structural features of model transmembrane peptides that conduct lipid scrambling as well as the interactions between the peptides and the surrounding lipids by means of experimental and simulation techniques. Peptides with two strongly hydrophilic residues located on the same side of the helices and at a deeper position in the membrane exhibited high scramblase activities. All-atom molecular dynamics simulations showed that the interactions between the hydrophilic residues and lipid head groups regulate the membrane thinning and disorder near the peptides in an order that correlates with the scramblase activity of the peptides. These results provide a basis for understanding the lipid scrambling mechanisms by transmembrane regions.

Reconstitution of Proteoliposomes for Phospholipid Scrambling and Nonselective Channel Assays.

Phospholipid scramblases catalyze the rapid trans-bilayer movement of lipids down their concentration gradients. This process is essential for numerous cellular signaling functions including cell fusion, blood coagulation, and apoptosis. The importance of scramblases is highlighted by the number of human diseases caused by mutations in these proteins. Because of their indispensable function, it is essential to understand and characterize the molecular function of phospholipid scramblases. Powerful tools to measure lipid transport in cells are available. However, these approaches provide limited mechanistic insights into the molecular bases of scrambling. Here we describe in detail an in vitro phospholipid scramblase assay and the accompanying analysis which allows for determination of the macroscopic rate constants associated with phospholipid scrambling. Notably, members of the TMEM16 family of scramblases also function as nonselective ion channels. To better understand the physiological relevance of this channel function as well as its relationship to the scrambling activity of the TMEM16s we also describe in detail an in vitro flux assay to measure nonselective channel activity. Together, these two assays can be used to investigate the dual activities of the TMEM16 scramblases/nonselective channels.

Cryo-EM Structures Reveal Bilayer Remodeling during Ca2+ Activation of a TMEM16 Scramblase

The plasma membranes of eukaryotic cells are organized asymmetrically for cellular function. At rest, polar and charged lipids are sequestered to the inner leaflet by the activity of ATP-driven pumps. Activation of a specialized class of membrane proteins – phospholipid scramblases – causes rapid collapse of this asymmetry and externalization of negatively charged phosphatidylserine molecules. As a result, extracellular signaling networks, controlling processes such as apoptosis, blood coagulation, membrane fusion and repair, are activated. The TMEM16 family of membrane proteins includes phospholipid scramblases and Cl- channels, all of which are Ca2+-dependent. Prior structural and functional analyses of the fungal TMEM16 scramblase from Nectria haematococca identified a membrane-exposed hydrophilic groove that serves as the lipid translocation pathway. In the TMEM16A channel, this pathway is sealed from the membrane, thus preventing lipid access and enabling ion permeation. However, the mechanisms underlying Ca2+-dependent gating of TMEM16 scramblases, and their effects on the surrounding lipid bilayer, remain poorly understood. Here we describe three high-resolution cryo-electron microscopy structures of a fungal scramblase from Aspergillus fumigatus, afTMEM16, reconstituted in lipid nanodiscs. Differences between the Ca2+-free and Ca2+-bound states reveal that Ca2+ binding induces a global rearrangement of the transmembrane and cytosolic regions, which causes the lipid pathway to open. Further, comparison of these structures and a third in the presence of a long-chain inhibitory lipid, together with functional experiments, reveal that scramblases cause profound remodeling of the surrounding membrane. Specifically, scramblase activation causes the bilayer to thin at the open lipid pathway and the outer leaflet to bend towards the center of the bilayer at the dimer interface. We propose a model in which trans-bilayer lipid movement is enabled by these membrane and protein rearrangements and provide a general mechanistic framework for phospholipid scrambling.

Structural basis of Ca2+-dependent activation and lipid transport by a TMEM16 scramblase.

The lipid distribution of plasma membranes of eukaryotic cells is asymmetric and phospholipid scramblases disrupt this asymmetry by mediating the rapid, nonselective transport of lipids down their concentration gradients. As a result, phosphatidylserine is exposed to the outer leaflet of membrane, an important step in extracellular signaling networks controlling processes such as apoptosis, blood coagulation, membrane fusion and repair. Several TMEM16 family members have been identified as Ca2+-activated scramblases, but the mechanisms underlying their Ca2+-dependent gating and their effects on the surrounding lipid bilayer remain poorly understood. Here, we describe three high-resolution cryo-electron microscopy structures of a fungal scramblase from Aspergillus fumigatus, afTMEM16, reconstituted in lipid nanodiscs. These structures reveal that Ca2+-dependent activation of the scramblase entails global rearrangement of the transmembrane and cytosolic domains. These structures, together with functional experiments, suggest that activation of the protein thins the membrane near the transport pathway to facilitate rapid transbilayer lipid movement.

Elementary Processes and Mechanisms of Interactions of Antimicrobial Peptides with Membranes-Single Giant Unilamellar Vesicle Studies.

To elucidate the mechanisms of action of antimicrobial peptides (AMPs) and to develop de novo designed peptides with activities similar to those of AMPs, it is essential to elucidate the detailed processes of AMP interactions with plasma membranes of bacterial and fungal cells and model membranes (lipid bilayers). In this mini-review, we summarize the present state of knowledge of the interactions of AMPs with lipid vesicles obtained using the single giant unilamellar vesicle (GUV) method. Currently, three modes of action of AMPs on GUVs have been defined. The elementary processes of interactions of AMPs with lipid vesicles revealed by the single GUV method, and the advantages of this technique, are described and discussed. For example, the single GUV method can be used to determine rate constants of AMP-induced pore formation or local rupture and membrane permeation of internal contents through the pore or the local rupture, the transbilayer movement of lipids, and the relationship between the location of AMPs and pore formation. Effects of membrane tension and of asymmetric lipid packing in the bilayer on AMP-induced pore formation also are described. On the basis of these data, we discuss the present state of understanding of the interaction of AMPs with lipid bilayers and future prospects for AMP studies.

Effect of membrane tension on transbilayer movement of lipids.

The stretching of plasma membranes of cells and lipid bilayers of vesicles affects the physical properties of the membrane as well as the functions of proteins/peptides in the membranes. Here, we examined the effect of membrane tension on the rate constant of the transbilayer movement (kFF) of fluorescent probe-labeled lipids using a new method. Specifically, we recently reported [Hasan et al., Langmuir 34, 3349 (2018)] the development of a technique that employs giant unilamellar vesicles (GUVs) with asymmetric lipid compositions in two monolayers. In the present work, we found that the kFF greatly increased with tension without leakage of water-soluble fluorescent probes from the GUV lumen (i.e., without the formation of pores in the GUV membrane). We discussed the plausible mechanisms for the effect of tension on the transbilayer movement of lipids. As one of the mechanisms, we hypothesized that the transbilayer movement of lipids occurs through the lateral diffusion of lipids in the walls of hydrophilic pre-pores.

Lipid diffusion in the distal and proximal leaflets of supported lipid bilayer membranes studied by single particle tracking.

Supported lipid bilayers (SLBs) have been studied extensively as simple but powerful models for cellular membranes. Yet, potential differences in the dynamics of the two leaflets of a SLB remain poorly understood. Here, using single particle tracking, we obtain a detailed picture of bilayer dynamics. We observe two clearly separate diffusing populations, fast and slow, that we associate with motion in the distal and proximal leaflets of the SLB, respectively, based on fluorescence quenching experiments. We estimate diffusion coefficients using standard techniques as well as a new method based on the blur of images due to motion. Fitting the observed diffusion coefficients to a two-leaflet membrane hydrodynamic model allows for the simultaneous determination of the intermonolayer friction coefficient and the substrate-membrane friction coefficient, without any prior assumptions on the strengths of the relevant interactions. Remarkably, our calculations suggest that the viscosity of the interfacial water confined between the membrane and the substrate is elevated by ∼104 as compared to bulk water. Using hidden Markov model analysis, we then obtain insight into the transbilayer movement of lipids. We find that lipid flip-flop dynamics are very fast, with half times in the range of seconds. Importantly, we find little evidence for membrane defect mediated lipid flip-flop for SLBs at temperatures well above the solid-to-liquid transition, though defects seem to be involved when the SLBs are cooled down. Our work thus shows that the combination of single particle tracking and advanced hydrodynamic modeling provides a powerful means to obtain insight into membrane dynamics.

Probing phosphoethanolamine-containing lipids in membranes with duramycin/cinnamycin and aegerolysin proteins.

In this mini-review, we summarize current knowledge about the lipid-binding characteristics of two types of toxins used to visualize the membrane distribution of phosphoethanolamine-containing lipid species: the glycerophospholipid, phosphatidylethanolamine (PE) and the sphingolipid, ceramide phosphoethanolamine (CPE). The lantibiotic cinnamycin and the structurally-related peptide duramycin produced by some Gram-positive bacteria were among the first toxins characterized by their specificity for PE which is widely present in animal kingdoms from bacteria to mammals. These toxins promoted their binding to PE-containing membranes by changing membrane curvature and by inducing transbilayer lipid movement. The recognition of the conical shape and negative curvature adopted by the PE species within the membrane, is important to understand how lipid-peptide interaction can occur. Three mushroom-derived proteins belonging to the aegerolysin family, pleurotolysin A2, ostreolysin and erylysin A were recently described as efficient tools to visualize the membrane distribution of CPE which is found in trace amounts in mammalian cells but in higher amounts in some developmental stages of lower eukaryotes like Trypanosoma and in invertebrates such as Drosophila. The recent development of lantibiotic-based PE-specific and aegerolysin-based CPE-specific probes is useful to visualize and specify the role of these lipids in various pathophysiological events such as cell division, apoptosis, tumor vasculature and parasite developmental stages.

Protease‐activated receptor 4 is more important than protease‐activated receptor 1 for the thrombin‐induced procoagulant effect on platelets

Protease-activated receptor 4 is more important than protease-activated receptor 1 for the thrombin-induced procoagulant effect on platelets

Asymmetric supported lipid bilayer formation via methyl-β-cyclodextrin mediated lipid exchange: influence of asymmetry on lipid dynamics and phase behavior.

Supported lipid bilayers (SLBs) are broadly used as minimal membrane models and commonly produced by vesicle fusion (VF) on solid supports. Despite its advantages, VF does not allow the controlled formation of bilayers that mimic the leaflet asymmetry in lipid composition normally found in biological systems. Here we present a simple, quick, and versatile method to produce SLBs with a desired asymmetric lipid composition which is stable for ca. 4 h. We apply methyl-β-cyclodextrin mediated lipid exchange to SLBs formed by VF to enrich the upper leaflet of the bilayer with sphingomyelin. The bilayer asymmetry is assessed by fluorescence correlation spectroscopy, measuring the lipid mobility separately in each leaflet. To check the compatibility of the method with the most common protein reconstitution approaches, we report the production of asymmetric SLBs (aSLBs) in the presence of a glycosylphosphatidylinositol-anchored protein, reconstituted in the bilayer both, via direct protein insertion, and via proteoliposomes fusion. We finally apply aSLBs to study phase separation and transbilayer lipid movement of raft-mimicking lipid mixtures. The observed differences in terms of phase separation in symmetric and asymmetric SLBs with the same overall lipid composition provide further experimental evidence that the transversal lipid distribution affects the overall lipid miscibility and allow to temporally investigate leaflet mixing.

Interaction of Polyethylenimine with Model Cell Membranes Studied by Linear and Nonlinear Spectroscopic Techniques

Polyethylenimine (PEI) has been widely used as a transfection agent for gene delivery, but it is cytotoxic and can lead to cell apoptosis. Although several apoptotic mechanisms have been proposed, a molecular level understanding of PEI/cell membrane interaction can help develop further insight into such cytotoxicity. We combined sum frequency generation (SFG) vibrational spectroscopy and attenuated total-internal reflection Fourier transform infrared (ATR-FTIR) spectroscopy to study the effect of PEI on lipid transbilayer movement in supported bilayers (serving as model cell membranes) as a function of lipid composition, PEI concentration, and temperature. For both dipalmitoylphosphatidylglycerol (DPPG) and distearoylphosphatidylcholine (DSPC) bilayers, PEI molecules showed no significant effect on lipid translocation at room temperature (21 °C). In contrast, significant lipid translocation was observed near the physiological temperature (39 °C), indicating the ability of PEI to induce lipid translocation...

Breaking asymmetry: phospholipid scrambling by GPCRs and TMEM16 proteins (351.2)

Polar lipids must flip rapidly, and often bidirectionally, across membranes to support cellular life. For example, phospholipids are synthesized on the cytoplasmic face of the endoplasmic reticulum (ER) and must be apportioned between the luminal and cytoplasmic leaflets for uniform expansion of the ER during cell growth. Transbilayer movement of lipids is also needed for the generation, maintenance and dissipation of transbilayer lipid asymmetry at the plasma membrane. As flipping is energetically costly, specialized transporters increase its intrinsically low rate to a physiologically relevant level. While some of these transporters couple ATP hydrolysis to lipid movement, many function without any discernible metabolic energy input. The molecular identification of these latter ‘ATP‐independent flippases’, also termed ‘scramblases’, has eluded researchers for decades. We now report the first examples of this novel class of proteins: rhodopsin, a prototypical G protein‐coupled receptor, is a constitutively active, ATP‐independent phospholipid flippase (Menon et al. (2011) Curr. Biol. 21: 149), and afTMEM16, a fungal homolog of the TMEM16 family of ion channels is a Ca2+‐dependent phospholipid scramblase (Malvezzi et al. (2013) Nature Commun. 4: 2367). Both proteins break transbilayer lipid asymmetry.