Large-scale fluid/fluid phase separation of proteins and lipids in giant plasma membrane vesicles

The interplay of composition and mechanics in the thermodynamics of asymmetric ternary lipid membranes

Eukaryotic lipid membranes are both compositionally complex and strongly asymmetric. Preferential lipid interactions enable coexistence between two fluid phases and an associated critical point, while bilayer asymmetry leads to leaflet-specific values for many observables-most saliently composition, but also a difference in leaflet tensions, for which we introduced the term "differential stress." Lipid mixing thermodynamics has been extensively studied, notably in idealized ternary model systems, and interest in asymmetry has grown significantly in the past decade, but their interplay remains poorly understood. Here we propose a conceptual framework for the thermodynamics of asymmetric ternary lipid membranes. Cholesterol emerges as an essential actor playing two different roles: first, it controls lipid mixing; second, it couples the compositional phase points of the two leaflets by achieving chemical equilibrium between them. Since differential stress can squeeze cholesterol from one leaflet into the other, this couples mechanical properties such as lateral stresses and curvature torques directly to mixing thermodynamics. Using coarse-grained simulations, we explore implications for leaflet coexistence, mechanical stability of giant vesicles, and differential stress driven phase segregation in a single leaflet. We hope this framework enables a fresh look at some persistent puzzles in this field, most notably the elusive nature of lipid rafts.

Loss of lipid asymmetry facilitates plasma membrane blebbing by decreasing membrane lipid packing

Membrane blebs have important roles in cell migration, apoptosis, and intercellular communication through extracellular vesicles (EVs). While plasma membranes (PM) typically maintain phosphatidylserine (PS) on their cytoplasmic leaflet, most blebs have PS exposed on their outer leaflet, revealing that loss of steady-state lipid asymmetry often accompanies PM blebbing. How these changes in PM lipid organization regulate membrane properties and affect bleb formation remains unknown. We confirmed that lipid scrambling through the scramblase TMEM16F is essential for chemically induced membrane blebbing across cell types, with the kinetics of PS exposure being tightly coupled to the kinetics of bleb formation. Measurement of lipid packing with environment-sensitive probes revealed that lipid scrambling changes the physical properties of the PM, reducing lipid packing and facilitating the bilayer bending required for bleb formation. Accordingly, reducing lipid packing of the PM through cholesterol extraction, elevated temperature, or treatment with biological amphiphiles promoted blebbing in the absence of TMEM16F. Consistent with these cellular observations, blebbing in Caenorhabditis elegans embryos measured via EV production was significantly reduced by depleting the TMEM16-homolog ANOH-2. Our findings suggest that changing membrane biophysical properties by lipid scrambling is an important contributor to the formation of blebs and EVs and potentially other cellular processes involving PM deformation.

Pattern formation of lipid domains in bilayer membranes

Phase separation plays an important role in spatial organization and material distribution of biological membranes, which are essential for crucial biological functions ranging from signaling and stress response to vesicle trafficking. Domains arising from demixing of molecules coarsen indefinitely unless growth is arrested at a finite size by additional mechanisms (e.g., membrane elasticity). The resulting finite-size domains self-organize into regular patterns such as stripes and dots, which are called modulated phases. Here, we examine the size and morphology of lipid domains with a minimal theoretical model that considers both the elastic deformation of the membrane and the chemical interactions between lipids, which are coupled by a preferred membrane curvature that depends on the local lipid composition. Microscopically, the coupling is caused by an asymmetry between leaflets which emerges after extra lipids (e.g., DPPC) are introduced to the outer leaflet. The additional lipid partitions preferentially to domains where it is enriched, creating a preferred curvature that depends on local composition. We use an amplitude expansion to determine the domain size and morphology of patterns that minimize the total free energy, which is validated by numerical simulations and compared against experiments in synthetic model membranes and cell-derived membranes. The morphology of patterns varies with membrane lipid composition following a complex morphological diagram, which is in good agreement with experiments. The domain size decreases monotonically with a membrane bending modulus but can be non-monotonic with surface tension. Our results offer testable predictions, such as pattern hysteresis upon cycling external stimuli, diverse pattern morphology near critical points, and non-monotonic dependence of the domain size on osmotic pressure, which motivate future experiments. The presented theoretical framework is generally applicable to pattern formation on deformable surfaces.

Elucidating the mechanical properties of asymmetric membranes by direct derivation of their energetics

The asymmetry between the two leaflets of a plasma membrane (PM) is widely accepted as an essential condition for most PM-associated biochemical processes. However, recent work has also shown that asymmetric bilayers can be significantly stiffer upon bending than symmetric ones, suggesting that the same asymmetry may hinder the ability of the PM to remodel itself. Here, we address this issue by combining all-atom molecular dynamics (MD) simulations with an enhanced sampling scheme that explicitly induces membrane deformations to quantify their free-energy cost. Examining small asymmetric POPC/DOPC bilayers, we find that a small density imbalance between the leaflets increases their bending rigidity compared to bilayers with minimal imbalance, or to symmetric bilayers of the same two lipids. This result is consistent with recently proposed theoretical models that identify differential stress as the main source of stiffening in asymmetric membranes. The first-principles approach used in this study is broadly applicable to other types of membrane, enabling further exploration of the interplay between asymmetry and curvature, or the simulation of specific biological conditions of the PM.

Nonequilibrium asymmetry in the living cell membrane

We will discuss how sustained nonequilibrium processes operating at the plasma membrane (PM) determine the dynamical organisation (both lateral and transverse) of lipids, their maintenance and control, under physiological conditions. These nonequilibrium processes include active contractile stresses arising from the inevitable interaction of the inner leaflet of the PM with the adjoining actomyosin cortex, and active flipping of specific lipids. Recently, we showed that the inner leaflet phosphatidylserine (PS) interacts with the actomyosin cortex and engages in a strong transbilayer coupling across the leaflets. Here we develop an active Flory-Huggins theory for the mesoscale segregation of liquid-ordered (lo)-liquid-disordered (ld) domains in an asymmetric membrane bilayer, that incorporates both active contractile stresses at the inner leaflet and transbilayer coupling across the leaflets. The interplay between chemical potential gradients, transbilayer coupling and active stresses drives a rich pattern of mesoscale lo domains - static, strongly fluctuating and moving active emulsions - even at temperatures beyond the equilibrium phase transition temperature. We study conditions under which domain registry and slippage could be observed. We end with a discussion on the role of active flippases on PS in maintaining the active mesoscale organisation.

Cold adaptation of harmful dinoflagellate facilitates their poleward colonization: Insights into extracellular polymeric substances and intracellular bio-macromolecules dynamics through in-situ FTIR imaging

While higher latitudes are becoming relatively warm ecosystem for phytoplankton, the rapid and active adaptation of harmful algal cells to cold conditions also contributes to their poleward colonization, which has scarcely been studied. We examined the adaptive mechanism to cold stress in Gymnodinium catenatum, a eurythermic species that has been recently reported to spread to higher latitudes. Using the in-situ focal plane array Fourier transform infrared spectroscopy (FPA-FTIR) imaging combined with transmission electron microscopy, we demonstrated that this dinoflagellate could adapt to cold stress by establishing two cell barriers: one consisting of the massive extracellular polymeric substances (EPS) that accumulated outside the cell and the other represented by lipid phase separation within the reshaped cellular microenvironment. Two-dimensional correlation (2D-COS) spectroscopy further revealed that intracellular bio-macromolecules (lipids, proteins, and carbohydrates) were organized in an ordered and purposeful manner to resist cold. Transcriptome analysis confirmed the inhibition of nicotinamide adenine dinucleotide (NADH) dehydrogenase and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) involved in protein and carbohydrate metabolism, in cold-treated cells. This study elucidated a flexible adaptation strategy of G. catenatum at the bio-macromolecular level and generally discussed the widespread colonization of harmful microalgae at higher latitudes.

Interpretable Multiscale Convolutional Neural Network for Classification and Feature Visualization of Weak Raman Spectra of Biomolecules at Cell Membranes

Raman spectroscopy in biological applications faces challenges due to complex spectra, characterized by peaks of varying widths and significant biological background noise. Convolutional neural networks (CNNs) are widely used for spectrum classification due to their ability to capture local peak features. In this study, we introduce a multiscale CNN designed to detect weak biomolecule signals and differentiate spectra with features that cannot be statistically distinguished. The approach is further enhanced by a new visualization technique tailored for multiscale spectral analysis, providing clear insights into classification results. Using the classification of cholera toxin B subunit (CTB)-treated versus untreated cell membrane samples, whose spectra cannot be statistically differentiated, the optimized multiscale CNN achieved superior performance compared to traditional machine learning methods and existing multiscale CNNs, with accuracy (99.22%), sensitivity (99.27%), specificity (99.16%), and precision (99.20%). Our new visualization method, based on gradients of activation maps with respect to class scores, generates saliency scores that capture sample variations, with decision-making relying on consistently identified peak features. By visualizing the effects of different kernel sizes, Grad-AM highlights features at varying scales, aligning closely with spectral features and enhancing CNN interpretability in complex biomolecular analysis. These advancements demonstrate the potential of our method to improve spectral analysis and reveal previously hidden peaks in complex biological environments.

Real-time visualization reveals Mycobacterium tuberculosis ESAT-6 disrupts phagosome-like compartment via fibril-mediated vesiculation

Mycobacterium tuberculosis (Mtb) evades host defense by hijacking and rupturing the phagosome. ESAT-6, a secreted virulence protein of Mtb, is known to be critical for phagosome rupture. However, the mechanism of ESAT-6-mediated disruption of the phagosomal membrane remains unknown. Using in vitro reconstitution, live-cell imaging, and numerical simulations, we discover that ESAT-6 polymerization forces remodeling and vesiculation of the phagosome-like compartment both in vitro and in vivo. Shallow insertion of ESAT-6 leads to tubular and bud-like deformations on the membrane facilitated by a reduction in membrane tension. Growing fibrils generate both radial and tangential forces causing local remodeling and shape transition of the membrane into buds. The ESAT-6-bound tensed membrane undergoes local changes in membrane curvature and lipid phase separation that assist the subsequent fission. Overall, the findings provide mechanistic insights into the long-standing question of phagosome disruption by Mtb for its escape.

Phase Separation Clustering of Poly Ubiquitin Cargos on Ternary Mixture Lipid Membranes by Synthetically Cross-Linked Ubiquitin Binder Peptides

Ubiquitylation is involved in various physiological processes, such as signaling and vesicle trafficking, whereas ubiquitin (UB) is considered an important clinical target. The polymeric addition of UB enables cargo molecules to be recognized specifically by multivalent binding interactions with UB-binding proteins, which results in various downstream processes. Recently, protein condensate formation by ubiquitylated proteins has been reported in many independent UB processes, suggesting its potential role in governing the spatial organization of ubiquitylated cargo proteins. We created modular polymeric UB binding motifs and polymeric UB cargos by synthetic bioconjugation and protein purification. Giant unilamellar vesicles with lipid raft composition were prepared to reconstitute the polymeric UB cargo organization on the membranes. Fluorescence imaging was used to observe the outcome. The polymeric UB cargos clustered on the membranes by forming a phase separation codomain during the interaction with the multivalent UB-binding conjugate. This phase separation was valence-dependent and strongly correlated with its potent ability to form protein condensate droplets in solution. Multivalent UB binding interactions exhibited a general trend toward the formation of phase-separated condensates and the resulting condensates were either in a liquid-like or solid-like state depending on the conditions and interactions. This suggests that the polymeric UB cargos on the plasma and endosomal membranes may use codomain phase separation to assist in the clustering of UB cargos on the membranes for cargo sorting. Our findings also indicate that such phase behavior model systems can be created by a modular synthetic approach that can potentially be used to further engineer biomimetic interactions in vitro.

The Importance of Bilayer Asymmetry in Biological Membranes: Insights from Model Membranes

This mini-review intends to highlight the importance of bilayer asymmetry. Biological membranes are complex structures that are a physical barrier separating the external environment from the cellular content. This complex bilayer comprises an extensive lipid repertory, suggesting that the different lipid structures might play a role in the membrane. Interestingly, this vast repertory of lipids is asymmetrically distributed between leaflets that form the lipid bilayer. Here, we discuss the properties of the plasma membrane from the perspective of experimental model membranes, consisting of simplified and controlled in vitro systems. We summarize some crucial features of the exoplasmic (outer) and cytoplasmic (inner) leaflets observed through investigations using symmetric and asymmetric membranes. Symmetric model membranes for the exoplasmic leaflet have a unique lipid composition that might form a coexistence of phases, namely the liquid disordered and liquid order phases. These phase domains may appear in different sizes and shapes depending on lipid composition and lipid-lipid interactions. In contrast, symmetric model membranes for the cytoplasmic leaflet form a fluid phase. We discuss the outcomes reported in the literature for asymmetric bilayers, which vary according to lipid compositions and, consequently, reflect different intra- and inter-leaflet interactions. Interestingly, the asymmetric bilayer could show induced domains in the inner leaflet, or it could decrease the tendency of the outer leaflet to phase separation. If cells regulate the lipid composition of the plasma membrane, they can adjust the existence and sizes of the domains by tuning the lipid composition.

Rapid assessment of the gate function and membrane properties of connexin-embedded giant plasma membrane vesicles in a microwell array

Giant plasma membrane vesicles (GPMVs) incorporating connexin proteins, referred to as connectosomes, serve as promising tools for studying cell membrane properties and intercellular communication. This study aimed to evaluate the membrane capacitance of connectosomes derived from HeLa cells and establish a method for assessing the gate function of connexin hemichannels. We investigated the behavior of dielectrophoresis (DEP) manipulation of connectosomes and HeLa cells by using microwell array electrodes. The frequency dependence of DEP force for connectosomes and HeLa cells suggested a low membrane capacitance of the connectosomes compared to that of HeLa cells. Positive DEP (p-DEP) was used to trap the connectosomes in the microwell array, where a relatively strong electric field was formed. This approach facilitated monitoring of the fluorescence intensity of individual connectosomes immediately after the solutions were exchanged, enhancing our ability to assess the release dynamics of fluorescent molecules and the hemichannel's open/closed states. The results confirmed that connexin hemichannels were regulated by the exterior concentration of Ca2+, allowing selective control over drug storage and release. The method developed in this study elucidates the functional properties of connectosomes and would provide a valuable platform for future applications in targeted drug delivery systems.

Influence of the glycocalyx on the size and mechanical properties of plasma membrane-derived vesicles

Recent studies have reported that the overexpression of MUC1 glycoproteins on cell surfaces changes the morphology of cell plasma membranes and increases the blebbing of vesicles from them, supporting the hypothesis that entropic forces exerted by MUC1 change the spontaneous curvature of cell membranes. However, how MUC1 is incorporated into and influences the size and biophysical properties of plasma-membrane-blebbed vesicles is not understood. Here we report single-vesicle-level characterization of giant plasma membrane vesicles (GPMVs) derived from cells overexpressing MUC1, revealing a 40× variation in MUC1 density between GPMVs from a single preparation and a strong correlation between GPMV size and MUC1 density. By dispersing GPMVs in aqueous liquid crystals (LCs), we show that the elasticity of the LC can be used to strain individual GPMVs into spindle-like shapes, consistent with the straining of fluid-like membranes. To quantify the influence of MUC1 on membrane mechanical properties, we analyze the shapes of strained GPMVs within a theoretical framework that integrates the effects of MUC1 density and GPMV size on strain. We measure the spontaneous curvature of GPMV membranes to be 2-10 μm-1 and weakly influenced by the 40× variation in MUC1 density, a conclusion we validate by performing independent experiments in which MUC1 is enzymatically removed from GPMVs. Overall, our study advances the understanding of heterogeneity in size and MUC1 density in GPMVs, and establishes single-vesicle-level methods for characterization of mechanical properties within a heterogeneous population of GPMVs. Furthermore, our measurements highlight differences between membrane properties of GPMVs and their parent cells.

Lipid Rafts in Signalling, Diseases, and Infections: What Can Be Learned from Fluorescence Techniques?

Lipid rafts are dynamic microdomains in the membrane, rich in cholesterol and sphingolipids, that are critical for biological processes like cell signalling, membrane trafficking, and protein organization. Their essential role is claimed in both physiological and pathological conditions, including cancer, neurodegenerative diseases, and viral infections, making them a key area of research. Fluorescence-based approaches, including super-resolution fluorescence microscopy techniques, enable precise analysis of the organization, dynamics, and interactions of these microdomains, thanks also to the innovative design of appropriate fluorescent probes. Moreover, these non-invasive approaches allow for the study of live cells, facilitating the collection of quantitative data under physiologically relevant conditions. This review synthesizes the latest insights into the role of lipid rafts in biological and pathological processes and underscores how fluorescence techniques have advanced our understanding of these critical microdomains. The findings emphasize the pivotal role of lipid rafts in health and disease, providing a foundation for future research and potential therapeutic interventions.

Ruthenium(II) Lipid-Mimics Drive Lipid Phase Separation to Arouse Autophagy-Ferroptosis Cascade for Photoimmunotherapy

Lipid-mediated phase separation is crucial for the formation of lipophilic spontaneous domain to regulate lipid metabolism and homeostasis, furtherly contributing to multiple cell death pathways. Herein, a series of Ru(II) lipid-mimics based on short chains or midchain lipids are developed. Among them, Ru-LipM with two dodecyl chains significantly induces natural lipid phase separation via hydrocarbon chain-melting phase transitions. Accompanied by the aggregation of Ru-LipM-labeled lipophilic membrane-less compartments, most polyunsaturated lipids are increased and the autophagic flux is retarded with the adaptor protein sequestosome 1 (p62). Upon low-dose irradiation, Ru-LipM further drives ferritinophagy, providing an additional source of labile iron and rendering cells more sensitive to ferroptosis. Meanwhile, the peroxidation of polyunsaturated lipids occurs due to the deactivation of glutathione peroxidase 4 (GPX4) and the overexpression of acyl-CoA synthetase long-chain family member 4 (ACSL4), leading to the immunogenic ferroptosis. Ultimately, both innate and adaptive immunity are invigorated, indicating the tremendous antitumor capability of Ru-LipM in vivo. This study presents an unprecedented discovery of small molecules capable of inducing and monitoring lipid phase separation, thereby eliciting robust immune responses in living cells. It provides a biosimulation strategy for constructing efficient metal-based immune activators.

Enzymatically Polymerized Organic Conductors on Native Lipid Membranes

The dual capability of conductive polymers to conduct ions and electrons, in combination with their flexible mechanical properties, makes them ideal for bioelectronic applications. This study explores the in situ enzymatic polymerization of water-soluble π-conjugated monomers on native lipid bilayers derived from the F11 cell line, mimicking mammalian neural membranes. Enzymatic polymerization was catalyzed using horseradish peroxidase (HRP) in the presence of oxidant hydrogen peroxide (H2O2) and monitored via electrochemical quartz crystal microbalance with dissipation (EQCM-D) and electrochemical impedance spectroscopy (EIS). Results showed polymerization with HRP. The structural properties of the formed polymer films were characterized ex situ using atomic force microscopy (AFM), while the quality of the F11 native lipid vesicles and bilayer was respectively assessed through dynamic light scattering (DLS) and fluorescence recovery after photobleaching (FRAP) techniques. This work demonstrates, for the first time, the feasibility of the in situ formation of conductive polymers on native lipid membranes, offering a promising approach for the development of minimally invasive neural electrodes to diagnose and treat neurological disorders.

Flotillin-2 dampens T cell antigen sensitivity and functionality

T cell receptor (TCR) engagement triggers T cell responses, yet how TCR-mediated activation is regulated at the plasma membrane remains unclear. Here, we report that deleting the membrane scaffolding protein Flotillin-2 (Flot2) increases T cell antigen sensitivity, resulting in enhanced TCR signaling and effector function in response to weak TCR stimulation. T cell-specific Flot2-deficient mice exhibited reduced tumor growth and enhanced immunity to infection. Flot2-null CD4+ T cells exhibited increased Th1 polarization, proliferation, Nur77 induction, and phosphorylation of ZAP70 and ERK1/2 upon weak TCR stimulation, indicating a sensitized TCR-triggering threshold. Single-cell RNA-Seq suggested that Flot2-null CD4+ T cells follow a similar route of activation as WT CD4+ T cells but exhibit higher occupancy of a discrete activation state under weak TCR stimulation. Given prior reports that TCR clustering influences sensitivity of T cells to stimuli, we evaluated TCR distribution with super-resolution microscopy. Flot2 ablation increased the number of surface TCR nanoclusters on naive CD4+ T cells. Collectively, we posit that Flot2 modulates T cell functionality to weak TCR stimulation, at least in part, by regulating surface TCR clustering. Our findings have implications for improving T cell reactivity in diseases with poor antigenicity, such as cancer and chronic infections.

Membrane lipid nanodomains modulate HCN pacemaker channels in nociceptor DRG neurons

Cell membranes consist of heterogeneous lipid nanodomains that influence key cellular processes. Using FRET-based fluorescent assays and fluorescence lifetime imaging microscopy (FLIM), we find that the dimension of cholesterol-enriched ordered membrane domains (OMD) varies considerably, depending on specific cell types. Particularly, nociceptor dorsal root ganglion (DRG) neurons exhibit large OMDs. Disruption of OMDs potentiated action potential firing in nociceptor DRG neurons and facilitated the opening of native hyperpolarization-activated cyclic nucleotide-gated (HCN) pacemaker channels. This increased neuronal firing is partially due to an increased open probability and altered gating kinetics of HCN channels. The gating effect on HCN channels is likely due to a direct modulation of their voltage sensors by OMDs. In animal models of neuropathic pain, we observe reduced OMD size and a loss of HCN channel localization within OMDs. Additionally, cholesterol supplementation inhibited HCN channels and reduced neuronal hyperexcitability in pain models. These findings suggest that disturbances in lipid nanodomains play a critical role in regulating HCN channels within nociceptor DRG neurons, influencing pain modulation.

Establishment of the Meyer-Overton correlation in an artificial membrane without protein

BACKGROUND

The potency of anesthetics with various structures increases exponentially with lipophilicity, which is the Meyer-Overton (MO) correlation discovered over 120 years ago. The MO correlation was also observed with various biological effects and chemicals, including alcohols; thus, the correlation represents a fundamental relationship between chemicals and organisms. The MO correlation was explained by the lipid and protein theories, although the principle remains unknown because these are still debating.

METHODS

The gentle hydration method was used to form giant unilamellar vesicles (GUVs) consisting of high- and low-melting phospholipids and cholesterol in the presence of n-alcohols (C2-C12). Confocal fluorescence microscopy was used to determine the percentage of GUVs with domains in relation to the n-alcohol concentrations.

RESULTS

n-Alcohols inhibited the domain formation of GUVs, and the half inhibitory concentration (IC50) in the aqueous phase (Cw) decreased exponentially with increasing chain length (lipophilicity). In contrast, the membrane concentrations (Cm) of alcohols for the inhibition, which is a product of the membrane-water partition coefficient and the IC50 values, remained constant irrespective of the chain length.

CONCLUSIONS

The MO correlation is established in GUVs, which supports the lipid theory. When alcohols reach the same critical concentration in the membrane, similar biological effects appear irrespective of the chain length, which is the principle underlying the MO correlation.

GENERAL SIGNIFICANCE

The protein theory states that a highly lipophilic compound targets minor membrane proteins due to the low Cw. However, our lipid theory states that the compound targets various membrane proteins due to the high Cm.

Cellular Output and Physicochemical Properties of the Membrane-Derived Vesicles Depend on Chemical Stimulants

Synthetic liposomes are widely used as drug delivery vehicles in biomedical treatments, such as for mRNA-based antiviral vaccines like those recently developed against SARS-CoV-2. Extracellular vesicles (EVs), which are naturally produced by cells, have emerged as a next-generation delivery system. However, key questions regarding their origin within cells remain unresolved. In this regard, plasma membrane vesicles (PMVs), which are essentially produced from the cellular plasma membrane (PM), present a promising alternative. Unfortunately, their properties relevant to biomedical applications have not be extensively studied. Therefore, we conducted a thorough investigation of the methods used in the production of PMVs. By leveraging advanced fluorescence techniques in microscopy and flow cytometry, we demonstrated a strong dependence of the physicochemical attributes of PMVs on the chemicals used during their production. Following established protocols employing chemicals such as paraformaldehyde (PFA), N-ethylmaleimide (NEM) or dl-dithiothreitol (DTT) and by developing a modified NEM-based method that involved a hypotonic shock step, we generated PMVs from THP-1 CD1d cells. We systematically compared key parameters such as vesicle output, their size distribution, vesicular content analysis, vesicular membrane lipid organization and the mobility of a transmembrane protein. Our results revealed distinct trends: PMVs isolated using NEM-based protocols closely resembled natural vesicles, whereas PFA induced significant molecular cross-linking, leading to notable changes in the biophysical properties of the vesicles. Furthermore, our novel NEM protocol enhanced the efficiency of PMV production. In conclusion, our study highlights the unique characteristics of chemically produced PMVs and offers insights into their potentially diverse yet valuable biological functions.

Cancer cell stiffening via CoQ10 and UBIAD1 regulates ECM signaling and ferroptosis in breast cancer

CoQ10 (Coenzyme Q10) is an essential fat-soluble metabolite that plays a key role in cellular metabolism. A less-known function of CoQ10 is whether it may act as a plasma membrane-stabilizing agent and whether this property can affect cancer development and progression. Here, we show that CoQ10 and its biosynthetic enzyme UBIAD1 play a critical role in plasmamembrane mechanical properties that are of interest for breast cancer (BC) progression and treatment. CoQ10 and UBIAD1 increase membrane fluidity leading to increased cell stiffness in BC. Furthermore, CoQ10 and UBIAD1 states impair ECM (extracellular matrix)-mediated oncogenic signaling and reduce ferroptosis resistance in BC settings. Analyses on human patients and mouse models reveal that UBIAD1 loss is associated with BC development and progression and UBIAD1 expression in BC limits CTCs (circulating tumor cells) survival and lung metastasis formation. Overall, this study reveals that CoQ10 and UBIAD1 can be further investigated to develop therapeutic interventions to treat BC patients with poor prognosis.

Probing Gag-Env dynamics at HIV-1 assembly sites using live-cell microscopy

Human immunodeficiency virus (HIV)-1 assembly is initiated by Gag binding to the inner leaflet of the plasma membrane (PM). Gag targeting is mediated by its N-terminally myristoylated matrix (MA) domain and PM phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]. Upon Gag assembly, envelope (Env) glycoproteins are recruited to assembly sites; this process depends on the MA domain of Gag and the Env cytoplasmic tail. To investigate the dynamics of Env recruitment, we applied a chemical dimerizer system to manipulate HIV-1 assembly by reversible PI(4,5)P2 depletion in combination with super resolution and live-cell microscopy. This approach enabled us to control and synchronize HIV-1 assembly and track Env recruitment to individual nascent assembly sites in real time. Single virion tracking revealed that Gag and Env are accumulating at HIV-1 assembly sites with similar kinetics. PI(4,5)P2 depletion prevented Gag PM targeting and Env cluster formation, confirming Gag dependence of Env recruitment. In cells displaying pre-assembled Gag lattices, PI(4,5)P2 depletion resulted in the disintegration of the complete assembly domain, as not only Gag but also Env clusters were rapidly lost from the PM. These results argue for the existence of a Gag-induced and -maintained membrane micro-environment, which attracts Env. Gag cluster dissociation by PI(4,5)P2 depletion apparently disrupts this micro-environment, resulting in the loss of Env from the former assembly domain.IMPORTANCEHuman immunodeficiency virus (HIV)-1 assembles at the plasma membrane of infected cells, resulting in the budding of membrane-enveloped virions. HIV-1 assembly is a complex process initiated by the main structural protein of HIV-1, Gag. Interestingly, HIV-1 incorporates only a few envelope (Env) glycoproteins into budding virions, although large Env accumulations surrounding nascent Gag assemblies are detected at the plasma membrane of HIV-expressing cells. The matrix domain of Gag and the Env cytoplasmatic tail play a role in Env recruitment to HIV-1 assembly sites and its incorporation into nascent virions. However, the regulation of these processes is incompletely understood. By combining a chemical dimerizer system to manipulate HIV-1 assembly with super resolution and live-cell microscopy, our study provides new insights into the interplay between Gag, Env, and host cell membranes during viral assembly and into Env incorporation into HIV-1 virions.

Lipid-driven interleaflet coupling of plasma membrane order regulates FcεRI signaling in mast cells

Interleaflet coupling-the influence of one leaflet on the properties of the opposing leaflet-is a fundamental plasma membrane organizational principle. This coupling is proposed to participate in maintaining steady-state biophysical properties of the plasma membrane, which in turn regulates some transmembrane signaling processes. A prominent example is antigen (Ag) stimulation of signaling by clustering transmembrane receptors for immunoglobulin E (IgE), FcεRI. This transmembrane signaling depends on the stabilization of ordered regions in the inner leaflet for sorting of intracellular signaling components. The resting inner leaflet has a lipid composition that is generally less ordered than the outer leaflet and that does not spontaneously phase separate in model membranes. We propose that interleaflet coupling can mediate ordering and disordering of the inner leaflet, which is poised in resting cells to reorganize upon stimulation. To test this in live cells, we first established a straightforward approach to evaluate induced changes in membrane order by measuring inner leaflet diffusion of lipid probes by imaging fluorescence correlation spectroscopy, by imaging fluorescence correlation spectroscopy (ImFCS), before and after methyl-α-cyclodexrin (mαCD)-catalyzed exchange of outer leaflet lipids (LEX) with exogenous order- or disorder-promoting phospholipids. We examined the functional impact of LEX by monitoring two Ag-stimulated responses: recruitment of cytoplasmic Syk kinase to the inner leaflet and exocytosis of secretory granules (degranulation). Based on the ImFCS data in resting cells, we observed global increase or decrease of inner leaflet order when outer leaflet is exchanged with order- or disorder-promoting lipids, respectively. We find that the degree of both stimulated Syk recruitment and degranulation correlates positively with LEX-mediated changes of inner leaflet order in resting cells. Overall, our results show that resting-state lipid ordering of the outer leaflet influences the ordering of the inner leaflet, likely via interleaflet coupling. This imposed lipid reorganization modulates transmembrane signaling stimulated by Ag clustering of IgE-FcεRI.

Endoplasmic reticulum: Monitoring and maintaining protein and membrane homeostasis in the endoplasmic reticulum by the unfolded protein response

The endoplasmic reticulum (ER) regulates essential cellular processes, including protein folding, lipid synthesis, and calcium homeostasis. The ER homeostasis is maintained by a conserved set of signaling cascades called the Unfolded Protein Response (UPR). How the UPR senses perturbations in ER homeostasis has been the subject of active research for decades. In metazoans, the UPR consists of three ER-membrane embedded sensors: IRE1, PERK and ATF6. These sensors detect the accumulation of misfolded proteins in the ER lumen and adjust protein folding capacity according to cellular needs. Early work revealed that the ER-resident chaperone BiP binds to all three UPR sensors in higher eukaryotes and BiP binding was suggested to regulate their activity. More recent data have shown that in higher eukaryotes the interaction of the UPR sensors with a complex network of chaperones and misfolded proteins modulates their activation and deactivation dynamics. Furthermore, emerging evidence suggests that the UPR monitors ER membrane integrity beyond protein folding defects. However, the mechanistic and structural basis of UPR activation by proteotoxic and lipid bilayer stress in higher eukaryotes remains only partially understood. Here, we review the current understanding of novel protein interaction networks and the contribution of the lipid membrane environment to UPR activation.

Transmembrane signaling through single-spanning receptors modulated by phase separation at the cell surface

A wide variety of transmembrane signals are transduced by cell-surface receptors that activate intracellular signaling molecules. In particular, receptor clustering in the plasma membrane plays a critical role in these processes. Single-spanning or single-pass transmembrane proteins are among the most significant types of membrane receptors, which include adhesion receptors, such as integrins, CD44, cadherins, and receptor tyrosine kinases. Elucidating the molecular mechanisms underlying the regulation of the activity of these receptors is of great significance. Liquid-liquid phase separation (LLPS) is a recently emerging paradigm in cellular physiology for the ubiquitous regulation of the spatiotemporal dynamics of various signaling pathways. This study describes the emerging features of transmembrane signaling through single-spanning receptors from the perspective of phase separation. Possible physicochemical modulations of LLPS-based transmembrane signaling are also discussed.

CaV1.3 channel clusters characterized by live-cell and isolated plasma membrane nanoscopy

A key player of excitable cells in the heart and brain is the L-type calcium channel CaV1.3. In the heart, it is required for voltage-dependent Ca2+-signaling, i.e., for controlling and modulating atrial cardiomyocyte excitation-contraction coupling. The clustering of CaV1.3 in functionally relevant channel multimers has not been addressed due to a lack of stoichiometric labeling combined with high-resolution imaging. Here, we developed a HaloTag-labeling strategy to visualize and quantify CaV1.3 clusters using STED nanoscopy to address the questions of cluster size and intra-cluster channel density. Channel clusters were identified in the plasma membrane of transfected live HEK293 cells as well as in giant plasma membrane vesicles derived from these cells that were spread on modified glass support to obtain supported plasma membrane bilayers (SPMBs). A small fraction of the channel clusters was colocalized with early and recycling endosomes at the membranes. STED nanoscopy in conjunction with live-cell and SPMB imaging enabled us to quantify CaV1.3 cluster sizes and their molecular density revealing significantly lower channel densities than expected for dense channel packing. CaV1.3 channel cluster size and molecular density were increased in SPMBs after treatment of the cells with the sympathomimetic compound isoprenaline, suggesting a regulated channel cluster condensation mechanism.

A combined lipidomic and proteomic profiling of Arabidopsis thaliana plasma membrane

The plant plasma membrane (PM) plays a key role in perception of environmental signals, and set-up of adaptive responses. An exhaustive and quantitative description of the whole set of lipids and proteins constituting the PM is necessary to understand how these components allow to fulfill such essential physiological functions. Here we provide by state-of-the-art approaches the first combined reference of the plant PM lipidome and proteome from Arabidopsis thaliana suspension cell culture. We identified and quantified a reproducible core set of 2165 proteins, which is by far the largest set of available data concerning this plant PM proteome. Using the same samples, combined lipidomic approaches, allowing the identification and quantification of an unprecedented repertoire of 414 molecular species of lipids showed that sterols, phospholipids, and sphingolipids are present in similar proportions in the plant PM. Within each lipid class, the precise amount of each lipid family and the relative proportion of each molecular species were further determined, allowing to establish the complete lipidome of Arabidopsis PM, and highlighting specific characteristics of the different molecular species of lipids. Results obtained point to a finely tuned adjustment of the molecular characteristics of lipids and proteins. More than a hundred proteins related to lipid metabolism, transport, or signaling have been identified and put in perspective of the lipids with which they are associated. This set of data represents an innovative resource to guide further research relative to the organization and functions of the plant PM.

Shear-Induced Nonequilibrium Patterns in Lipid Bilayer Membranes Exhibiting Phase Separation

The nonequilibrium dynamics of a fluid lipid membrane under external stimuli is an important issue that spans disciplines such as soft matter, biophysical chemistry, and interface science. This study investigated the dynamic response of lipid vesicles with order-disorder phase separation, which mimics a plasma membrane heterogeneity, to shear flow. Lipid vesicles were immobilized in a microfluidic chamber, and shear-induced nonequilibrium patterns on the membrane surface were observed by an optical microscope. We found that phase-separated membranes exhibit a dissipative structure of stripe patterns along the vortex flow on the membrane surface, and the number of stripes increased with the flow rate. At a high flow rate, the membrane exhibited a stripe-to-wave transition, where striped domains often migrated and the replacement of two different phases happened at vortex centers with time. We obtained a dynamic phase diagram of the shear-induced wave pattern by changing the flow rate, membrane components, and temperature. These findings could provide insight into the dissipative structures of lipid membranes out of equilibrium and flow-mediated mechanotransduction of biological membranes.

Flotillin-2 dampens T cell antigen-sensitivity and functionality

T cell receptor (TCR) engagement triggers T cell responses, yet how TCR-mediated activation is regulated at the plasma membrane remains unclear. Here, we report that deleting the membrane scaffolding protein Flotillin-2 (Flot2) increases T cell antigen sensitivity, resulting in enhanced TCR signaling and effector function to weak TCR stimulation. T cell-specific Flot2-deficient mice exhibited reduced tumor growth and enhanced immunity to infection. Flot2-null CD4 + T cells exhibited increased T helper 1 polarization, proliferation, Nur77 induction, and phosphorylation of ZAP70 and LCK upon weak TCR stimulation, indicating a sensitized TCR-triggering threshold. Single cell-RNA sequencing suggested that Flot2 - null CD4 + T cells follow a similar route of activation as wild-type CD4 + T cells but exhibit higher occupancy of a discrete activation state under weak TCR stimulation. Given prior reports that TCR clustering influences sensitivity of T cells to stimuli, we evaluated TCR distribution with super-resolution microscopy. Flot2 ablation increased the number of surface TCR nanoclusters on naïve CD4 + T cells. Collectively, we posit that Flot2 modulates T cell functionality to weak TCR stimulation, at least in part, by regulating surface TCR clustering. Our findings have implications for improving T cell reactivity in diseases with poor antigenicity, such as cancer and chronic infections.

Characterization of domain formation in complex membranes

A widely known property of lipid membranes is their tendency to undergo a separation into disordered (Ld) and ordered (Lo) domains. This impacts the local structure of the membrane relevant for the physical (e.g., enhanced electroporation) and biological (e.g., protein sorting) significance of these regions. The increase in computing power, advancements in simulation software, and more detailed information about the composition of biological membranes shifts the study of these domains into the focus of classical molecular dynamics simulations. In this chapter, we present a versatile yet robust analysis pipeline that can be easily implemented and adapted for a wide range of lipid compositions. It employs Gaussian-based Hidden Markov Models to predict the hidden order states of individual lipids by describing their structure through the area per lipid and the average SCC order parameters per acyl chain. Regions of the membrane with a high correlation between ordered lipids are identified by employing the Getis-Ord local spatial autocorrelation statistic on a Voronoi tessellation of the lipids. As an example, the approach is applied to two distinct systems at a coarse-grained resolution, demonstrating either a strong tendency towards phase separation (1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (DIPC), cholesterol) or a weak tendency toward phase separation (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PUPC), cholesterol). Explanations of the steps are complemented by coding examples written in Python, providing both a comprehensive understanding and practical guidance for a seamless integration of the workflow into individual projects.

Cell Line and Media Composition Influence the Production of Giant Plasma Membrane Vesicles

Giant plasma membrane vesicles (GPMVs) have been utilized as a model to study phase separation in the plasma membrane. Additionally, GPMVs have been employed as vehicle for delivering molecular cargo, including small molecule drugs and nanoparticles. Nearly all examples of GPMV production use a defined salt buffer that is a stark contrast to typical cell culture medium. In this study, we demonstrate that the addition of formaldehyde and dithiothreitol to a standard culture medium was capable of generating GPMVs at a concentration equal to or higher than the traditional production buffer. These methods were evaluated for two human cell lines: kidney endothelial and Schwann cells (SCs). Morphological properties of the resultant GPMVs exhibited no significant differences between the two formulations. Factors such as pH and seeding density significantly influenced the production of GPMVs in both mediums. The cell type and seeding density was shown to influence the number of GPMVs to the greatest extent. SCs yield more GPMVs at higher seeding densities compared to endothelial cells. Stability of the membrane of the GPMVs produced in both mediums was evaluated by monitoring passive diffusion of two fluorescently tagged dextrans (3 and 10 kDa). Regardless of the production formulation or cell type, approximately 85% GPMVs are impermeable to either dextran. Cold storage for on-demand use and shipping are essential for broader use of GPMVs. Toward this aim, we have evaluated the GMPV number and morphologies following storage at -80 °C and in liquid nitrogen. A significant loss of the GPMV number, ∼30%, was observed following storage across production formulations as well as cell types. Our results indicate that smaller GMPVs, <5 μm are more stable for preservation. In conclusion, GPMVs can be produced in a broad range of formulations, exhibit a high degree of stability, and can undergo cold storage for further adoption.

Effects of grafted polymers on the lipid membrane fluidity

Since the membrane fluidity controls the cellular functions, it is important to identify the factors that determine the cell membrane viscosity. Cell membranes are composed of not only lipids and proteins but also polysaccharide chain-anchored molecules, such as glycolipids. To reveal the effects of grafted polymers on the membrane fluidity, in this study, we measured the membrane viscosity of polymer-grafted giant unilamellar vesicles (GUVs), which were prepared by introducing the poly (ethylene glycol) (PEG)-anchored lipids to the ternary GUVs composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and cholesterol. The membrane viscosity was obtained from the velocity field on the GUV generated by applying a point force, based on the hydrodynamic model proposed by Henle and Levine. The velocity field was visualized by a motion of the circular liquid ordered (Lo) domains formed by a phase separation. With increasing PEG density, the membrane viscosity of PEG-grafted GUVs increased gradually in the mushroom region and significantly in the brush region. We propose a hydrodynamic model that includes the excluded volume effect of PEG chains to explain the increase in membrane viscosity in the mushroom region. This work provides a basic understanding of how grafted polymers affect the membrane fluidity.

Curcumin Modulates the Membrane Raft Integrity via Phase Separation and Induces CD44 Shedding in Tumor Cells

CD44 is a transmembrane cell adhesion molecule that is cleaved by the membrane proteinase, a disintegrin and metalloproteinase 10 (ADAM10), on the cell surface via ectodomain shedding after cholesterol depletion. Lipid raft-mediated CD44 shedding is essential for cancer cell invasion. As cell-cell and cell-matrix adhesions are critical for cancer progression, lipid raft-targeting agents may be effective for cancer therapy. Here, we found that curcumin and its derivatives induced the ADAM10-mediated shedding of CD44 in tumor cells. We also found that curcumin and the derivatives are membrane-active compounds whose effect depends on its planar backbone and the spatial arrangement of methoxy groups substituted on the two aromatic rings using giant unilamellar and plasma membrane vesicles. Curcumin and its derivatives with rigid backbones and hydroxy groups exerted membrane-domain-modulating activity, which may account for their pleiotropic effects via multiple signaling pathways involving membrane receptors. This study provides a basis for the use of membrane-active compounds, such as curcuminoids, to elucidate the roles of lipid rafts in cellular signaling, regulation of membrane-bound ADAM metalloproteinases, and the development of novel membrane lipid-based therapies.

Lipid Peroxidation Drives Liquid-Liquid Phase Separation and Disrupts Raft Protein Partitioning in Biological Membranes

The peroxidation of membrane lipids by free radicals contributes to aging, numerous diseases, and ferroptosis, an iron-dependent form of cell death. Peroxidation changes the structure and physicochemical properties of lipids, leading to bilayer thinning, altered fluidity, and increased permeability of membranes in model systems. Whether and how lipid peroxidation impacts the lateral organization of proteins and lipids in biological membranes, however, remains poorly understood. Here, we employ cell-derived giant plasma membrane vesicles (GPMVs) as a model to investigate the impact of lipid peroxidation on ordered membrane domains, often termed membrane rafts. We show that lipid peroxidation induced by the Fenton reaction dramatically enhances the phase separation propensity of GPMVs into coexisting liquid-ordered (Lo) and liquid-disordered (Ld) domains and increases the relative abundance of the disordered phase. Peroxidation also leads to preferential accumulation of peroxidized lipids and 4-hydroxynonenal (4-HNE) adducts in the disordered phase, decreased lipid packing in both Lo and Ld domains, and translocation of multiple classes of raft proteins out of ordered domains. These findings indicate that the peroxidation of plasma membrane lipids disturbs many aspects of membrane rafts, including their stability, abundance, packing, and protein and lipid composition. We propose that these disruptions contribute to the pathological consequences of lipid peroxidation during aging and disease and thus serve as potential targets for therapeutic intervention.

Multispherical shapes of vesicles with intramembrane domains

Phase separation of biomembranes into two fluid phases, a and b, leads to the formation of vesicles with intramembrane a- and b-domains. These vesicles can attain multispherical shapes consisting of several spheres connected by closed membrane necks. Here, we study the morphological complexity of these multispheres using the theory of curvature elasticity. Vesicles with two domains form two-sphere shapes, consisting of one a- and one b-sphere, connected by a closed ab-neck. The necks' effective mean curvature is used to distinguish positive from negative necks. Two-sphere shapes of two-domain vesicles can attain four different morphologies that are governed by two different stability conditions. The closed ab-necks are compressed by constriction forces which induce neck fission and vesicle division for large line tensions and/or large spontaneous curvatures. Multispherical shapes with one ab-neck and additional aa- and bb-necks involve several stability conditions, which act to reduce the stability regimes of the multispheres. Furthermore, vesicles with more than two domains form multispheres with more than one ab-neck. The multispherical shapes described here represent generalized constant-mean-curvature surfaces with up to four constant mean curvatures. These shapes are accessible to experimental studies using available methods for giant vesicles prepared from ternary lipid mixtures.

Experimentally determined leaflet-leaflet phase diagram of an asymmetric lipid bilayer

We have determined the partial leaflet-leaflet phase diagram of an asymmetric lipid bilayer at ambient temperature using asymmetric giant unilamellar vesicles (aGUVs). Symmetric GUVs with varying amounts of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine and DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) were hemifused to a supported lipid bilayer (SLB) composed of DOPC, resulting in lipid exchange between their outer leaflets. The GUVs and SLB contained a red and green lipid fluorophore, respectively, thus enabling the use of confocal fluorescence imaging to determine both the extent of lipid exchange (quantified for individual vesicles by the loss of red intensity and gain of green intensity) and the presence or absence of phase separation in aGUVs. Consistent with previous reports, we found that hemifusion results in large variation in outer leaflet exchange for individual GUVs, which allowed us to interrogate the phase behavior at multiple points within the asymmetric composition space of the binary mixture. When initially symmetric GUVs showed coexisting gel and fluid domains, aGUVs with less than ~50% outer leaflet exchange were also phase-separated. In contrast, aGUVs with greater than 50% outer leaflet exchange were uniform and fluid. In some cases, we also observed three coexisting bilayer-spanning phases: two registered phases and an anti-registered phase. These results suggest that a relatively large unfavorable midplane interaction between ordered and disordered phases in opposing leaflets (i.e., a midplane surface tension) can overwhelm the driving force for lateral phase separation within one of the leaflets, resulting in an asymmetric bilayer with two uniformly mixed leaflets that is poised to phase-separate upon leaflet scrambling.

Quantitative image mean squared displacement (iMSD) analysis of the dynamics of Aquaporin 2 within the membrane of live cells

Nanodomains are a biological membrane phenomenon which have a large impact on various cellular processes. They are often analysed by looking at the lateral dynamics of membrane lipids or proteins. The localization of the plasma membrane protein aquaporin-2 in nanodomains has so far been unknown. In this study, we use total internal reflection fluorescence microscopy to image Madin-Darby Canine Kidney (MDCK) cells expressing aquaporin-2 tagged with mEos 3.2. Then, image mean squared displacement (iMSD) approach was used to analyse the diffusion of aquaporin-2, revealing that aquaporin-2 is confined within membrane nanodomains. Using iMSD analysis, we found that the addition of the drug forskolin increases the diffusion of aquaporin-2 within the confined domains, which is in line with previous studies. Finally, we observed an increase in the size of the membrane domains and the extent of trapping of aquaporin-2 after stimulation with forskolin.

The Membrane Phase Transition Gives Rise to Responsive Plasma Membrane Structure and Function

Several groups have recently reported evidence for the emergence of domains in cell plasma membranes when membrane proteins are organized by ligand binding or assembly of membrane proximal scaffolds. These domains recruit and retain components that favor the liquid-ordered phase, adding to a decades-old literature interrogating the contribution of membrane phase separation in plasma membrane organization and function. Here we propose that both past and present observations are consistent with a model in which membranes have a high compositional susceptibility, arising from their thermodynamic state in a single phase that is close to a miscibility phase transition. This rigorous framework naturally allows for both transient structure in the form of composition fluctuations and long-lived structure in the form of induced domains. In this way, the biological tuning of plasma membrane composition enables a responsive compositional landscape that facilitates and augments cellular biochemistry vital to plasma membrane functions.

A Survey of Models of Cell Membranes: Toward a New Understanding of Membrane Organization

The cell membrane, the boundary that separates living cells from their environment, has been the subject of study for over a century. The fluid-mosaic model of Singer and Nicolson in 1972 proposed the plasma membrane as a two-dimensional fluid composed of lipids and proteins. Fifty years hence, advances in biophysical and biochemical tools, particularly optical imaging techniques, have allowed for a better understanding of the physical nature, organization, and composition of cell membranes. This has been made possible by visualizing membrane heterogeneities and their dynamics and appreciating the asymmetrical arrangement of lipids in living cell membranes. Despite these advances, mechanisms underlying the local spatiotemporal organization of membrane components remain unclear. This review surveys various models of membrane organization, culminating in a new model that incorporates nonequilibrium processes and forces exerted by interactions with extramembrane elements such as the actin cytoskeleton. The proposed model provides a comprehensive understanding of membrane organization, taking into account the dynamic nature of the cell membrane and its interactions with its immediate environment.

Lipid peroxidation drives liquid-liquid phase separation and disrupts raft protein partitioning in biological membranes

The peroxidation of membrane lipids by free radicals contributes to aging, numerous diseases, and ferroptosis, an iron-dependent form of cell death. Peroxidation changes the structure, conformation and physicochemical properties of lipids, leading to major membrane alterations including bilayer thinning, altered fluidity, and increased permeability. Whether and how lipid peroxidation impacts the lateral organization of proteins and lipids in biological membranes, however, remains poorly understood. Here, we employ cell-derived giant plasma membrane vesicles (GPMVs) as a model to investigate the impact of lipid peroxidation on ordered membrane domains, often termed membrane rafts. We show that lipid peroxidation induced by the Fenton reaction dramatically enhances phase separation propensity of GPMVs into co-existing liquid ordered (raft) and liquid disordered (non-raft) domains and increases the relative abundance of the disordered, non-raft phase. Peroxidation also leads to preferential accumulation of peroxidized lipids and 4-hydroxynonenal (4-HNE) adducts in the disordered phase, decreased lipid packing in both raft and non-raft domains, and translocation of multiple classes of proteins out of rafts. These findings indicate that peroxidation of plasma membrane lipids disturbs many aspects of membrane rafts, including their stability, abundance, packing, and protein and lipid composition. We propose that these disruptions contribute to the pathological consequences of lipid peroxidation during aging and disease, and thus serve as potential targets for therapeutic intervention.

The plasma membrane of focal adhesions has a high content of cholesterol and phosphatidylcholine with saturated acyl chains

Cellular functions, such as differentiation and migration, are regulated by the extracellular microenvironment, including the extracellular matrix (ECM). Cells adhere to ECM through focal adhesions (FAs) and sense the surrounding microenvironments. Although FA proteins have been actively investigated, little is known about the lipids in the plasma membrane at FAs. In this study, we examine the lipid composition at FAs with imaging and biochemical approaches. Using the cholesterol-specific probe D4 with total internal reflection fluorescence microscopy and super-resolution microscopy, we show an enrichment of cholesterol at FAs simultaneously with FA assembly. Furthermore, we establish a method to isolate the lipid from FA-rich fractions, and biochemical quantification of the lipids reveals that there is a higher content of cholesterol and phosphatidylcholine with saturated fatty acid chains in the lipids of the FA-rich fraction than in either the plasma membrane fraction or the whole-cell membrane. These results demonstrate that plasma membrane at FAs has a locally distinct lipid composition compared to the bulk plasma membrane.

Membrane free-energy landscapes derived from atomistic dynamics explain nonuniversal cholesterol-induced stiffening

All lipid membranes have inherent morphological preferences and resist deformation. Yet adaptations in membrane shape can and do occur at multiple length scales. While this plasticity is crucial for cellular physiology, the factors controlling the morphological energetics of lipid bilayers and the dominant mechanisms of membrane remodeling remain to be fully understood. An ongoing debate regarding the universality of the stiffening effect of cholesterol underscores the challenges facing this field, both experimentally and theoretically, even for simple lipid mixtures. On the computational side, we have argued that enhanced-sampling all-atom molecular dynamics simulations are uniquely suited for the quantification of membrane conformational energetics, as they minimize a priori assumptions and permit analysis of bilayers in deformed states. To showcase this approach, we examine reported inconsistencies between alternative experimental measurements of bending moduli for cholesterol-enriched membranes. Specifically, we analyze lipid bilayers with different chain saturation and compute free-energy landscapes for curvature deformations distributed over areas from ∼5 to ∼60 nm2 . These enhanced simulations, totaling over 100 μs of sampling time, enable us to directly quantify both bending and tilt moduli and to dissect the contributing factors and molecular mechanisms of curvature generation at each length scale. Our results show that the effects of cholesterol on bending rigidity are lipid-specific and suggest that this specificity arises from differences in the torsional dynamics of the acyl chains. In summary, we demonstrate that quantitative relationships can now be established between lipid structure and bending energetics, paving the way for addressing open fundamental questions in cell membrane mechanics.

Lipid packing in biological membranes governs protein localization and membrane permeability

Plasma membrane (PM) heterogeneity has long been implicated in various cellular functions. However, mechanistic principles governing functional regulations of lipid environment are not well understood due to the inherent complexities associated with the relevant length and timescales that limit both direct experimental measurements and their interpretation. In this context, computer simulations hold immense potential to investigate molecular-level interactions and mechanisms that lead to PM heterogeneity and its functions. Herein, we investigate spatial and dynamic heterogeneity in model membranes with coexisting liquid ordered and liquid disordered phases and characterize the membrane order in terms of the local topological changes in lipid environment using the nonaffine deformation framework. Furthermore, we probe the packing defects in these membranes, which can be considered as the conjugate of membrane order assessed in terms of the nonaffine parameter. In doing so, we formalize the connection between membrane packing and local membrane order and use that to explore the mechanistic principles behind their functions. Our observations suggest that heterogeneity in mixed phase membranes is a consequence of local lipid topology and its temporal evolution, which give rise to disparate lipid packing in ordered and disordered domains. This in turn governs the distinct nature of packing defects in these domains that can play a crucial role in preferential localization of proteins in mixed phase membranes. Furthermore, we observe that lipid packing also leads to contrasting distribution of free volume in the membrane core region in ordered and disordered membranes, which can lead to distinctive membrane permeability of small molecules. Our results, thus, indicate that heterogeneity in mixed phase membranes closely governs the membrane functions that may emerge from packing-related basic design principles.

Designing a green-emitting viscosity-sensitive 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) probe for plasma membrane viscosity imaging

Viscosity is a key characteristic of lipid membranes - it governs the passive diffusion of solutes and affects the lipid raft formation and membrane fluidity. Precise determination of viscosity values in biological systems is of great interest and viscosity-sensitive fluorescent probes offer a convenient solution for this task. In this work we present a novel membrane-targeting and water-soluble viscosity probe BODIPY-PM, which is based on one of the most frequently used probes BODIPY-C10. Despite its regular use, BODIPY-C10 suffers from poor integration into liquid-ordered lipid phases and lack of water solubility. Here, we investigate the photophysical characteristics of BODIPY-PM and demonstrate that solvent polarity only slightly affects the viscosity-sensing qualities of BODIPY-PM. In addition, with fluorescence lifetime imaging microscopy (FLIM), we imaged microviscosity in complex biological systems - large unilamellar vesicles (LUVs), tethered bilayer membranes (tBLMs) and live lung cancer cells. Our study showcases that BODIPY-PM preferentially stains the plasma membranes of live cells, equally well partitions into both liquid-ordered and liquid-disordered phases and reliably distinguishes lipid phase separation in tBLMs and LUVs.

A Photoswitchable Solvatochromic Dye for Probing Membrane Ordering by RESOLFT Super-resolution Microscopy

A switchable solvatochromic fluorescent dyad can be used to map ordering of lipids in vesicle membranes at a resolution better than the diffraction limit. Combining a Nile Red fluorophore with a photochromic spironaphthoxazine quencher allows the fluorescence to be controlled using visible light, via photoswitching and FRET quenching. Synthetic lipid vesicles of varying composition were imaged with an average 2.5-fold resolution enhancement, compared to the confocal images. Ratiometric detection was used to probe the membrane polarity, and domains of different lipid ordering were distinguished within the same membrane.

DNA-Origami Line-Actants Control Domain Organization and Fission in Synthetic Membranes

Cells can precisely program the shape and lateral organization of their membranes using protein machinery. Aiming to replicate a comparable degree of control, here we introduce DNA-origami line-actants (DOLAs) as synthetic analogues of membrane-sculpting proteins. DOLAs are designed to selectively accumulate at the line-interface between coexisting domains in phase-separated lipid membranes, modulating the tendency of the domains to coalesce. With experiments and coarse-grained simulations, we demonstrate that DOLAs can reversibly stabilize two-dimensional analogues of Pickering emulsions on synthetic giant liposomes, enabling dynamic programming of membrane lateral organization. The control afforded over membrane structure by DOLAs extends to three-dimensional morphology, as exemplified by a proof-of-concept synthetic pathway leading to vesicle fission. With DOLAs we lay the foundations for mimicking, in synthetic systems, some of the critical membrane-hosted functionalities of biological cells, including signaling, trafficking, sensing, and division.

An isoform of the giant protein titin is a master regulator of human T lymphocyte trafficking

Response to multiple microenvironmental cues and resilience to mechanical stress are essential features of trafficking leukocytes. Here, we describe unexpected role of titin (TTN), the largest protein encoded by the human genome, in the regulation of mechanisms of lymphocyte trafficking. Human T and B lymphocytes express five TTN isoforms, exhibiting cell-specific expression, distinct localization to plasma membrane microdomains, and different distribution to cytosolic versus nuclear compartments. In T lymphocytes, the LTTN1 isoform governs the morphogenesis of plasma membrane microvilli independently of ERM protein phosphorylation status, thus allowing selectin-mediated capturing and rolling adhesions. Likewise, LTTN1 controls chemokine-triggered integrin activation. Accordingly, LTTN1 mediates rho and rap small GTPases activation, but not actin polymerization. In contrast, chemotaxis is facilitated by LTTN1 degradation. Finally, LTTN1 controls resilience to passive cell deformation and ensures T lymphocyte survival in the blood stream. LTTN1 is, thus, a critical and versatile housekeeping regulator of T lymphocyte trafficking.

Membrane protein isolation and structure determination in cell-derived membrane vesicles

Integral membrane protein structure determination traditionally requires extraction from cell membranes using detergents or polymers. Here, we describe the isolation and structure determination of proteins in membrane vesicles derived directly from cells. Structures of the ion channel Slo1 from total cell membranes and from cell plasma membranes were determined at 3.8 Å and 2.7 Å resolution, respectively. The plasma membrane environment stabilizes Slo1, revealing an alteration of global helical packing, polar lipid, and cholesterol interactions that stabilize previously unresolved regions of the channel and an additional ion binding site in the Ca2+ regulatory domain. The two methods presented enable structural analysis of both internal and plasma membrane proteins without disrupting weakly interacting proteins, lipids, and cofactors that are essential to biological function.

Phosphatidylinositol 4,5-Bisphosphate Sensing Lipid Raft via Inter-Leaflet Coupling Regulated by Acyl Chain Length of Sphingomyelin

Phosphatidylinositol 4,5-bisphosphate (PIP₂) is an important molecule located at the inner leaflet of cell membrane, where it serves as anchoring sites for a cohort of membrane-associated molecules and as a broad-reaching signaling intermediate. The lipid raft is thought as the major platform recruiting proteins for signal transduction and also known to mediate PIP₂ accumulation across the membrane. While the significance of this cross-membrane coupling is increasingly appreciated, it remains unclear whether and how PIP₂ senses the dynamic change of the ordered lipid domains over the packed hydrophobic core of the bilayer. Herein, by means of molecular dynamic simulation, we reveal that inner PIP₂ molecules can sense the outer lipid domain via inter-leaflet coupling, and the coupling manner is dictated by the acyl chain length of sphingomyelin (SM) partitioned to the lipid domain. Shorter SM promotes membrane domain registration, whereby PIP₂ accumulates beneath the domain across the membrane. In contrast, the anti-registration is thermodynamically preferred if the lipid domain has longer SM due to the hydrophobic mismatch between the corresponding acyl chains in SM and PIP₂. In this case, PIP₂ is expelled by the domain with a higher diffusivity. These results provide molecular insights into the regulatory mechanism of correlation between the outer lipid domain and inner PIP₂, both of which are critical components for cell signal transduction.

Micropatterning of functional lipid bilayer assays for quantitative bioanalysis

Interactions of the cell with its environment are mediated by the cell membrane and membrane-localized molecules. Supported lipid bilayers have enabled the recapitulation of the basic properties of cell membranes and have been broadly used to further our understanding of cellular behavior. Coupled with micropatterning techniques, lipid bilayer platforms have allowed for high throughput assays capable of performing quantitative analysis at a high spatiotemporal resolution. Here, an overview of the current methods of the lipid membrane patterning is presented. The fabrication and pattern characteristics are briefly described to present an idea of the quality and notable features of the methods, their utilizations for quantitative bioanalysis, as well as to highlight possible directions for the advanced micropatterning lipid membrane assays.

Cholesterol- and actin-centered view of the plasma membrane: updating the Singer-Nicolson fluid mosaic model to commemorate its 50th anniversary†

Two very polarized views exist for understanding the cellular plasma membrane (PM). For some, it is the simple fluid described by the original Singer-Nicolson fluid mosaic model. For others, due to the presence of thousands of molecular species that extensively interact with each other, the PM forms various clusters and domains that are constantly changing and therefore, no simple rules exist that can explain the structure and molecular dynamics of the PM. In this article, we propose that viewing the PM from its two predominant components, cholesterol and actin filaments, provides an excellent and transparent perspective of PM organization, dynamics, and mechanisms for its functions. We focus on the actin-induced membrane compartmentalization and lipid raft domains coexisting in the PM and how they interact with each other to perform PM functions. This view provides an important update of the fluid mosaic model.