Mechanisms of membrane deformation

Protein Recognition of Glycosphingolipids in Membranes: Mechanistic and Quantitative Insights

Recognition of glycosphingolipids (GSLs) in cell membranes by glycan-binding proteins (GBPs) is essential for diverse biological processes. However, owing to deficiencies in available analytical methods, the thermodynamics of GBP-GSL interactions remains poorly characterized. Native mass spectrometry (nMS) analysis performed using soluble GSL-containing model membranes provides a direct readout of the identity and stoichiometry of bound GSL ligands and, under certain conditions, can inform on affinity. Yet, for multivalent GBPs capable of engaging multiple model membranes simultaneously, data analysis relies on untested assumptions, which has limited adoption of the assay. Here, we apply mass photometry to quantify a series of high-affinity interactions between glycolipids in soluble model membranes (nanodiscs) and mono- and multivalent GBPs and compare with binding data acquired with nMS. Remarkably, the mass photometry results indicate that glycolipids are distributed nonstatistically across the lipid bilayer and engage in clustering that is sensitive to GBP binding. Moreover, the affinities and stoichiometries (of bound nanodiscs) measured for multivalent GBPs are strongly modulated by glycolipid clustering, which can overwhelm avidity gains from multivalent binding. After normalization for the number of GBP binding sites and glycolipid content, the affinities from mass photometry are found to be, overall, in good agreement with native nMS-derived affinities. Collectively, the findings of this study provide critically needed affinity and stoichiometry benchmarks for assay validation and significant new insights into the mechanisms of GBP recognition of GSLs in model membranes, which serve as a foundation for understanding binding in natural cellular environments.

The role of nonlinear axonal membrane capacitance in modulating ion channel cooperativity in action potential dynamics: Studies on Hodgkin-Huxley's model

Hodgkin-Huxley's (HH) model of action potential (AP) has been modified in view of the nonlinear membrane capacitance of the axon of a neuron as well as the cooperation among the participating ion channels in the axon. Previous studies of action potential behavior based on computational analysis of modified HH models with either nonlinear axonal membrane capacitance or ion channel cooperativity show significant changes in action potential dynamics, e.g. AP peak, hyperpolarization amplitude, spike threshold, rapid onset, etc. As shown in the present paper, the combined effect of the nonlinear capacitance and ion channel cooperativity displays qualitatively similar results that are quantitatively different. For example, the nonlinear membrane capacitance leads to a reduction in the ion channel cooperativity effect on the action potential dynamics. The reason for this combined effect is thought to be axonal membrane distortion and depolarization caused by the varying membrane potential.

Morphology remodelling and membrane channel formation in synthetic cells via reconfigurable DNA nanorafts

The shape of biological matter is central to cell function at different length scales and determines how cellular components recognize, interact and respond to one another. However, their shapes are often transient and hard to reprogramme. Here we construct a synthetic cell model composed of signal-responsive DNA nanorafts, biogenic pores and giant unilamellar vesicles (GUVs). We demonstrate that reshaping of DNA rafts at the nanoscale can be coupled to reshaping of GUVs at the microscale. The nanorafts collectively undergo reversible transitions between isotropic and short-range local order on the lipid membrane, programmably remodelling the GUV shape. Assisted by the biogenic pores, during GUV shape recovery the locally ordered DNA rafts perforate the membrane, forming sealable synthetic channels for large cargo transport. Our work outlines a versatile platform for interfacing reconfigurable DNA nanostructures with synthetic cells, expanding the potential of DNA nanotechnology in synthetic biology.

Salivary proteins modulate Candida albicans virulence and may prevent oropharingeal candidiasis

Oral candidiasis can be presented in different ways due to the virulence factors of its etiology such as Candida albicans that have developed an effective set of these factors that are able to improve its pathogenesis. The role of salivary immunological components in the development of candidiasis can provide insights for the development of new methodologies aiming to control this disease. The aim of this study was to evaluate the antifungal activity of two salivary components, histatin 5 and lactoferrin on C. albicans viability and virulence using a fluconazole resistant C. albicans clinical strain. Results showed that histatin 5 and lactoferrin decreased cell viability, and the cell surface hydrophobicity was increased by 18% in presence of 151 µg/mL of histatin 5 but was not altered by lactoferrin. It was observed the reduction of 69.3% in the expression of mannoproteins on C. albicans surface in the presence of 151 µg/mL of histatin, but proteolytic activity of serine proteinases was not inhibited by any of the proteins. Histatin 5 altered cell ultrastructure predominantly in the cytoplasmic compartment. However, this peptide does not interfere with mitochondrial function neither in membrane permeability of the yeasts. The association index between C. albicans and epithelial cells was increased by 51% in presence of 151 µg/mL of histatin. Results suggest that histatin 5 and lactoferrin affects viability and virulence of C. albicans at physiological levels, and the maintenance of these levels may be essential in the prevention of oropharyngeal candidiasis. Exogenous administration of these proteins may become a therapeutic alternative for resistant strains of C. albicans, circumventing toxicity issues, considering their constitutive features.

Actin dynamics switches two distinct modes of endosomal fusion in yolk sac visceral endoderm cells

Membranes undergo various patterns of deformation during vesicle fusion, but how this membrane deformation is regulated and contributes to fusion remains unknown. In this study, we developed a new method of observing the fusion of individual late endosomes and lysosomes by using mouse yolk sac visceral endoderm cells that have huge endocytic vesicles. We found that there were two distinct fusion modes that were differently regulated. In homotypic fusion, two late endosomes fused quickly, whereas in heterotypic fusion they fused to lysosomes slowly. Mathematical modeling showed that vesicle size is a critical determinant of these fusion types and that membrane fluctuation forces can overcome the vesicle size effects. We found that actin filaments were bound to late endosomes and forces derived from dynamic actin remodeling were necessary for quick fusion during homotypic fusion. Furthermore, cofilin played a role in endocytic fusion by regulating actin turnover. These data suggest that actin promotes vesicle fusion for efficient membrane trafficking in visceral endoderm cells.

Membrane curvature sensing and symmetry breaking of the M2 proton channel from Influenza A

The M2 proton channel aids in the exit of mature influenza viral particles from the host plasma membrane through its ability to stabilize regions of high negative Gaussian curvature (NGC) that occur at the neck of budding virions. The channels are homo-tetramers that contain a cytoplasm-facing amphipathic helix (AH) that is necessary and sufficient for NGC generation; however, constructs containing the transmembrane spanning helix, which facilitates tetramerization, exhibit enhanced curvature generation. Here, we used all-atom molecular dynamics (MD) simulations to explore the conformational dynamics of M2 channels in lipid bilayers revealing that the AH is dynamic, quickly breaking the fourfold symmetry observed in most structures. Next, we carried out MD simulations with the protein restrained in four- and twofold symmetric conformations to determine the impact on the membrane shape. While each pattern was distinct, all configurations induced pronounced curvature in the outer leaflet, while conversely, the inner leaflets showed minimal curvature and significant lipid tilt around the AHs. The MD-generated profiles at the protein-membrane interface were then extracted and used as boundary conditions in a continuum elastic membrane model to calculate the membrane-bending energy of each conformation embedded in different membrane surfaces characteristic of a budding virus. The calculations show that all three M2 conformations are stabilized in inward-budding, concave spherical caps and destabilized in outward-budding, convex spherical caps, the latter reminiscent of a budding virus. One of the C2-broken symmetry conformations is stabilized by 4 kT in NGC surfaces with the minimum energy conformation occurring at a curvature corresponding to 33 nm radii. In total, our work provides atomistic insight into the curvature sensing capabilities of M2 channels and how enrichment in the nascent viral particle depends on protein shape and membrane geometry.

Light-Activated Synthetic Rotary Motors in Lipid Membranes Induce Shape Changes Through Membrane Expansion

Membranes are the key structures to separate and spatially organize cellular systems. Their rich dynamics and transformations during the cell cycle are orchestrated by specific membrane-targeted molecular machineries, many of which operate through energy dissipation. Likewise, man-made light-activated molecular rotary motors have previously shown drastic effects on cellular systems, but their physical roles on and within lipid membranes remain largely unexplored. Here, the impact of rotary motors on well-defined biological membranes is systematically investigated. Notably, dramatic mechanical transformations are observed in these systems upon motor irradiation, indicative of motor-induced membrane expansion. The influence of several factors on this phenomenon is systematically explored, such as motor concentration and membrane composition., Membrane fluidity is found to play a crucial role in motor-induced deformations, while only minor contributions from local heating and singlet oxygen generation are observed. Most remarkably, the membrane area expansion under the influence of the motors continues as long as irradiation is maintained, and the system stays out-of-equilibrium. Overall, this research contributes to a comprehensive understanding of molecular motors interacting with biological membranes, elucidating the multifaceted factors that govern membrane responses and shape transitions in the presence of these remarkable molecular machines, thereby supporting their future applications in chemical biology.

Membrane contacts with the endoplasmic reticulum modulate plastid morphology and behaviour

Plastid behaviour often occurs in tandem with endoplasmic reticulum (ER) dynamics. In order to understand the underlying basis for such linked behaviour we have used time-lapse imaging-based analysis of plastid movement and pleomorphy, including the extension and retraction of stromules. Stable transgenic plants that simultaneously express fluorescent fusion proteins targeted to the plastid stroma, and the ER along with BnCLIP1-eGFP, an independent plastid envelope localized membrane contact site (MCS) marker were utilized. Our experiments strongly suggest that transient MCS formed between the plastid envelope and the ER are responsible for their concomitant behaviour.

Photo-Lipids: Light-Sensitive Nano-Switches to Control Membrane Properties

Biological membranes are described as a complex mixture of lipids and proteins organized according to thermodynamic principles. This chemical and spatial complexity can lead to specialized functional membrane domains enriched with specific lipids and proteins. The interaction between lipids and proteins restricts their lateral diffusion and range of motion, thus altering their function. One approach to investigating these membrane properties is to use chemically accessible probes. In particular, photo-lipids, which contain a light-sensitive azobenzene moiety that changes its configuration from trans- to cis- upon light irradiation, have recently gained popularity for modifying membrane properties. These azobenzene-derived lipids serve as nanotools for manipulating lipid membranes in vitro and in vivo. Here, we will discuss the use of these compounds in artificial and biological membranes as well as their application in drug delivery. We will focus mainly on changes in the membrane's physical properties as well as lipid membrane domains in phase-separated liquid-ordered/liquid-disordered bilayers driven by light, and how these changes in membrane physical properties alter transmembrane protein function.

Mechanobiology and survival strategies of circulating tumor cells: a process towards the invasive and metastatic phenotype

Metastatic progression is the deadliest feature of cancer. Cancer cell growth, invasion, intravasation, circulation, arrest/adhesion and extravasation require specific mechanical properties to allow cell survival and the completion of the metastatic cascade. Circulating tumor cells (CTCs) come into contact with the capillary bed during extravasation/intravasation at the beginning of the metastatic cascade. However, CTC mechanobiology and survival strategies in the bloodstream, and specifically in the microcirculation, are not well known. A fraction of CTCs can extravasate and colonize distant areas despite the biomechanical constriction forces that are exerted by the microcirculation and that strongly decrease tumor cell survival. Furthermore, accumulating evidence shows that several CTC adaptations, via molecular factors and interactions with blood components (e.g., immune cells and platelets inside capillaries), may promote metastasis formation. To better understand CTC journey in the microcirculation as part of the metastatic cascade, we reviewed how CTC mechanobiology and interaction with other cell types in the bloodstream help them to survive the harsh conditions in the circulatory system and to metastasize in distant organs.

Membrane Curvature: The Inseparable Companion of Autophagy

Autophagy is a highly conserved recycling process of eukaryotic cells that degrades protein aggregates or damaged organelles with the participation of autophagy-related proteins. Membrane bending is a key step in autophagosome membrane formation and nucleation. A variety of autophagy-related proteins (ATGs) are needed to sense and generate membrane curvature, which then complete the membrane remodeling process. The Atg1 complex, Atg2-Atg18 complex, Vps34 complex, Atg12-Atg5 conjugation system, Atg8-phosphatidylethanolamine conjugation system, and transmembrane protein Atg9 promote the production of autophagosomal membranes directly or indirectly through their specific structures to alter membrane curvature. There are three common mechanisms to explain the change in membrane curvature. For example, the BAR domain of Bif-1 senses and tethers Atg9 vesicles to change the membrane curvature of the isolation membrane (IM), and the Atg9 vesicles are reported as a source of the IM in the autophagy process. The amphiphilic helix of Bif-1 inserts directly into the phospholipid bilayer, causing membrane asymmetry, and thus changing the membrane curvature of the IM. Atg2 forms a pathway for lipid transport from the endoplasmic reticulum to the IM, and this pathway also contributes to the formation of the IM. In this review, we introduce the phenomena and causes of membrane curvature changes in the process of macroautophagy, and the mechanisms of ATGs in membrane curvature and autophagosome membrane formation.

Generation of nanoscopic membrane curvature for membrane trafficking

Curved membranes are key features of intracellular organelles, and their generation involves dynamic protein complexes. Here we describe the fundamental mechanisms such as the hydrophobic insertion, scaffolding and crowding mechanisms these proteins use to produce membrane curvatures and complex shapes required to form intracellular organelles and vesicular structures involved in endocytosis and secretion. For each mechanism, we discuss its cellular functions as well as the underlying physical principles and the specific membrane properties required for the mechanism to be feasible. We propose that the integration of individual mechanisms into a highly controlled, robust process of curvature generation often relies on the assembly of proteins into coats. How cells unify and organize the curvature-generating factors at the nanoscale is presented for three ubiquitous coats central for membrane trafficking in eukaryotes: clathrin-coated pits, caveolae, and COPI and COPII coats. The emerging theme is that these coats arrange and coordinate curvature-generating factors in time and space to dynamically shape membranes to accomplish membrane trafficking within cells.

Cell-Derived Vesicles with Increased Stability and On-Demand Functionality by Equipping Their Membrane with a Cross-Linkable Copolymer

Cell-derived vesicles retain the cytoplasm and much of the native cell membrane composition. Therefore, they are attractive for investigations of membrane biophysics, drug delivery systems, and complex molecular factories. However, their fragility and aggregation limit their applications. Here, the mechanical properties and stability of giant plasma membrane vesicles (GPMVs) are enhanced by decorating them with a specifically designed diblock copolymer, cholesteryl-poly[2-aminoethyl methacrylate-b-poly(ethylene glycol) methyl ether acrylate]. When cross-linked, this polymer brush enhances the stability of the GPMVs. Furthermore, the pH-responsiveness of the copolymer layer allows for a controlled cargo loading/release, which may enable various bioapplications. Importantly, the cross-linked-copolymer GPMVs are not cytotoxic and preserve in vitro membrane integrity and functionality. This effective strategy to equip the cell-derived vesicles with stimuli-responsive cross-linkable copolymers is expected to open a new route to the stabilization of natural membrane systems and overcome barriers to biomedical applications.

Mem3DG: Modeling membrane mechanochemical dynamics in 3D using discrete differential geometry

Biomembranes adopt varying morphologies that are vital to cellular functions. Many studies use computational modeling to understand how various mechanochemical factors contribute to membrane shape transformations. Compared with approximation-based methods (e.g., finite element method [FEM]), the class of discrete mesh models offers greater flexibility to simulate complex physics and shapes in three dimensions; its formulation produces an efficient algorithm while maintaining coordinate-free geometric descriptions. However, ambiguities in geometric definitions in the discrete context have led to a lack of consensus on which discrete mesh model is theoretically and numerically optimal; a bijective relationship between the terms contributing to both the energy and forces from the discrete and smooth geometric theories remains to be established. We address this and present an extensible framework, Mem3DG, for modeling 3D mechanochemical dynamics of membranes based on discrete differential geometry (DDG) on triangulated meshes. The formalism of DDG resolves the inconsistency and provides a unifying perspective on how to relate the smooth and discrete energy and forces. To demonstrate, Mem3DG is used to model a sequence of examples with increasing mechanochemical complexity: recovering classical shape transformations such as 1) biconcave disk, dumbbell, and unduloid; and 2) spherical bud on spherical, flat-patch membrane; investigating how the coupling of membrane mechanics with protein mobility jointly affects phase and shape transformation. As high-resolution 3D imaging of membrane ultrastructure becomes more readily available, we envision Mem3DG to be applied as an end-to-end tool to simulate realistic cell geometry under user-specified mechanochemical conditions.

α-Synuclein-induced deformation of small unilamellar vesicles

α-Synuclein is a small neuronal protein that reversibly associates with lipid membranes. The membrane interactions are believed to be central to the healthy function of this protein involved in synaptic plasticity and neurotransmitter release. α-Synuclein has been speculated to induce vesicle fusion as well as fission, processes which are analogous to each other but proceed in different directions and involve different driving forces. In the current work, we analyse α-synuclein-induced small unilamellar vesicle deformation from a thermodynamics point of view. We show that the structures interpreted in the literature as fusion intermediates are in fact a stable deformed state and neither fusion nor vesicle clustering occurs. We speculate on the driving force for the observed deformation and put forward a hypothesis that α-synuclein self-assembly on the lipid membrane precedes and induces membrane remodelling.

Flow-driven competition between two capsules passing through a narrow pore

By incorporating a distance function into the finite element simulation, we investigate the flow-driven competition between two soft capsules passing through a narrow pore, employing the arbitrary Lagrangian-Eulerian formulation to satisfy the boundary conditions for fluid flow and capsule deformation. In our simulations, the motion and deformation of the capsules can be described in an intuitive manner, and the order in which capsules of different sizes pass through a pore can be clearly determined. Meanwhile, when the capsules are near the narrow pore, the change of the flow field is also very interesting and can be expressed intuitively. It is shown that, driven by the Poiseuille flow, the larger capsule has a stronger tendency to pass through the pore than the small one, which can be attributed to the greater resistance and the volume advantage of the larger capsule. In addition, we demonstrate that this tendency can be reversed by changing the inlet velocity and setting the initial position of the smaller capsule closer to the axis of the pore. And as long as the large one passes through first, the small one will offset the axis to the same orientation as the initial, while the large one always moves along the axis.

Dynamic interplay between cell membrane tension and clathrin-mediated endocytosis

Deformability of the plasma membrane, the outermost surface of metazoan cells, allows cells to be dynamic, mobile and flexible. Factors that affect this deformability, such as tension on the membrane, can regulate a myriad of cellular functions, including membrane resealing, cell motility, polarisation, shape maintenance, membrane area control and endocytic vesicle trafficking. This review focuses on mechanoregulation of clathrin-mediated endocytosis (CME). We first delineate the origins of cell membrane tension and the factors that yield to its spatial and temporal fluctuations within cells. We then review the recent literature demonstrating that tension on the membrane is a fast-acting and reversible regulator of CME. Finally, we discuss tension-based regulation of endocytic clathrin coat formation during physiological processes.

Recent developments in membrane curvature sensing and induction by proteins

BACKGROUND

Membrane-bound intracellular organelles have characteristic shapes attributed to different local membrane curvatures, and these attributes are conserved across species. Over the past decade, it has been confirmed that specific proteins control the large curvatures of the membrane, whereas many others due to their specific structural features can sense the curvatures and bind to the specific geometrical cues. Elucidating the interplay between sensing and induction is indispensable to understand the mechanisms behind various biological processes such as vesicular trafficking and budding.

SCOPE OF REVIEW

We provide an overview of major classes of membrane proteins and the mechanisms of curvature sensing and induction. We then discuss the importance of membrane elastic characteristics to induce the membrane shapes similar to intracellular organelles. Finally, we survey recently available assays developed for studying the curvature sensing and induction by many proteins.

MAJOR CONCLUSIONS

Recent theoretical/computational modeling along with experimental studies have uncovered fascinating connections between lipid membrane and protein interactions. However, the phenomena of protein localization and synchronization to generate spatiotemporal dynamics in membrane morphology are yet to be fully understood.

GENERAL SIGNIFICANCE

The understanding of protein-membrane interactions is essential to shed light on various biological processes. This further enables the technological applications of many natural proteins/peptides in therapeutic treatments. The studies of membrane dynamic shapes help to understand the fundamental functions of membranes, while the medicinal roles of various macromolecules (such as proteins, peptides, etc.) are being increasingly investigated.

Fascin-induced actin protrusions are suppressed by dendritic networks in giant unilamellar vesicles

The interactions between actin networks and cell membrane are immensely important for eukaryotic cell functions including cell shape changes, motility, polarity establishment, and adhesion. Actin-binding proteins are known to compete and cooperate using a finite amount of actin monomers to form distinct actin networks. How actin-bundling protein fascin and actin-branching protein Arp2/3 complex compete to remodel membranes is not entirely clear. To investigate fascin- and Arp2/3-mediated actin network remodeling, we applied a reconstitution approach encapsulating bundled and dendritic actin networks inside giant unilamellar vesicles (GUVs). Independently reconstituted, membrane-bound Arp2/3 nucleation forms an actin cortex in GUVs, whereas fascin mediates formation of actin bundles that protrude out of GUVs. Coencapsulating both fascin and Arp2/3 complex leads to polarized dendritic aggregates and significantly reduces membrane protrusions, irrespective of whether the dendritic network is membrane bound or not. However, reducing Arp2/3 complex while increasing fascin restores membrane protrusion. Such changes in network assembly and the subsequent interplay with membrane can be attributed to competition between fascin and Arp2/3 complex to utilize a finite pool of actin.

Oxygen Enrichment Membranes for Kuwait Power Plants: A Case Study

Power plants are considered as the major source of carbon dioxide pollution in Kuwait. The gas is released from the combustion of fuel with air to convert water into steam. It has been proven that the use of enriched oxygen can reduce fuel consumption and minimize emissions. In this study, UniSim (Honeywell, Charlotte, NC, USA) was used to estimate the fuel savings and carbon dioxide emissions of the largest power plant in Kuwait (Alzour). Results showed that at 30 mol% oxygen, the fuel consumption was lowered by 8%, with a reduction in carbon dioxide emissions by 3524 tons per day. An economic analysis was performed on the use of a membrane unit to produce 30 mol% oxygen. At current market prices, the unit is not economical. However, the system can achieve a payback duration of 3 years if natural gas price increases to USD 6.74 or the compressor cost decreases to USD 52 per kW. Currently, the research and development sector is targeting a membrane fabrication cost of less than USD 10 per m² to make the membrane process more attractive.

Performance Evaluation and Fouling Propensity of Forward Osmosis (FO) Membrane for Reuse of Spent Dialysate

The number of chronic renal disease patients has shown a significant increase in recent decades over the globe. Hemodialysis is the most commonly used treatment for renal replacement therapy (RRT) and dominates the global dialysis market. As one of the most water-consuming treatments in medical procedures, hemodialysis has room for improvement in reducing wastewater effluent. In this study, we investigated the technological feasibility of introducing the forward osmosis (FO) process for spent dialysate reuse. A 30 LMH of average water flux has been achieved using a commercial TFC membrane with high water permeability and salt removal. The water flux increased up to 23% with increasing flowrate from 100 mL/min to 500 mL/min. During 1 h spent dialysate treatment, the active layer facing feed solution (AL-FS) mode showed relatively higher flux stability with a 4–6 LMH of water flux reduction while the water flux decreased significantly at the active layer facing draw solution (AL-DS) mode with a 10–12 LMH reduction. In the pressure-assisted forward osmosis (PAFO) condition, high reverse salt flux was observed due to membrane deformation. During the membrane filtration process, scaling occurred due to the influence of polyvalent ions remaining on the membrane surface. Membrane fouling exacerbated the flux and was mainly caused by organic substances such as urea and creatinine. The results of this experiment provide an important basis for future research as a preliminary experiment for the introduction of the FO technique to hemodialysis.

Mechanical Adaptability of Tumor Cells in Metastasis

The most dangerous aspect of cancer lies in metastatic progression. Tumor cells will successfully form life-threatening metastases when they undergo sequential steps along a journey from the primary tumor to distant organs. From a biomechanics standpoint, growth, invasion, intravasation, circulation, arrest/adhesion, and extravasation of tumor cells demand particular cell-mechanical properties in order to survive and complete the metastatic cascade. With metastatic cells usually being softer than their non-malignant counterparts, high deformability for both the cell and its nucleus is thought to offer a significant advantage for metastatic potential. However, it is still unclear whether there is a finely tuned but fixed mechanical state that accommodates all mechanical features required for survival throughout the cascade or whether tumor cells need to dynamically refine their properties and intracellular components at each new step encountered. Here, we review the various mechanical requirements successful cancer cells might need to fulfill along their journey and speculate on the possibility that they dynamically adapt their properties accordingly. The mechanical signature of a successful cancer cell might actually be its ability to adapt to the successive microenvironmental constraints along the different steps of the journey.

Comparative Study of Curvature Sensing Mediated by F-BAR and an Intrinsically Disordered Region of FBP17

Membrane curvature has emerged as an intriguing physical principle underlying biological signaling and membrane trafficking. The CIP4/FBP17/Toca-1 F-BAR subfamily is unique in the BAR family because its structurally folded F-BAR domain does not contain any hydrophobic motifs that insert into membrane. Although widely assumed so, whether the banana-shaped F-BAR domain alone can sense curvature has never been experimentally demonstrated. Using a nanobar-supported lipid bilayer system, we found that the F-BAR domain of FBP17 displayed minimal curvature sensing in vitro. In comparison, an alternatively spliced intrinsically disordered region (IDR) adjacent to the F-BAR domain has the membrane curvature-sensing ability greatly exceeding that of F-BAR domain alone. In living cells, the presence of the IDR delayed the recruitment of FBP17 in curvature-coupled cortical waves. Collectively, we propose that contrary to the common belief, FBP17's curvature-sensing capability largely originates from IDR, and not the F-BAR domain alone.

Generation of interconnected vesicles in a liposomal cell model

We introduce an experimental method based upon a glass micropipette microinjection technique for generating a multitude of interconnected vesicles (IVs) in the interior of a single giant unilamellar phospholipid vesicle (GUV) serving as a cell model system. The GUV membrane, consisting of a mixture of soybean polar lipid extract and anionic phosphatidylserine, is adhered to a multilamellar lipid vesicle that functions as a lipid reservoir. Continuous IV formation was achieved by bringing a micropipette in direct contact with the outer GUV surface and subjecting it to a localized stream of a Ca²⁺ solution from the micropipette tip. IVs are rapidly and sequentially generated and inserted into the GUV interior and encapsulate portions of the micropipette fluid content. The IVs remain connected to the GUV membrane and are interlinked by short lipid nanotubes and resemble beads on a string. The vesicle chain-growth from the GUV membrane is maintained for as long as there is the supply of membrane material and Ca²⁺ solution, and the size of the individual IVs is controlled by the diameter of the micropipette tip. We also demonstrate that the IVs can be co-loaded with high concentrations of neurotransmitter and protein molecules and displaying a steep calcium ion concentration gradient across the membrane. These characteristics are analogous to native secretory vesicles and could, therefore, serve as a model system for studying secretory mechanisms in biological systems.

Biomimetic Models to Investigate Membrane Biophysics Affecting Lipid-Protein Interaction

Biological membranes are highly dynamic in their ability to orchestrate vital mechanisms including cellular protection, organelle compartmentalization, cellular biomechanics, nutrient transport, molecular/enzymatic recognition, and membrane fusion. Controlling lipid composition of different membranes allows cells to regulate their membrane characteristics, thus modifying their physical properties to permit specific protein interactions and drive structural function (membrane deformation facilitates vesicle budding and fusion) and signal transduction. Yet, how lipids control protein structure and function is still poorly understood and needs systematic investigation. In this review, we explore different in vitro membrane models and summarize our current understanding of the interplay between membrane biophysical properties and lipid-protein interaction, taken as example few proteins involved in muscular activity (dystrophin), digestion and Legionella pneumophila effector protein DrrA. The monolayer model with its movable barriers aims to mimic any membrane deformation while surface pressure modulation imitates lipid packing and membrane curvature changes. It is frequently used to investigate peripheral protein binding to the lipid headgroups. Examples of how lipid lateral pressure modifies protein interaction and organization within the membrane are presented using various biophysical techniques. Interestingly, the shear elasticity and surface viscosity of the monolayer will increase upon specific protein(s) binding, supporting the importance of such mechanical link for membrane stability. The lipid bilayer models such as vesicles are not only used to investigate direct protein binding based on the lipid nature, but more importantly to assess how local membrane curvature (vesicles with different size) influence the binding properties of a protein. Also, supported lipid bilayer model has been used widely to characterize diffusion law of lipids within the bilayer and/or protein/biomolecule binding and diffusion on the membrane. These membrane models continue to elucidate important advances regarding the dynamic properties harmonizing lipid-protein interaction.

Membrane rolling induced by bacterial toxins

Membrane curvature effects are important in numerous cellular processes and many membrane interacting proteins induce spontaneous curvature upon membrane binding. Shiga and cholera toxins both belong to the AB5 family of toxins and consist of a toxic A subunit and a membrane-binding pentameric B subunit. Shiga and cholera toxins induce tubular membrane invaginations in cells and GUVs due to curvature effects and the toxins are known from MD simulations to induce curvature. Membrane invaginations have been linked to uptake of the toxins into cells. As a novel model system to experimentally characterize curvature-inducing proteins, we study the morphology induced in planar membrane patches. It was previously shown that annexins induce distinct morphologies in membrane patches including membrane rolling. In this study we show that the B subunits of Shiga and cholera toxins (STxB, CTxB) both induce roll-up of cell-sized membrane patches. Rolling starts from the free membrane edges of the patch and is completed within a few seconds. We characterize the branched roll morphology and find experimental estimates for the spontaneous curvature of the toxins based on the topography of rolls. The estimates are in agreement with previous MD simulations. We quantify the dynamics of rolling as induced by the toxins and demonstrate agreement with a theoretical model of the rolling dynamics. The model solves the equation of motion for a membrane roll and includes viscous drag and adhesion to the support. The results suggest that membrane rolling may be a general phenomenon displayed by many proteins that induce negative curvature in membranes with free edges.

Tuning intercellular adhesion with membrane-anchored oligonucleotides

Adhesive interactions between cells play an integral role in development, differentiation and regeneration. Existing methods for controlling cell-cell cohesion and adhesion by manipulating protein expression are constrained by biological interdependencies, e.g. coupling of cadherins to actomyosin force-feedback mechanisms. We use oligonucleotides conjugated to PEGylated lipid anchors (ssDNAPEGDPPE) to introduce artificial cell-cell adhesion that is largely decoupled from the internal cytoskeleton. We describe cell-cell doublets with a mechanical model based on isotropic, elastic deformation of spheres to estimate the adhesion at the cell-cell interface. Physical manipulation of adhesion by modulating the PEG-lipid to ssDNAPEGDPPE ratio, and conversely treating with actin-depolymerizing cytochalasin D, resulted in decreases and increases in doublet contact area, respectively. Our data are relevant to the ongoing discussion over mechanisms of tissue surface tension and in agreement with models based on opposing cortical and cohesive forces. PEG-lipid modulation of doublet geometries resulted in a well-defined curve indicating continuity, enabling prescriptive calibration for controlling doublet geometry. Our study demonstrates tuning of basic doublet adhesion, laying the foundation for more complex multicellular adhesion control independent of protein expression.

Inception Mechanisms of Tunneling Nanotubes

Tunneling nanotubes (TNTs) are thin membranous tubes that interconnect cells, representing a novel route of cell-to-cell communication and spreading of pathogens. TNTs form between many cell types, yet their inception mechanisms remain elusive. We review in this study general concepts related to the formation and stability of membranous tubular structures with a focus on a deviatoric elasticity model of membrane nanodomains. We review experimental evidence that tubular structures initiate from local membrane bending facilitated by laterally distributed proteins or anisotropic membrane nanodomains. We further discuss the numerical results of several theoretical and simulation models of nanodomain segregation suggesting the mechanisms of TNT inception and stability. We discuss the coupling of nanodomain segregation with the action of protruding cytoskeletal forces, which are mostly provided in eukaryotic cells by the polymerization of f-actin, and review recent inception mechanisms of TNTs in relation to motor proteins.

Protein Delivery into the Cell Cytosol using Non-Viral Nanocarriers

Protein delivery into cells is a potentially transformative tool for treating "undruggable" targets in diseases associated with protein deficiencies or mutations. The vast majority of these targets are accessed via the cytosol, a challenging prospect for proteins with therapeutic and diagnostic relevance. In this review we will present promising non-viral approaches for intracellular and ultimately cytosolic delivery of proteins using nanocarriers. We will also discuss the mechanistic properties that govern the efficacy of nanocarrier-mediated protein delivery, applications of nanomaterials, and key challenges and opportunities in the use of nanocarriers for intracellular protein delivery.

Extracellular membrane vesicles in the three domains of life and beyond

Cells from all three domains of life, Archaea, Bacteria and Eukarya, produce extracellular vesicles (EVs) which are sometimes associated with filamentous structures known as nanopods or nanotubes. The mechanisms of EV biogenesis in the three domains remain poorly understood, although studies in Bacteria and Eukarya indicate that the regulation of lipid composition plays a major role in initiating membrane curvature. EVs are increasingly recognized as important mediators of intercellular communication via transfer of a wide variety of molecular cargoes. They have been implicated in many aspects of cell physiology such as stress response, intercellular competition, lateral gene transfer (via RNA or DNA), pathogenicity and detoxification. Their role in various human pathologies and aging has aroused much interest in recent years. EVs can be used as decoys against viral attack but virus-infected cells also produce EVs that boost viral infection. Here, we review current knowledge on EVs in the three domains of life and their interactions with the viral world.

Transition from curvature sensing to generation in a vesicle driven by protein binding strength and membrane tension

The ability of proteins to sense and/or generate membrane curvature is crucial for many biological processes inside the cell. We introduce a model for the binding and unbinding of curvature inducing proteins on vesicles using Dynamic Triangulation Monte Carlo (DTMC) simulations. In our study, the interaction between membrane curvature and protein binding is characterised by the binding affinity parameter μ, which indicates the interaction strength. We demonstrate that both sensing and generation of curvature can be observed in the same system as a function of the protein binding affinity on the membrane. Our results show that at low μ values, proteins only sense membrane curvature, whereas at high μ values, they induce curvature. The transition between sensing and generation regimes is marked by a sharp change in the μ-dependence of the protein bound fraction. We present ways to quantitatively characterise these two regimes. We also observe that imposing tension on the membrane (through internal excess pressure for liposomes) extends the region of curvature sensing in the parameter space.

The role of traction in membrane curvature generation

Curvature of biological membranes can be generated by a variety of molecular mechanisms including protein scaffolding, compositional heterogeneity, and cytoskeletal forces. These mechanisms have the net effect of generating tractions (force per unit length) on the bilayer that are translated into distinct shapes of the membrane. Here, we demonstrate how the local shape of the membrane can be used to infer the traction acting locally on the membrane. We show that buds and tubes, two common membrane deformations studied in trafficking processes, have different traction distributions along the membrane and that these tractions are specific to the molecular mechanism used to generate these shapes. Furthermore, we show that the magnitude of an axial force applied to the membrane as well as that of an effective line tension can be calculated from these tractions. Finally, we consider the sensitivity of these quantities with respect to uncertainties in material properties and follow with a discussion on sources of uncertainty in membrane shape.

Competition between TIAM1 and Membranes Balances Endophilin A3 Activity in Cancer Metastasis

Normal cells acquire aggressive behavior by modifying signaling pathways. For instance, alteration of endocytosis profoundly impacts both proliferation and migration during tumorigenesis. Here we investigate the mechanisms that enable the endocytic machinery to coordinate these processes. We show that a membrane curvature-sensing protein, endophilin A3, promotes growth and migration of colon cancer cells through two competing mechanisms: an endocytosis pathway that is required for proliferation and a GTPase regulatory pathway that controls cell motility. EndoA3 stimulates cell migration by binding the Rac GEF TIAM1 leading to activation of small GTPases. Competing interactions of EndoA3 with membrane versus TIAM1 modulate hyperproliferative and metastatic phenotypes. Disruption of EndoA3-membrane interactions stimulates TIAM1 and small GTPases in vitro, and further promotes pro-metastatic phenotypes in vivo. Together, these results uncover a coupling mechanism, by which EndoA3 promotes growth and migration of colon cancers, by linking membrane dynamics to GTPase regulation.

Revisiting the Role of Clathrin-Mediated Endoytosis in Synaptic Vesicle Recycling

Without robust mechanisms to efficiently form new synaptic vesicles (SVs), the tens to hundreds of SVs typically present at the neuronal synapse would be rapidly used up, even at modest levels of neuronal activity. SV recycling is thus critical for synaptic physiology and proper function of sensory and nervous systems. Yet, more than four decades after it was originally proposed that the SVs are formed and recycled locally at the presynaptic terminals, the mechanisms of endocytic processes at the synapse are heavily debated. Clathrin-mediated endocytosis, a type of endocytosis that capitalizes on the clathrin coat, a number of adaptor and accessory proteins, and the GTPase dynamin, is well understood, while the contributions of clathrin-independent fast endocytosis, kiss-and-run, bulk endocytosis and ultrafast endocytosis are still being evaluated. This review article revisits and summarizes the current knowledge on the SV reformation with a focus on clathrin-mediated endocytosis, and it discusses the modes of SV formation from endosome-like structures at the synapse. Given the importance of this topic, future advances in this active field are expected to contribute to better comprehension of neurotransmission, and to have general implications for neuroscience and medicine.

Membrane shape-mediated wave propagation of cortical protein dynamics

Immune cells exhibit stimulation-dependent traveling waves in the cortex, much faster than typical cortical actin waves. These waves reflect rhythmic assembly of both actin machinery and peripheral membrane proteins such as F-BAR domain-containing proteins. Combining theory and experiments, we develop a mechanochemical feedback model involving membrane shape changes and F-BAR proteins that render the cortex an interesting dynamical system. We show that such cortical dynamics manifests itself as ultrafast traveling waves of cortical proteins, in which the curvature sensitivity-driven feedback always constrains protein lateral diffusion in wave propagation. The resulting protein wave propagation mainly reflects the spatial gradient in the timing of local protein recruitment from cytoplasm. We provide evidence that membrane undulations accompany these protein waves and potentiate their propagation. Therefore, membrane shape change and protein curvature sensitivity may have underappreciated roles in setting high-speed cortical signal transduction rhythms.

Traveling waves in the cell cortex can propagate much faster than actin waves, and the mechanism is unknown. Here the authors propose a mechanochemical feedback model for traveling waves that incorporates membrane shape changes and recruitment of F-BAR proteins that enables fast wave propagation.

Microvesicle Involvement in Shiga Toxin-Associated Infection

Shiga toxin is the main virulence factor of enterohemorrhagic Escherichia coli, a non-invasive pathogen that releases virulence factors in the intestine, causing hemorrhagic colitis and, in severe cases, hemolytic uremic syndrome (HUS). HUS manifests with acute renal failure, hemolytic anemia and thrombocytopenia. Shiga toxin induces endothelial cell damage leading to platelet deposition in thrombi within the microvasculature and the development of thrombotic microangiopathy, mostly affecting the kidney. Red blood cells are destroyed in the occlusive capillary lesions. This review focuses on the importance of microvesicles shed from blood cells and their participation in the prothrombotic lesion, in hemolysis and in the transfer of toxin from the circulation into the kidney. Shiga toxin binds to blood cells and may undergo endocytosis and be released within microvesicles. Microvesicles normally contribute to intracellular communication and remove unwanted components from cells. Many microvesicles are prothrombotic as they are tissue factor- and phosphatidylserine-positive. Shiga toxin induces complement-mediated hemolysis and the release of complement-coated red blood cell-derived microvesicles. Toxin was demonstrated within blood cell-derived microvesicles that transported it to renal cells, where microvesicles were taken up and released their contents. Microvesicles are thereby involved in all cardinal aspects of Shiga toxin-associated HUS, thrombosis, hemolysis and renal failure.

Binding of the GTPase Sar1 to a Lipid Membrane Monolayer: Insertion and Orientation Studied by Infrared Reflection⁻Absorption Spectroscopy

Membrane-interacting proteins are polyphilic polymers that engage in dynamic protein–protein and protein–lipid interactions while undergoing changes in conformation, orientation and binding interfaces. Predicting the sites of interactions between such polypeptides and phospholipid membranes is still a challenge. One example is the small eukaryotic GTPase Sar1, which functions in phospholipid bilayer remodeling and vesicle formation as part of the multimeric coat protein complex (COPII). The membrane interaction of Sar1 is strongly dependent on its N-terminal 23 amino acids. By monolayer adsorption experiments and infrared reflection-absorption spectroscopy (IRRAS), we elucidate the role of lipids in inducing the amphipathicity of this N-terminal stretch, which inserts into the monolayer as an amphipathic helix (AH). The AH inserting angle is determined and is consistent with the philicities and spatial distribution of the amino acid monomers. Using an advanced method of IRRAS data evaluation, the orientation of Sar1 with respect to the lipid layer prior to the recruitment of further COPII proteins is determined. The result indicates that only a slight reorientation of the membrane-bound Sar1 is needed to allow coat assembly. The time-course of the IRRAS analysis corroborates a role of slow GTP hydrolysis in Sar1 desorption from the membrane.

Formation and Stability of Lipid Membrane Nanotubes

Lipid membrane nanotubes are abundant in living cells, even though tubules are energetically less stable than sheet-like structures. According to membrane elastic theory, the tubular endoplasmic reticulum (ER), with its high area-to-volume ratio, appears to be particularly unstable. We explore how tubular membrane structures can nevertheless be induced and why they persist. In Monte Carlo simulations of a fluid-elastic membrane model subject to thermal fluctuations and without constraints on symmetry, we find that a steady increase in the area-to-volume ratio readily induces tubular structures. In simulations mimicking the ER wrapped around the cell nucleus, tubules emerge naturally as the membrane area increases. Once formed, a high energy barrier separates tubules from the thermodynamically favored sheet-like membrane structures. Remarkably, this barrier persists even at large area-to-volume ratios, protecting tubules against shape transformations despite enormous driving forces toward sheet-like structures. Molecular dynamics simulations of a molecular membrane model confirm the metastability of tubular structures. Volume reduction by osmotic regulation and membrane area growth by lipid production and by fusion of small vesicles emerge as powerful factors in the induction and stabilization of tubular membrane structures.

CURVATURE-DRIVEN MOLECULAR FLOW ON MEMBRANE SURFACE

This work presents a mathematical model for the localization of multiple species of diffusion molecules on membrane surfaces. Morphological change of bilayer membrane in vivo is generally modulated by proteins. Most of these modulations are associated with the localization of related proteins in the crowded lipid environments. We start with the energetic description of the distributions of molecules on curved membrane surface, and define the spontaneous curvature of bilayer membrane as a function of the molecule concentrations on membrane surfaces. A drift-diffusion equation governs the gradient flow of the surface molecule concentrations. We recast the energetic formulation and the related governing equations by using an Eulerian phase field description to define membrane morphology. Computational simulations with the proposed mathematical model and related numerical techniques predict (i) the molecular localization on static membrane surfaces at locations with preferred mean curvatures, and (ii) the generation of preferred mean curvature which in turn drives the molecular localization.

Membrane remodeling by amyloidogenic and non-amyloidogenic proteins studied by EPR

The advancement in site-directed spin labeling of proteins has enabled EPR studies to expand into newer research areas within the umbrella of protein-membrane interactions. Recently, membrane remodeling by amyloidogenic and non-amyloidogenic proteins has gained a substantial interest in relation to driving and controlling vital cellular processes such as endocytosis, exocytosis, shaping of organelles like endoplasmic reticulum, Golgi and mitochondria, intracellular vesicular trafficking, formation of filopedia and multivesicular bodies, mitochondrial fusion and fission, and synaptic vesicle fusion and recycling in neurotransmission. Misregulation in any of these processes due to an aberrant protein (mutation or misfolding) or alteration of lipid metabolism can be detrimental to the cell and cause disease. Dissection of the structural basis of membrane remodeling by proteins is thus quite necessary for an understanding of the underlying mechanisms, but it remains a formidable task due to the difficulties of various common biophysical tools in monitoring the dynamic process of membrane binding and bending by proteins. This is largely since membranes generally complicate protein structure analysis and this problem is amplified for structural analysis in the presence of different types of membrane curvatures. Recent EPR studies on membrane remodeling by proteins show that a significant structural information can be generated to delineate the role of different protein modules, domains and individual amino acids in the generation of membrane curvature. These studies also show how EPR can complement the data obtained by high resolution techniques such as X-ray and NMR. This perspective covers the application of EPR in recent studies for understanding membrane remodeling by amyloidogenic and non-amyloidogenic proteins that is useful for researchers interested in using or complimenting EPR to gain better understanding of membrane remodeling. We also discuss how a single protein can generate different type of membrane curvatures using specific conformations for specific membrane structures and how EPR is a versatile tool well-suited to analyze subtle alterations in structures under such modifying conditions which otherwise would have been difficult using other biophysical tools.

Fast Simulation of Lipid Vesicle Deformation Using Spherical Harmonic Approximation

Lipid vesicles appear ubiquitously in biological systems. Understanding how the mechanical and intermolecular interactions deform vesicle membranes is a fundamental question in biophysics. In this article we develop a fast algorithm to compute the surface configurations of lipid vesicles by introducing surface harmonic functions to approximate the membrane surface. This parameterization allows an analytical computation of the membrane curvature energy and its gradient for the efficient minimization of the curvature energy using a nonlinear conjugate gradient method. Our approach drastically reduces the degrees of freedom for approximating the membrane surfaces compared to the previously developed finite element and finite difference methods. Vesicle deformations with a reduced volume larger than 0.65 can be well approximated by using as small as 49 surface harmonic functions. The method thus has a great potential to reduce the computational expense of tracking multiple vesicles which deform for their interaction with external fields.

High cell-surface density of HER2 deforms cell membranes

Breast cancers (BC) with HER2 overexpression (referred to as HER2 positive) progress more aggressively than those with normal expression. Targeted therapies against HER2 can successfully delay the progression of HER2-positive BC, but details of how this overexpression drives the disease are not fully understood. Using single-molecule biophysical approaches, we discovered a new effect of HER2 overexpression on disease-relevant cell biological changes in these BC. We found HER2 overexpression causes deformation of the cell membranes, and this in turn disrupts epithelial features by perturbing cell-substrate and cell-cell contacts. This membrane deformation does not require receptor signalling activities, but results from the high levels of HER2 on the cell surface. Our finding suggests that early-stage morphological alterations of HER2-positive BC cells during cancer progression can occur in a physical and signalling-independent manner.

Controlling amphiphilic copolymer self-assembly morphologies based on macrocycle/anion recognition and nucleotide-induced payload release

We report here a new approach to creating diversiform copolymer-derived self-assembly morphologies that relies on macrocycle/anion recognition in aqueous media. This approach exploits the anion binding features of a water-soluble form of the so-called 'Texas-sized' molecular box. When this tetracationic receptor is added to an aqueous solution of an amphiphilic copolymer bearing tethered carboxylate anion substituents, binding occurs to form a macrocycle/polymer complex. As the concentration of the box-like receptor increases, the relative hydrophilic fraction of the copolymer complex likewise increases. This leads to changes in the overall morphology of the self-assembled ensemble. The net result is an environmentally controllable system that mimics on a proof-of-concept level the structural evolution of organelles seen in living cells. The macrocycle/anion interactions respond in differing degrees to three key biological species, namely ATP, ADP, and AMP, which may be used as "inputs" to induce disassembly of these vehicles. As a result of this triggering and the nature of the morphological changes induced, the present copolymer system is capable of capturing and releasing in controlled manner various test payloads, including hydrophobic and hydrophilic fluorophores. The copolymer displays low inherent cytotoxicity as inferred from cell proliferation assays involving the HUVEC and HepG2 cell lines.

Tunneling nanotubes mediate the transfer of stem cell marker CD133 between hematopoietic progenitor cells

Deciphering all mechanisms of intercellular communication used by hematopoietic progenitors is important, not only for basic stem cell research, but also in view of their therapeutic relevance. Here, we investigated whether these cells can produce the thin F-actin-based plasma membrane protrusions referred to as tunneling nanotubes (TNTs), which are known to bridge cells over long distances without contact with the substratum and transfer cargo molecules along them in various biological processes. We found that human primary CD34⁺ hematopoietic progenitors and leukemic KG1a cells develop such structures upon culture on primary mesenchymal stromal cells or specific extracellular-matrix-based substrata. Time-lapse video microscopy revealed that cell dislodgement is the primary mechanism responsible for TNT biogenesis. Surprisingly, we found that, among various cluster of differentiation (CD) markers, only the stem cell antigen CD133 is transferred between cells. It is selectively and directionally transported along the surface of TNTs in small clusters, such as cytoplasmic phospho-myosin light chain 2, suggesting that the latter actin motor protein might be implicated in this process. Our data provide new insights into the biology of hematopoietic progenitors that can contribute to our understanding of all facets of intercellular communication in the bone marrow microenvironment under healthy or cancerous conditions.