The mechanochemistry of endocytosis

Enhanced Adhesion of Mildly Positively Charged Vesicles to Endothelial Cells with Shed Glycocalyx

The glycocalyx of endothelial cells is a dynamic, gel-like layer of glycoproteins, proteoglycans, and glycolipids that lines the luminal surface of blood vessels, playing a critical role in vascular permeability, mechanotransduction, and protection against shear stress. In this study, we investigated the in vitro adhesion of giant unilamellar vesicles (GUVs) composed of 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). Specifically, we examined mildly positively charged DOTAP-DMPC (20:80) GUVs, based on positively charged DOTAP and neutral DMPC but exhibiting an overall mild positive charge in physiological buffer, and neutral DMPC GUVs, which show a negative charge in physiological buffer. Adhesion to human umbilical vein endothelial cells (HUVEC) was studied under three culture conditions: dynamic (intact glycocalyx), static (underdeveloped glycocalyx), and glycocalyx-shed (degraded glycocalyx). Vesicles were produced via electroformation, stained with Texas Red dye, and perfused over endothelial cells at a controlled velocity to simulate slow blood flow. Adhesion was tracked using fluorescence microscopy combined with cell segmentation techniques. Adhesion of DOTAP-DMPC vesicles was significantly enhanced-by approximately 3.5-fold-on glycocalyx-shed cells compared to cells with an intact glycocalyx. In contrast, DMPC vesicles showed no adhesion under any condition. Analysis of vesicle size distributions revealed no significant differences between adherent and nonadherent vesicles or between DOTAP-DMPC and DMPC vesicles. These findings provide insights into the role of the endothelial glycocalyx in regulating adhesion, with potential implications for tumor cell interactions with the endothelium and mechanisms underlying DOTAP-based transfection.

In Vitro and In-Silico Assessment of Gaussian Curvature-driven Internalization Kinetics of Nanoparticles

Nanoparticles have been of significant interest in various biomedical domains such as drug delivery, gene delivery, cytotoxicity analysis, and imaging. Despite the synthesis of a variety of nanoparticles, their cellular uptake efficiency remains a substantial obstacle, with only a small fraction of delivered nanoparticles (NPs) have been reported to traverse the cell membrane within 24 h. Consequently, higher doses are often necessitated, leading to increased toxicity concerns. In this investigation, we illustrate that nanoparticles having negative Gaussian curvature demonstrate rapid and efficient internalization into cells by lowering the energy barrier for membrane bending. Specifically, three types of gold nanoparticles; gold nanorods (GNR), gold nanodogbones at pH 4 (GDB4), and gold nanodogbones at pH 6 (GDB6) were synthesized, with Gaussian curvatures of 0, -166.91, and -376.62, respectively. Cellular uptake studies conducted via ICP-OES analysis reveal that GDB6 is taken up 140% more in A549 cells and 77% more in NIH3T3 cells compared to GNR. Confocal microscopy-based uptake studies further confirm the higher uptake of GDB6 compared to GNR. Additionally, molecular simulations indicate that GDB nanoparticles exhibit a significantly larger free energy change during translocation compared to GNR, emphasizing the impact of nanoparticle shape on uptake and translocation through the membrane and validating the efficacy of negative Gaussian curvature in enhancing cellular uptake, consistent with experimental observations. Overall, our findings emphasize the importance of nanoparticle curvature modulation in maximizing cellular uptake efficiency for improved biomedical applications, providing valuable insights into the design of nanomaterials for drug delivery purposes.

Connecting single-molecule and superresolution microscopies to cell biology through theoretical modeling

Recent developments of single-molecule and superresolution microscopies reveal novel spatial-temporal features of various cellular processes with unprecedented details, and greatly facilitate the development of theoretical models. In this review, we synthesize our view of how to meaningfully integrate these experimental approaches with theoretical modeling to obtain deeper understanding of the physical mechanisms of cell biology.

Roles of membrane mechanics-mediated feedback in membrane traffic

Synthesizing the recent progresses, we present our perspectives on how local modulations of membrane curvature, tension, and bending energy define the feedback controls over membrane traffic processes. We speculate the potential mechanisms of, and the control logic behind, the different membrane mechanics-mediated feedback in endocytosis and exo-endocytosis coupling. We elaborate the path forward with the open questions for theoretical considerations and the grand challenges for experimental validations.

Coaching ribosome biogenesis from the nuclear periphery

Severe invagination of the nuclear envelope is a hallmark of cancers, aging, neurodegeneration, and infections. However, the outcomes of nuclear invagination remain unclear. This work identified a new function of nuclear invagination: regulating ribosome biogenesis. With expansion microscopy, we observed frequent physical contact between nuclear invaginations and nucleoli. Surprisingly, the higher the invagination curvature, the more ribosomal RNA and pre-ribosomes are made in the contacted nucleolus. By growing cells on nanopillars that generate nuclear invaginations with desired curvatures, we can increase and decrease ribosome biogenesis. Based on this causation, we repressed the ribosome levels in breast cancer and progeria cells by growing cells on low-curvature nanopillars, indicating that overactivated ribosome biogenesis can be rescued by reshaping nuclei. Mechanistically, high-curvature nuclear invaginations reduce heterochromatin and enrich nuclear pore complexes, which promote ribosome biogenesis. We anticipate that our findings will serve as a foundation for further studies on nuclear deformation.

Alternative mechanisms of Notch activation by partitioning into distinct endosomal domains

Different membrane microdomain compositions provide unique environments that can regulate signaling receptor function. We identify microdomains on the endosome membrane of Drosophila endosomes, enriched in lipid-raft or clathrin/ESCRT-0, which are associated with Notch activation by distinct, ligand-independent mechanisms. Transfer of Notch between microdomains is regulated by Deltex and Suppressor of deltex ubiquitin ligases and is limited by a gate-keeper role for ESCRT complexes. Ubiquitination of Notch by Deltex recruits it to the clathrin/ESCRT-0 microdomain and enhances Notch activation by an ADAM10-independent/TRPML-dependent mechanism. This requirement for Deltex is bypassed by the downregulation of ESCRT-III. In contrast, while ESCRT-I depletion also activates Notch, it does so by an ADAM10-dependent/TRPML-independent mechanism and Notch is retained in the lipid raft-like microdomain. In the absence of such endosomal perturbation, different activating Notch mutations also localize to different microdomains and are activated by different mechanisms. Our findings demonstrate the interplay between Notch regulators, endosomal trafficking components, and Notch genetics, which defines membrane locations and activation mechanisms.

Membrane curvature catalyzes actin nucleation through nano-scale condensation of N-WASP-FBP17

Actin remodeling is spatiotemporally regulated by surface topographical cues on the membrane for signaling across diverse biological processes. Yet, the mechanism dynamic membrane curvature prompts quick actin cytoskeletal changes in signaling remain elusive. Leveraging the precision of nanolithography to control membrane curvature, we reconstructed catalytic reactions from the detection of nano-scale curvature by sensing molecules to the initiation of actin polymerization, which is challenging to study quantitatively in living cells. We show that this process occurs via topographical signal-triggered condensation and activation of the actin nucleation-promoting factor (NPF), Neuronal Wiskott-Aldrich Syndrome protein (N-WASP), which is orchestrated by curvature-sensing BAR-domain protein FBP17. Such N-WASP activation is fine-tuned by optimizing FBP17 to N-WASP stoichiometry over different curvature radii, allowing a curvature-guided macromolecular assembly pattern for polymerizing actin network locally. Our findings shed light on the intricate relationship between changes in curvature and actin remodeling via spatiotemporal regulation of NPF/BAR complex condensation.

Forceful patterning: theoretical principles of mechanochemical pattern formation

Biological pattern formation is essential for generating and maintaining spatial structures from the scale of a single cell to tissues and even collections of organisms. Besides biochemical interactions, there is an important role for mechanical and geometrical features in the generation of patterns. We review the theoretical principles underlying different types of mechanochemical pattern formation across spatial scales and levels of biological organization.

Formation of protein-mediated bilayer tubes is governed by a snapthrough transition

Plasma membrane tubes are ubiquitous in cellular membranes and in the membranes of intracellular organelles. They play crucial roles in trafficking, ion transport, and cellular motility. These tubes can be formed due to localized forces acting on the membrane or by the curvature induced by membrane-bound proteins. Here, we present a mathematical framework to model cylindrical tubular protrusions formed by proteins that induce anisotropic spontaneous curvature. Our analysis revealed that the tube radius depends on an effective tension that includes contributions from the bare membrane tension and the protein-induced curvature. We also found that the length of the tube undergoes an abrupt transition from a short, dome-shaped membrane to a long cylinder and this transition is characteristic of a snapthrough instability. Finally, we show that the snapthrough instability depends on the different parameters including coat area, bending modulus, and extent of protein-induced curvature. Our findings have implications for tube formation due to BAR-domain proteins in processes such as endocytosis, t-tubule formation in myocytes, and cristae formation in mitochondria.

Membrane compression by synaptic vesicle exocytosis triggers ultrafast endocytosis

Compensatory endocytosis keeps the membrane surface area of secretory cells constant following exocytosis. At chemical synapses, clathrin-independent ultrafast endocytosis maintains such homeostasis. This endocytic pathway is temporally and spatially coupled to exocytosis; it initiates within 50 ms at the region immediately next to the active zone where vesicles fuse. However, the coupling mechanism is unknown. Here, we demonstrate that filamentous actin is organized as a ring, surrounding the active zone at mouse hippocampal synapses. Assuming the membrane area conservation is due to this actin ring, our theoretical model suggests that flattening of fused vesicles exerts lateral compression in the plasma membrane, resulting in rapid formation of endocytic pits at the border between the active zone and the surrounding actin-enriched region. Consistent with model predictions, our data show that ultrafast endocytosis requires sufficient compression by exocytosis of multiple vesicles and does not initiate when actin organization is disrupted, either pharmacologically or by ablation of the actin-binding protein Epsin1. Our work suggests that membrane mechanics underlie the rapid coupling of exocytosis to endocytosis at synapses.

PLC regulates spontaneous glutamate release triggered by extracellular calcium and readily releasable pool size in neocortical neurons

Introduction

Dynamic physiological changes in brain extracellular calcium ([Ca²⁺]_o) occur when high levels of neuronal activity lead to substantial Ca²⁺ entry via ion channels reducing local [Ca²⁺]_o. Perturbations of the extracellular microenvironment that increase [Ca²⁺]_o are commonly used to study how [Ca²⁺] regulates neuronal activity. At excitatory synapses, the Ca²⁺-sensing receptor (CaSR) and other G-protein coupled receptors link [Ca²⁺]_o and spontaneous glutamate release. Phospholipase C (PLC) is activated by G-proteins and is hypothesized to mediate this process.

Methods

Patch-clamping cultured neocortical neurons, we tested how spontaneous glutamate release was affected by [Ca²⁺]_o and inhibition of PLC activity. We used hypertonic sucrose (HS) to evaluate the readily releasable pool (RRP) and test if it was affected by inhibition of PLC activity.

Results

Spontaneous glutamate release substantially increased with [Ca²⁺]_o, and inhibition of PLC activity, with U73122, abolished this effect. PLC-β1 is an abundant isoform in the neocortex, however, [Ca²⁺]_o-dependent spontaneous release was unchanged in PLC-β1 null mutants (PLC-β1^-/-). U73122 completely suppressed this response in PLC-β1^-/- neurons, indicating that this residual [Ca²⁺]_o-sensitivity may be mediated by other PLC isoforms. The RRP size was substantially reduced after incubation in U73122, but not U73343. Phorbol esters increased RRP size after PLC inhibition.

Discussion

Together these data point to a strong role for PLC in mediating changes in spontaneous release elicited by [Ca²⁺]_o and other extracellular cues, possibly by modifying the size of the RRP.

Spatiotemporal organization and correlation of tip-focused exocytosis and endocytosis in regulating pollen tube tip growth

Pollen tube polar growth is a key cellular process during plant fertilization and is regulated by tip-focused exocytosis and endocytosis. However, the spatiotemporal dynamics and localizations of apical exocytosis and endocytosis in the tip region are still a matter of debate. Here, we use a refined spinning-disk confocal microscope coupled with fluorescence recovery after photobleaching for sustained live imaging and quantitative analysis of rapid vesicular activities in growing pollen tube tips. We traced and analyzed the occurrence site of exocytic plasma membrane-targeting of Arabidopsis secretory carrier membrane protein 4 and its subsequent endocytosis in tobacco pollen tube tips. We demonstrated that the pollen tube apex is the site for both vesicle polar exocytic fusion and endocytosis to take place. In addition, we disrupted either tip-focused exocytosis or endocytosis and found that their dynamic activities are closely correlated with one another basing on the spatial organization of actin fringe. Collectively, our findings attempt to propose a new exocytosis and endocytosis-coordinated yin-yang working model underlying the apical membrane organization and dynamics during pollen tube tip growth.

Modeling membrane reshaping driven by dynamic protein assemblies

Remodeling of membranes in living systems is almost universally coupled to self-assembly of soluble proteins. Proteins assemble into semi-rigid shells that reshape attached membranes, and into filaments that protrude membranes. These assemblies are temporary, building from reversible protein and membrane interactions that must nucleate in the proper location. The interactions are strongly influenced by the nonequilibrium environment of the cell, such as gradients of components or active modifications by kinases. From a modeling perspective, understanding mechanisms and control thus requires 1. time-dependent approaches that ideally incorporate 2. macromolecular structure, 3. out-of-equilibrium processes, and 4. deformable membranes over microns and seconds. Realistically, tradeoffs must be made with these last three features. However, we see recent developments from the highly coarsened molecule-based scale, the continuum reaction-diffusion scale, and hybrid approaches as stimulating efforts in diverse applications. We discuss here methodological advances and progress towards simulating these processes as they occur physiologically.

Membrane curvature as a signal to ensure robustness of diverse cellular processes

An increasing corpus of research has demonstrated that membrane shape, generated either by the external environment of the cell or by intrinsic mechanisms such as cytokinesis and vesicle or organelle formation, is an important parameter in the control of diverse cellular processes. In this review we discuss recent findings that demonstrate how membrane curvature (from nanometer to micron length-scales) alters protein function. We describe an expanding toolkit for experimentally modulating membrane curvature to reveal effects on protein function, and discuss how membrane curvature - far from being a passive consequence of the physical environment and the internal protein activity of a cell - is an important signal that controls protein affinity and enzymatic activity to ensure robust forward progression of key processes within the cell.

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.

The endocytic protein machinery as an actin-driven membrane-remodeling machine

In clathrin-mediated endocytosis, a principal membrane trafficking route of all eukaryotic cells, forces are applied to invaginate the plasma membrane and form endocytic vesicles. These forces are provided by specific endocytic proteins and the polymerizing actin cytoskeleton. One of the best-studied endocytic systems is endocytosis in yeast, known for its simplicity, experimental amenability, and overall similarity to human endocytosis. Importantly, the yeast endocytic protein machinery generates and transmits tremendous force to bend the plasma membrane, making this system beneficial for mechanistic studies of cellular force-driven membrane reshaping. This review summarizes important protein players, molecular functions, applied forces, and open questions and perspectives of this robust, actin-powered membrane-remodeling protein machine.

The CD63 homologs, Tsp42Ee and Tsp42Eg, restrict endocytosis and promote neurotransmission through differential regulation of synaptic vesicle pools

The Tetraspanin (Tsp), CD63, is a transmembrane component of late endosomes and facilitates vesicular trafficking through endosomal pathways. Despite being widely expressed in the human brain and localized to late endosomes, CD63's role in regulating endo- and exocytic cycling at the synapse has not been investigated. Synaptic vesicle pools are highly dynamic and disruptions in the mobilization and replenishment of these vesicle pools have adverse neuronal effects. We find that the CD63 homologs, Tsp42Ee and Tsp42Eg, are expressed at the Drosophila neuromuscular junction to regulate synaptic vesicle pools through both shared and unique mechanisms. Tsp42Ee and Tsp42Eg negatively regulate endocytosis and positively regulate neurotransmitter release. Both tsp mutants show impaired locomotion, reduced miniature endplate junctional current frequencies, and increased endocytosis. Expression of human CD63 in Drosophila neurons leads to impaired endocytosis suggesting the role of Tsps in endocytosis is conserved. We further show that Tsps influence the synaptic cytoskeleton and membrane composition by regulating Futsch loop formation and synaptic levels of SCAR and PI(4,5)P2. Finally, Tsp42Ee and Tsp42Eg influence the synaptic localization of several vesicle-associated proteins including Synapsin, Synaptotagmin, and Cysteine String Protein. Together, our results present a novel function for Tsps in the regulation of vesicle pools and provide insight into the molecular mechanisms of Tsp-related synaptic dysfunction.

Regulation of membrane scission in yeast endocytosisDepartment of Biochemistry and National Centre of Competence in Research, Chemical Biology, University of Geneva, Geneva, Switzerland

During clathrin-mediated endocytosis, a flat plasma membrane is shaped into an invagination that undergoes scission to form a vesicle. In mammalian cells, the force that drives the transition from invagination to vesicle is primarily provided by the GTPase dynamin that acts in concert with crescent-shaped BAR domain proteins. In yeast cells, the mechanism of endocytic scission is unclear. The yeast BAR domain protein complex Rvs161/167 (Rvs) nevertheless plays an important role in this process: deletion of Rvs dramatically reduces scission efficiency. A mechanistic understanding of the influence of Rvs on scission however, remains incomplete. We used quantitative live-cell imaging and genetic manipulation to understand the recruitment and function of Rvs and other late-stage proteins at yeast endocytic sites. We found that arrival of Rvs at endocytic sites is timed by interaction of its BAR domain with specific membrane curvature. A second domain of Rvs167 - the SH3 domain - affects localization efficiency of Rvs. We show that Myo3, one of the two type-I myosins in Saccharomyces cerevisiae, has a role in recruiting Rvs167 via the SH3 domain. Removal of the SH3 domain also affects assembly and disassembly of actin and impedes membrane invagination. Our results indicate that both BAR and SH3 domains are important for the role of Rvs as a regulator of scission. We tested other proteins implicated in vesicle formation in Saccharomyces cerevisiae, and found that neither synaptojanins nor dynamin contribute directly to membrane scission. We propose that recruitment of Rvs BAR domains delays scission and allows invaginations to grow by stabilizing them. We also propose that vesicle formation is dependent on the force exerted by the actin network.

Induced nanoscale membrane curvature bypasses the essential endocytic function of clathrin

During clathrin-mediated endocytosis (CME), flat plasma membrane is remodeled to produce nanometer-scale vesicles. The mechanisms underlying this remodeling are not completely understood. The ability of clathrin to bind membranes of distinct geometries casts uncertainty on its specific role in curvature generation/stabilization. Here, we used nanopatterning to produce substrates for live-cell imaging, with U-shaped features that bend the ventral plasma membrane of a cell into shapes resembling energetically unfavorable CME intermediates. This induced membrane curvature recruits CME proteins, promoting endocytosis. Upon AP2, FCHo1/2, or clathrin knockdown, CME on flat substrates is severely diminished. However, induced membrane curvature recruits CME proteins in the absence of FCHo1/2 or clathrin and rescues CME dynamics/cargo uptake after clathrin (but not AP2 or FCHo1/2) knockdown. Induced membrane curvature enhances CME protein recruitment upon branched actin assembly inhibition under elevated membrane tension. These data establish that membrane curvature assists in CME nucleation and that the essential function of clathrin during CME is to facilitate curvature evolution, rather than scaffold protein recruitment.

Integrating protein copy numbers with interaction networks to quantify stoichiometry in clathrin-mediated endocytosis

Proteins that drive processes like clathrin-mediated endocytosis (CME) are expressed at copy numbers within a cell and across cell types varying from hundreds (e.g. auxilin) to millions (e.g. clathrin). These variations contain important information about function, but without integration with the interaction network, they cannot capture how supply and demand for each protein depends on binding to shared and distinct partners. Here we construct the interface-resolved network of 82 proteins involved in CME and establish a metric, a stoichiometric balance ratio (SBR), that quantifies whether each protein in the network has an abundance that is sub- or super-stoichiometric dependent on the global competition for binding. We find that highly abundant proteins (like clathrin) are super-stoichiometric, but that not all super-stoichiometric proteins are highly abundant, across three cell populations (HeLa, fibroblast, and neuronal synaptosomes). Most strikingly, within all cells there is significant competition to bind shared sites on clathrin and the central AP-2 adaptor by other adaptor proteins, resulting in most being in excess supply. Our network and systematic analysis, including response to perturbations of network components, show how competition for shared binding sites results in functionally similar proteins having widely varying stoichiometries, due to variations in both abundance and their unique network of binding partners.

Large self-assembled clathrin lattices spontaneously disassemble without sufficient adaptor proteins

Clathrin-coated structures must assemble on cell membranes to internalize receptors, with the clathrin protein only linked to the membrane via adaptor proteins. These structures can grow surprisingly large, containing over 20 clathrin, yet they often fail to form productive vesicles, instead aborting and disassembling. We show that clathrin structures of this size can both form and disassemble spontaneously when adaptor protein availability is low, despite high abundance of clathrin. Here, we combine recent in vitro kinetic measurements with microscopic reaction-diffusion simulations and theory to differentiate mechanisms of stable vs unstable clathrin assembly on membranes. While in vitro conditions drive assembly of robust, stable lattices, we show that concentrations, geometry, and dimensional reduction in physiologic-like conditions do not support nucleation if only the key adaptor AP-2 is included, due to its insufficient abundance. Nucleation requires a stoichiometry of adaptor to clathrin that exceeds 1:1, meaning additional adaptor types are necessary to form lattices successfully and efficiently. We show that the critical nucleus contains ~25 clathrin, remarkably similar to sizes of the transient and abortive structures observed in vivo. Lastly, we quantify the cost of bending the membrane under our curved clathrin lattices using a continuum membrane model. We find that the cost of bending the membrane could be largely offset by the energetic benefit of forming curved rather than flat structures, with numbers comparable to experiments. Our model predicts how adaptor density can tune clathrin-coated structures from the transient to the stable, showing that active energy consumption is therefore not required for lattice disassembly or remodeling during growth, which is a critical advance towards predicting productive vesicle formation.

Sterols lower energetic barriers of membrane bending and fission necessary for efficient clathrin-mediated endocytosis

Clathrin-mediated endocytosis (CME) is critical for cellular signal transduction, receptor recycling, and membrane homeostasis in mammalian cells. Acute depletion of cholesterol disrupts CME, motivating analysis of CME dynamics in the context of human disorders of cholesterol metabolism. We report that inhibition of post-squalene cholesterol biosynthesis impairs CME. Imaging of membrane bending dynamics and the CME pit ultrastructure reveals prolonged clathrin pit lifetimes and shallow clathrin-coated structures, suggesting progressive impairment of curvature generation correlates with diminishing sterol abundance. Sterol structural requirements for efficient CME include 3′ polar head group and B-ring conformation, resembling the sterol structural prerequisites for tight lipid packing and polarity. Furthermore, Smith-Lemli-Opitz fibroblasts with low cholesterol abundance exhibit deficits in CME-mediated transferrin internalization. We conclude that sterols lower the energetic costs of membrane bending during pit formation and vesicular scission during CME and suggest that reduced CME activity may contribute to cellular phenotypes observed within disorders of cholesterol metabolism.

Anderson et al. demonstrate that sterol abundance and identity play a dominant role in facilitating clathrin-mediated endocytosis. Detailed analyses of clathrin-coated pits under sterol depletion support a requirement for sterol-mediated membrane bending during multiple stages of endocytosis, implicating endocytic dysfunction within the pathogenesis of disorders of cholesterol metabolism.

Biomembranes undergo complex, non-axisymmetric deformations governed by Kirchhoff-Love kinematicsand revealed by a three-dimensional computational framework

Biomembranes play a central role in various phenomena like locomotion of cells, cell-cell interactions, packaging and transport of nutrients, transmission of nerve impulses, and in maintaining organelle morphology and functionality. During these processes, the membranes undergo significant morphological changes through deformation, scission, and fusion. Modelling the underlying mechanics of such morphological changes has traditionally relied on reduced order axisymmetric representations of membrane geometry and deformation. Axisymmetric representations, while robust and extensively deployed, suffer from their inability to model-symmetry breaking deformations and structural bifurcations. To address this limitation, a three-dimensional computational mechanics framework for high fidelity modelling of biomembrane deformation is presented. The proposed framework brings together Kirchhoff–Love thin-shell kinematics, Helfrich-energy-based mechanics, and state-of-the-art numerical techniques for modelling deformation of surface geometries. Lipid bilayers are represented as spline-based surface discretizations immersed in a three-dimensional space; this enables modelling of a wide spectrum of membrane geometries, boundary conditions, and deformations that are physically admissible in a three-dimensional space. The mathematical basis of the framework and its numerical machinery are presented, and their utility is demonstrated by modelling three classical, yet non-trivial, membrane deformation problems: formation of tubular shapes and their lateral constriction, Piezo1-induced membrane footprint generation and gating response, and the budding of membranes by protein coats during endocytosis. For each problem, the full three-dimensional membrane deformation is captured, potential symmetry-breaking deformation paths identified, and various case studies of boundary and load conditions are presented. Using the endocytic vesicle budding as a case study, we also present a ‘phase diagram’ for its symmetric and broken-symmetry states.

Safety Evaluation of Nanotechnology Products

Nanomaterials are now being used in a wide variety of biomedical applications. Medical and health-related issues, however, have raised major concerns, in view of the potential risks of these materials against tissue, cells, and/or organs and these are still poorly understood. These particles are able to interact with the body in countless ways, and they can cause unexpected and hazardous toxicities, especially at cellular levels. Therefore, undertaking in vitro and in vivo experiments is vital to establish their toxicity with natural tissues. In this review, we discuss the underlying mechanisms of nanotoxicity and provide an overview on in vitro characterizations and cytotoxicity assays, as well as in vivo studies that emphasize blood circulation and the in vivo fate of nanomaterials. Our focus is on understanding the role that the physicochemical properties of nanomaterials play in determining their toxicity.

Curvature-driven feedback on aggregation-diffusion of proteins in lipid bilayers

Membrane bending is an extensively studied problem from both modeling and experimental perspectives because of the wide implications of curvature generation in cell biology. Many of the curvature generating aspects in membranes can be attributed to interactions between proteins and membranes. These interactions include protein diffusion and formation of aggregates due to protein-protein interactions in the plane of the membrane. Recently, we developed a model that couples the in-plane flow of lipids and diffusion of proteins with the out-of-plane bending of the membrane. Building on this work, here, we focus on the role of explicit aggregation of proteins on the surface of the membrane in the presence of membrane bending and diffusion. We develop a comprehensive framework that includes lipid flow, membrane bending, the entropy of protein distribution, along with an explicit aggregation potential and derive the governing equations for the coupled system. We compare this framework to the Cahn-Hillard formalism to predict the regimes in which the proteins form patterns on the membrane. We demonstrate the utility of this model using numerical simulations to predict how aggregation and diffusion, when coupled with curvature generation, can alter the landscape of membrane-protein interactions.

Multiple roles for actin in secretory and endocytic pathways

Actin filaments play multiple roles in the secretory pathway and in endosome dynamics in mammals, including maintenance of Golgi structure, release of membrane cargo from the trans-Golgi network (TGN), endocytosis, and endosomal sorting dynamics. In addition, TGN carrier transport and endocytosis both occur by multiple mechanisms in mammals. Actin likely plays a role in at least four mammalian endocytic pathways, five pathways for membrane release from the TGN, and three processes involving endosomes. Also, the mammalian Golgi structure is highly dynamic, and actin is likely important for these dynamics. One challenge for many of these processes is the need to deal with other membrane-associated structures, such as the cortical actin network at the plasma membrane or the matrix that surrounds the Golgi. Arp2/3 complex is a major actin assembly factor in most of the processes mentioned, but roles for formins and tandem WH2-motif-containing assembly factors are being elucidated and are anticipated to grow with further study. The specific role for actin has not been defined for most of these processes, but is likely to involve the generation of force for membrane dynamics, either by actin polymerization itself or by myosin motor activity. Defining these processes mechanistically is necessary for understanding membrane dynamics in general, as well as pathways that utilize these processes, such as autophagy.

Investigation of the pathway dependent endocytosis of gold nanoparticles by surface-enhanced Raman scattering

Endocytosis is a critical mechanism providing not only internalization of biomacromolecular structures but also communication with the environment where cells reside. Due to being the first step at the interaction interface, the route of cellular uptake has a major role governing the intracellular destinations and behaviors of molecular and non-molecular species including nanoparticles. To this end, various methods employing variety of techniques are investigated. In this study, surface-enhanced Raman spectroscopy (SERS) based approach for the investigation of endocytosis of gold nanoparticles (AuNPs) is reported. Internalization pathways of AuNPs were examined by flow cytometry via specific inhibitors for each endocytosis pathway type using three model cell lines Beas-2b, A549 and PNT1A. Macropinocytosis was blocked by cytochalasin D (CytoD), clathrin mediated endocytosis (CME) by sucrose (Scr), and caveolae mediated endocytosis (CE) by filipin (Fil). The results showed that cell type dependent AuNPs internalization affects not only the response of the cells to the inhibitors but also the obtained SERS spectra. SERS spectra of PNT1A cells treated with inhibitors was influenced most. The inhibition of each endocytosis pathway significantly affected the SERS spectral pattern and the spectral changes in different endocytosis pathways were clearly discriminated from each other. This means that SERS can significantly contribute to the investigation of different endosomal pathways from single living cells without any disruption of the cells or labeling.

Value of models for membrane budding

The budding of membranes and curvature generation is common to many forms of trafficking in cells. Clathrin-mediated endocytosis, as a prototypical example of trafficking, has been studied in great detail using a variety of experimental systems and methods. Recently, advances in experimental methods have led to great strides in insights on the molecular mechanisms and the spatiotemporal dynamics of the protein machinery associated with membrane curvature generation. These advances have been ably supported by computational models, which have given us insights into the underlying mechanical principles of clathrin-mediated endocytosis. On the other hand, targeted experimental perturbation of membranes has lagged behind that of proteins in cells. In this area, modeling is especially critical to interpret experimental measurements in a mechanistic context. Here, we discuss the contributions made by these models to our understanding of endocytosis and identify opportunities to strengthen the connections between models and experiments.

Membrane signalosome: where biophysics meets systems biology

We opine on the recent advances in experiments and modeling of modular signaling complexes assembled on mammalian cell membranes (membrane signalosomes) in the context of several applications including intracellular trafficking, cell migration, and immune response. Characterizing the individual components of the membrane assemblies at the nanoscale, ranging from protein-lipid and protein-protein interactions, to membrane morphology, and the energetics of emergent assemblies at the subcellular to cellular scales pose significant challenges. Overcoming these challenges through the iterative coupling of multiscale modeling and experiment can be transformative in terms of addressing the gaps between structural biology and super-resolution microscopy, as it holds the key to the discovery of fundamental mechanisms behind the emergence of function in the membrane signalosome.

Emerging roles of the MAGE protein family in stress response pathways

The melanoma antigen (MAGE) proteins all contain a MAGE homology domain. MAGE genes are conserved in all eukaryotes and have expanded from a single gene in lower eukaryotes to ∼40 genes in humans and mice. Whereas some MAGEs are ubiquitously expressed in tissues, others are expressed in only germ cells with aberrant reactivation in multiple cancers. Much of the initial research on MAGEs focused on exploiting their antigenicity and restricted expression pattern to target them with cancer immunotherapy. Beyond their potential clinical application and role in tumorigenesis, recent studies have shown that MAGE proteins regulate diverse cellular and developmental pathways, implicating them in many diseases besides cancer, including lung, renal, and neurodevelopmental disorders. At the molecular level, many MAGEs bind to E3 RING ubiquitin ligases and, thus, regulate their substrate specificity, ligase activity, and subcellular localization. On a broader scale, the MAGE genes likely expanded in eutherian mammals to protect the germline from environmental stress and aid in stress adaptation, and this stress tolerance may explain why many cancers aberrantly express MAGEs Here, we present an updated, comprehensive review on the MAGE family that highlights general characteristics, emphasizes recent comparative studies in mice, and describes the diverse functions exerted by individual MAGEs.

Effects of foliar application of graphene oxide on cadmium uptake by lettuce

Although graphene oxide (GO) has been widely used to enhance soil quality and crop yield, there is currently little information regarding the effects of foliar application of GO on cadmium (Cd) toxicity to plants. In this study, we investigated the response to GO in lettuce cultivated under Cd stress in hydroponic conditions. Lettuce was grown from seeds in a nutrient solution supplemented with 2 mg/L Cd and the leaves were sprayed with 0, 30, and 60 mg/L GO. The results indicated that application of 30 mg/L GO significantly increased the total length, surface area, average diameter, and hair number of lettuce roots, and effectively alleviated the negative effects of Cd on root growth. Furthermore, foliar application of 30 mg/L GO, but not 60 mg/L GO, significantly improved the quality of lettuce, including reduction in Cd accumulation in leaves and roots and increase in soluble sugar, protein, and vitamin C content. Transmission electron microscopy revealed that GO nanoparticles, which entered the leaves and were subsequently transported to the roots via the vascular system (phloem), reduced the damaging effect of Cd on cellular organelles, including the cell wall and membrane, chloroplasts, and starch granules. The effect may be attributed to the absorption of GO by lettuce cells, where it fixed Cd2+, thus reducing Cd2+ bioavailability, or to the improvement of Cd tolerance through regulation of lettuce metabolic pathways. Gaussian simulation analysis revealed that Cd caused significant changes in the GO molecule, resulting in detachment of an epoxy group from the GO carbon ring and breakage of OH bonds in hydroxyl groups, whereupon the oxygen freed from the OH bond formed a new bond with Cd. Collectively, these results indicate that foliar application of 30 mg/L GO can enhance the tolerance of lettuce to Cd, promote plant growth, and improve nutritional quality.

Protein crowding mediates membrane remodeling in upstream ESCRT-induced formation of intraluminal vesicles

As part of the lysosomal degradation pathway, the endosomal sorting complexes required for transport (ESCRT-0 to -III/VPS4) sequester receptors at the endosome and simultaneously deform the membrane to generate intraluminal vesicles (ILVs). Whereas ESCRT-III/VPS4 have an established function in ILV formation, the role of upstream ESCRTs (0 to II) in membrane shape remodeling is not understood. Combining experimental measurements and electron microscopy analysis of ESCRT-III-depleted cells with a mathematical model, we show that upstream ESCRT-induced alteration of the Gaussian bending rigidity and their crowding in concert with the transmembrane cargo on the membrane induce membrane deformation and facilitate ILV formation: Upstream ESCRT-driven budding does not require ATP consumption as only a small energy barrier needs to be overcome. Our model predicts that ESCRTs do not become part of the ILV, but localize with a high density at the membrane neck, where the steep decline in the Gaussian curvature likely triggers ESCRT-III/VPS4 assembly to enable neck constriction and scission.

Nonaxisymmetric Shapes of Biological Membranes from Locally Induced Curvature

In various biological processes such as endocytosis and caveolae formation, the cell membrane is locally deformed into curved morphologies. Previous models to study membrane morphologies resulting from locally induced curvature often only consider the possibility of axisymmetric shapes-an indeed unphysical constraint. Past studies predict that the cell membrane buds at low resting tensions and stalls at a flat pit at high resting tensions. In this work, we lift the restriction to axisymmetry to study all possible membrane morphologies. Only if the resting tension of the membrane is low, we reproduce axisymmetric membrane morphologies. When the resting tension is moderate to high, we show that 1) axisymmetric membrane pits are unstable and 2) nonaxisymmetric ridge-shaped structures are energetically favorable. Furthermore, we find the interplay between intramembrane viscous flow and the rate of induced curvature affects the membrane's ability to transition into nonaxisymmetric ridges and axisymmetric buds. In particular, we show that axisymmetric buds are favored when the induced curvature is rapidly increased, whereas nonaxisymmetric ridges are favored when the curvature is slowly increased. Our results hold relevant implications for biological processes such as endocytosis and physical phenomena like phase separation in lipid bilayers.

Loss of MAGEL2 in Prader-Willi syndrome leads to decreased secretory granule and neuropeptide production

Prader-Willi syndrome (PWS) is a developmental disorder caused by loss of maternally imprinted genes on 15q11-q13, including melanoma antigen gene family member L2 (MAGEL2). The clinical phenotypes of PWS suggest impaired hypothalamic neuroendocrine function; however, the exact cellular defects are unknown. Here, we report deficits in secretory granule (SG) abundance and bioactive neuropeptide production upon loss of MAGEL2 in humans and mice. Unbiased proteomic analysis of Magel2pΔ/m+ mice revealed a reduction in components of SG in the hypothalamus that was confirmed in 2 PWS patient-derived neuronal cell models. Mechanistically, we show that proper endosomal trafficking by the MAGEL2-regulated WASH complex is required to prevent aberrant lysosomal degradation of SG proteins and reduction of mature SG abundance. Importantly, loss of MAGEL2 in mice, NGN2-induced neurons, and human patients led to reduced neuropeptide production. Thus, MAGEL2 plays an important role in hypothalamic neuroendocrine function, and cellular defects in this pathway may contribute to PWS disease etiology. Moreover, these findings suggest unanticipated approaches for therapeutic intervention.

Principles of self-organization and load adaptation by the actin cytoskeleton during clathrin-mediated endocytosis

Force generation by actin assembly shapes cellular membranes. An experimentally constrained multiscale model shows that a minimal branched actin network is sufficient to internalize endocytic pits against membrane tension. Around 200 activated Arp2/3 complexes are required for robust internalization. A newly developed molecule-counting method determined that ~200 Arp2/3 complexes assemble at sites of clathrin-mediated endocytosis in human cells. Simulations predict that actin self-organizes into a radial branched array with growing ends oriented toward the base of the pit. Long actin filaments bend between attachment sites in the coat and the base of the pit. Elastic energy stored in bent filaments, whose presence was confirmed by cryo-electron tomography, contributes to endocytic internalization. Elevated membrane tension directs more growing filaments toward the base of the pit, increasing actin nucleation and bending for increased force production. Thus, spatially constrained actin filament assembly utilizes an adaptive mechanism enabling endocytosis under varying physical constraints.

The outer membrane of a cell is a tight but elastic barrier that controls what enters or leaves the cell. Large molecules typically cannot cross this membrane unaided. Instead, to enter the cell, they must be packaged into a pocket of the membrane that is then pulled inside. This process, called endocytosis, shuttles material into a cell hundreds of times a minute.

Endocytosis relies on molecular machines that assemble and disassemble at the membrane as required. One component, a protein called actin, self-assembles near the membrane into long filaments with many repeated subunits. These filaments grow against the membrane, pulling it inwards. But it was not clear how actin filaments organize in such a way that allows them to pull on the membrane with enough force – and without a template to follow.

Akamatsu et al. set about identifying how actin operates during endocytosis by using computer simulations that were informed by measurements made in living cells. The simulations included information about the location of actin and other essential molecules, along with the details of how these molecules work individually and together. Akamatsu et al. also developed a method to count the numbers of molecules of a key protein at individual sites of endocytosis. High-resolution imaging was then used to create 3D pictures of actin and endocytosis in action in human cells grown in the laboratory.

The analysis showed the way actin filaments arrange themselves depends on the starting positions of a few key molecules that connect to actin. Imaging confirmed that, like a pole-vaulting pole, the flexible actin filaments bend to store energy and then release it to pull the membrane inwards during endocytosis. Finally, the simulations predicted that the collection of filaments adapts its shape and size in response to the resistance of the elastic membrane. This makes the system opportunistic and adaptable to the unpredictable environment within cells.

Emergent membrane morphologies in relaxed and tense membranes in presence of reversible adhesive pinning interactions

The morphologies of cell membranes, and specifically the local curvature distributions are determined either by its intrinsic components such as lipids and membrane-associated proteins or by the adhesion forces due to membrane interactions with the cytoskeleton, extracellular matrix (ECM) and other cells in the tissue, as well as physical variables such as membrane and frame tensions. We present a computational analysis for a model of pinned membranes based on the dynamically triangulated Monte Carlo (MC) model for membranes. We show that membrane adhesion to ECM or a substrate promotes curvature generation on cell membranes, and this process depends on the excess area, or equivalently membrane tension, and the density of adhesion sites. This biophysics based model predicts adhesion induced biogenesis of microvesicles in cell membranes. For a moderate density of adhesion sites and high excess membrane area, an increase in membrane tension can result in the formation of microvesicles and tubules on the membrane. We also demonstrate the significance of intrinsically curved proteins in promoting vesiculation on pinned membranes. The results presented here are relevant to the understanding of microvesicle biogenesis and curved membrane topographies due to physical factors such as substrate stiffness and ECM interactions.

Synaptojanin and Endophilin Mediate Neck Formation during Ultrafast Endocytosis

Ultrafast endocytosis generates vesicles from the plasma membrane as quickly as 50 ms in hippocampal neurons following synaptic vesicle fusion. The molecular mechanism underlying the rapid maturation of these endocytic pits is not known. Here we demonstrate that synaptojanin-1, and its partner endophilin-A, function in ultrafast endocytosis. In the absence of synaptojanin or endophilin, the membrane is rapidly invaginated, but pits do not become constricted at the base. The 5-phosphatase activity of synaptojanin is involved in formation of the neck, but 4-phosphatase is not required. Nevertheless, these pits are eventually cleaved into vesicles; within a 30-s interval, synaptic endosomes form and are resolved by clathrin-mediated budding. Then synaptojanin and endophilin function at a second step to aid with the removal of clathrin coats from the regenerated vesicles. These data together suggest that synaptojanin and endophilin can mediate membrane remodeling on a millisecond timescale during ultrafast endocytosis.

Biophysics at the coffee shop: lessons learned working with George Oster

Over the past 50 years, the use of mathematical models, derived from physical reasoning, to describe molecular and cellular systems has evolved from an art of the few to a cornerstone of biological inquiry. George Oster stood out as a pioneer of this paradigm shift from descriptive to quantitative biology not only through his numerous research accomplishments, but also through the many students and postdocs he mentored over his long career. Those of us fortunate enough to have worked with George agree that his sharp intellect, physical intuition, and passion for scientific inquiry not only inspired us as scientists but also greatly influenced the way we conduct research. We would like to share a few important lessons we learned from George in honor of his memory and with the hope that they may inspire future generations of scientists.

Unraveling Polymeric Nanoparticles Cell Uptake Pathways: Two Decades Working to Understand Nanoparticles Journey to Improve Gene Therapy

Polymeric nanoparticles have aroused an increasing interest in the last decades as novel advanced delivery systems to improve the treatment of many diseases. Hard work has been performed worldwide designing and developing polymeric nanoparticles using different building blocks, which target specific cell types, trying to avoid bioaccumulation and degradation pathways. The main handicap of the design is to understand the final fate and the journey that the nanoparticle will follow, which is intimately ligated with the chemical and physical properties of the nanoparticles themselves and specific factors of the targeted cells. Although the huge number of published scientific articles regarding polymeric nanoparticles for biomedical applications, their use in clinics is still limited. This fact could be explained by the limited data reporting the interaction of the huge diversity of polymeric nanoparticles with cells. This knowledge is essential to understand nanoparticle uptake and trafficking inside cells to the subcellular target structure.In this chapter, we aim to contribute to this field of knowledge by: (1) summarizing the polymeric nanoparticles properties and cellular factors that influence nanoparticle endocytosis and (2) reviewing the endocytic pathways classified as a function of nanoparticle size and as a function of the receptor playing a role. The revision of previously reported endocytic pathways for particular polymeric nanoparticles could facilitate scientist involved in this field to easily delineate efficient delivery systems based on polymeric nanoparticles.

Molecular mechanisms of force production in clathrin-mediated endocytosis

During clathrin-mediated endocytosis (CME), a flat patch of membrane is invaginated and pinched off to release a vesicle into the cytoplasm. In yeast CME, over 60 proteins-including a dynamic actin meshwork-self-assemble to deform the plasma membrane. Several models have been proposed for how actin and other molecules produce the forces necessary to overcome the mechanical barriers of membrane tension and turgor pressure, but the precise mechanisms and a full picture of their interplay are still not clear. In this review, we discuss the evidence for these force production models from a quantitative perspective and propose future directions for experimental and theoretical work that could clarify their various contributions.

Modeling Membrane Curvature Generation due to Membrane⁻Protein Interactions

To alter and adjust the shape of the plasma membrane, cells harness various mechanisms of curvature generation. Many of these curvature generation mechanisms rely on the interactions between peripheral membrane proteins, integral membrane proteins, and lipids in the bilayer membrane. Mathematical and computational modeling of membrane curvature generation has provided great insights into the physics underlying these processes. However, one of the challenges in modeling these processes is identifying the suitable constitutive relationships that describe the membrane free energy including protein distribution and curvature generation capability. Here, we review some of the commonly used continuum elastic membrane models that have been developed for this purpose and discuss their applications. Finally, we address some fundamental challenges that future theoretical methods need to overcome to push the boundaries of current model applications.

Dissipative structures in biological systems: bistability, oscillations, spatial patterns and waves

The goal of this review article is to assess how relevant is the concept of dissipative structure for understanding the dynamical bases of non-equilibrium self-organization in biological systems, and to see where it has been applied in the five decades since it was initially proposed by Ilya Prigogine. Dissipative structures can be classified into four types, which will be considered, in turn, and illustrated by biological examples: (i) multistability, in the form of bistability and tristability, which involve the coexistence of two or three stable steady states, or in the form of birhythmicity, which involves the coexistence between two stable rhythms; (ii) temporal dissipative structures in the form of sustained oscillations, illustrated by biological rhythms; (iii) spatial dissipative structures, known as Turing patterns; and (iv) spatio-temporal structures in the form of propagating waves. Rhythms occur with widely different periods at all levels of biological organization, from neural, cardiac and metabolic oscillations to circadian clocks and the cell cycle; they play key roles in physiology and in many disorders. New rhythms are being uncovered while artificial ones are produced by synthetic biology. Rhythms provide the richest source of examples of dissipative structures in biological systems. Bistability has been observed experimentally, but has primarily been investigated in theoretical models in an increasingly wide range of biological contexts, from the genetic to the cell and animal population levels, both in physiological conditions and in disease. Bistable transitions have been implicated in the progression between the different phases of the cell cycle and, more generally, in the process of cell fate specification in the developing embryo. Turing patterns are exemplified by the formation of some periodic structures in the course of development and by skin stripe patterns in animals. Spatio-temporal patterns in the form of propagating waves are observed within cells as well as in intercellular communication. This review illustrates how dissipative structures of all sorts abound in biological systems.This article is part of the theme issue 'Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 1)'.

Biophysics of membrane curvature remodeling at molecular and mesoscopic lengthscales

At the micron scale, where cell organelles display an amazing complexity in their shape and organization, the physical properties of a biological membrane can be better-understood using continuum models subject to thermal (stochastic) undulations. Yet, the chief orchestrators of these complex and intriguing shapes are a specialized class of membrane associating often peripheral proteins called curvature remodeling proteins (CRPs) that operate at the molecular level through specific protein-lipid interactions. We review multiscale methodologies to model these systems at the molecular as well as at the mesoscopic and cellular scales, and also present a free energy perspective of membrane remodeling through the organization and assembly of CRPs. We discuss the morphological space of nearly planar to highly curved membranes, methods to include thermal fluctuations, and review studies that model such proteins as curvature fields to describe the emergent curved morphologies. We also discuss several mesoscale models applied to a variety of cellular processes, where the phenomenological parameters (such as curvature field strength) are often mapped to models of real systems based on molecular simulations. Much insight can be gained from the calculation of free energies of membranes states with protein fields, which enable accurate mapping of the state and parameter values at which the membrane undergoes morphological transformations such as vesiculation or tubulation. By tuning the strength, anisotropy, and spatial organization of the curvature-field, one can generate a rich array of membrane morphologies that are highly relevant to shapes of several cellular organelles. We review applications of these models to budding of vesicles commonly seen in cellular signaling and trafficking processes such as clathrin mediated endocytosis, sorting by the ESCRT protein complexes, and cellular exocytosis regulated by the exocyst complex. We discuss future prospects where such models can be combined with other models for cytoskeletal assembly, and discuss their role in understanding the effects of cell membrane tension and the mechanics of the extracellular microenvironment on cellular processes.

Interfacing Cells with Vertical Nanoscale Devices: Applications and Characterization

Measurements of the intracellular state of mammalian cells often require probes or molecules to breach the tightly regulated cell membrane. Mammalian cells have been shown to grow well on vertical nanoscale structures in vitro, going out of their way to reach and tightly wrap the structures. A great deal of research has taken advantage of this interaction to bring probes close to the interface or deliver molecules with increased efficiency or ease. In turn, techniques have been developed to characterize this interface. Here, we endeavor to survey this research with an emphasis on the interface as driven by cellular mechanisms.

Structure Versus Stochasticity-The Role of Molecular Crowding and Intrinsic Disorder in Membrane Fission

Cellular membranes must undergo remodeling to facilitate critical functions including membrane trafficking, organelle biogenesis, and cell division. An essential step in membrane remodeling is membrane fission, in which an initially continuous membrane surface is divided into multiple, separate compartments. The established view has been that membrane fission requires proteins with conserved structural features such as helical scaffolds, hydrophobic insertions, and polymerized assemblies. In this review, we discuss these structure-based fission mechanisms and highlight recent findings from several groups that support an alternative, structure-independent mechanism of membrane fission. This mechanism relies on lateral collisions among crowded, membrane-bound proteins to generate sufficient steric pressure to drive membrane vesiculation. As a stochastic process, this mechanism contrasts with the paradigm that deterministic protein structures are required to drive fission, raising the prospect that many more proteins may participate in fission than previously thought. Paradoxically, our recent work suggests that intrinsically disordered domains may be among the most potent drivers of membrane fission, owing to their large hydrodynamic radii and substantial chain entropy. This stochastic view of fission also suggests new roles for the structure-based fission proteins. Specifically, we hypothesize that in addition to driving fission directly, the canonical fission machines may facilitate the enrichment and organization of bulky disordered protein domains in order to promote membrane fission by locally amplifying protein crowding.

Membrane bending by actin polymerization

Actin polymerization provides driving force to aid several types of processes that involve pulling the plasma membrane into the cell, including phagocytosis, cellular entry of large viruses, and endocytosis. In endocytosis, actin polymerization is especially important under conditions of high membrane tension or high turgor pressure. Recent modeling efforts have shown how actin polymerization can give rise to a distribution of forces around the endocytic site, and explored how these forces affect the shape dynamics; experiments have revealed the structure of the endocytic machinery in increasing detail, and demonstrated key feedback interactions between actin assembly and membrane curvature. Here we provide a perspective on these findings and suggest avenues for future research.

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.