On the role of anisotropy of membrane constituents in formation of a membrane neck during budding of a multicomponent membrane

Topological Connection between Vesicles and Nanotubes in Single-Molecule Lipid Membranes Driven by Head-Tail Interactions

Lipid nanotube-vesicle networks are important channels for intercellular communication and transport of matter. Experimentally observed in neighboring mammalian cells but also reproduced in model membrane systems, a broad consensus exists on their formation and stability. Lipid membranes must be composed of at least two molecular components, each stabilizing low (generally a phospholipid) and high curvatures. Strong anisotropy or enhanced conical shape of the second amphiphile is crucial for the formation of nanotunnels. Anisotropic driving forces generally favor nanotube protrusions from vesicles. In this work, we report the unique case of topologically connected nanotubes-vesicles obtained in the absence of directional forces, in single-molecule membranes, composed of an anisotropic bolaform glucolipid, above its melting temperature, T_m. Cryo-TEM and fluorescence confocal microscopy show the interconnection between vesicles and nanotubes in a single-phase region, between 60 and 90 °C under diluted conditions. Solid-state NMR demonstrates that the glucolipid can assume two distinct configurations, head-head and head-tail. These arrangements, seemingly of comparable energy above the T_m, could explain the existence and stability of the topologically connected vesicles and nanotubes, which are generally not observed for classical single-molecule phospholipid-based membranes above their T_m.

Mechanical Principles Governing the Shapes of Dendritic Spines

Dendritic spines are small, bulbous protrusions along the dendrites of neurons and are sites of excitatory postsynaptic activity. The morphology of spines has been implicated in their function in synaptic plasticity and their shapes have been well-characterized, but the potential mechanics underlying their shape development and maintenance have not yet been fully understood. In this work, we explore the mechanical principles that could underlie specific shapes using a minimal biophysical model of membrane-actin interactions. Using this model, we first identify the possible force regimes that give rise to the classic spine shapes-stubby, filopodia, thin, and mushroom-shaped spines. We also use this model to investigate how the spine neck might be stabilized using periodic rings of actin or associated proteins. Finally, we use this model to predict that the cooperation between force generation and ring structures can regulate the energy landscape of spine shapes across a wide range of tensions. Thus, our study provides insights into how mechanical aspects of actin-mediated force generation and tension can play critical roles in spine shape maintenance.

On the Role of Curved Membrane Nanodomains, and Passive and Active Skeleton Forces in the Determination of Cell Shape and Membrane Budding

Biological membranes are composed of isotropic and anisotropic curved nanodomains. Anisotropic membrane components, such as Bin/Amphiphysin/Rvs (BAR) superfamily protein domains, could trigger/facilitate the growth of membrane tubular protrusions, while isotropic curved nanodomains may induce undulated (necklace-like) membrane protrusions. We review the role of isotropic and anisotropic membrane nanodomains in stability of tubular and undulated membrane structures generated or stabilized by cyto- or membrane-skeleton. We also describe the theory of spontaneous self-assembly of isotropic curved membrane nanodomains and derive the critical concentration above which the spontaneous necklace-like membrane protrusion growth is favorable. We show that the actin cytoskeleton growth inside the vesicle or cell can change its equilibrium shape, induce higher degree of segregation of membrane nanodomains or even alter the average orientation angle of anisotropic nanodomains such as BAR domains. These effects may indicate whether the actin cytoskeleton role is only to stabilize membrane protrusions or to generate them by stretching the vesicle membrane. Furthermore, we demonstrate that by taking into account the in-plane orientational ordering of anisotropic membrane nanodomains, direct interactions between them and the extrinsic (deviatoric) curvature elasticity, it is possible to explain the experimentally observed stability of oblate (discocyte) shapes of red blood cells in a broad interval of cell reduced volume. Finally, we present results of numerical calculations and Monte-Carlo simulations which indicate that the active forces of membrane skeleton and cytoskeleton applied to plasma membrane may considerably influence cell shape and membrane budding.

On the role of external force of actin filaments in the formation of tubular protrusions of closed membrane shapes with anisotropic membrane components

Biological membranes are composed of different components and there is no a priori reason to assume that all components are isotropic. It was previously shown that the anisotropic properties of membrane components may explain the stability of membrane tubular protrusions even without the application of external force. Our theoretical study focuses on the role of anisotropic membrane components in the stability of membrane tubular structures generated or stabilized by actin filaments. We show that the growth of the actin cytoskeleton inside the vesicle can induce the partial lateral segregation of different membrane components. The entropy of mixing of membrane components hinders the total lateral segregation of the anisotropic and isotropic membrane components. Self-assembled aggregates formed by anisotropic membrane components facilitate the growth of long membrane tubular protrusions. Protrusive force generated by actin filaments favors strong segregation of membrane components by diminishing the opposing effect of mixing entropy.

Multiscale simulations of protein-facilitated membrane remodeling

Protein-facilitated shape and topology changes of cell membranes are crucial for many biological processes, such as cell division, protein trafficking, and cell signaling. However, the inherently multiscale nature of membrane remodeling presents a considerable challenge for understanding the mechanisms and physics that drive this process. To address this problem, a multiscale approach that makes use of a diverse set of computational and experimental techniques is required. The atomistic simulations provide high-resolution information on protein-membrane interactions. Experimental techniques, like electron microscopy, on the other hand, resolve high-order organization of proteins on the membrane. Coarse-grained (CG) and mesoscale computational techniques provide the intermediate link between the two scales and can give new insights into the underlying mechanisms. In this Review, we present the recent advances in multiscale computational approaches established in our group. We discuss various CG and mesoscale approaches in studying the protein-mediated large-scale membrane remodeling.

Bud-neck scaffolding as a possible driving force in ESCRT-induced membrane budding

Membrane budding is essential for processes such as protein sorting and transport. Recent experimental results with ESCRT proteins reveal a novel budding mechanism, with proteins emerging in bud necks but separated from the entire bud surface. Using an elastic model, we show that ESCRT protein shapes are sufficient to spontaneously create experimentally observed structures, with protein-membrane interactions leading to protein scaffolds in bud-neck regions. Furthermore, the model reproduces experimentally observed budding directions and bud sizes. Finally, our results reveal that membrane-mediated sorting has the capability of creating structures more complicated than previously assumed.

Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins

Biological membranes constitute boundaries of cells and cell organelles. These membranes are soft fluid interfaces whose thermodynamic states are dictated by bending moduli, induced curvature fields, and thermal fluctuations. Recently, there has been a flood of experimental evidence highlighting active roles for these structures in many cellular processes ranging from trafficking of cargo to cell motility. It is believed that the local membrane curvature, which is continuously altered due to its interactions with myriad proteins and other macromolecules attached to its surface, holds the key to the emergent functionality in these cellular processes. Mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the protein, shape and amino acid composition of the protein, and its amino acid contents. The specificity of molecular interactions together with the cooperativity of multiple proteins induce and stabilize complex membrane shapes at the mesoscale. These shapes span a wide spectrum ranging from the spherical plasma membrane to the complex cisternae of the Golgi apparatus. Mapping the relation between the protein-induced deformations at the molecular scale and the resulting mesoscale morphologies is key to bridging cellular experiments across the various length scales. In this review, we focus on the theoretical and computational methods used to understand the phenomenology underlying protein-driven membrane remodeling. Interactions at the molecular scale can be computationally probed by all atom and coarse grained molecular dynamics (MD, CGMD), as well as dissipative particle dynamics (DPD) simulations, which we only describe in passing. We choose to focus on several continuum approaches extending the Canham - Helfrich elastic energy model for membranes to include the effect of curvature-inducing proteins and explore the conformational phase space of such systems. In this description, the protein is expressed in the form of a spontaneous curvature field. The approaches include field theoretical methods limited to the small deformation regime, triangulated surfaces and particle-based computational models to investigate the large-deformation regimes observed in the natural state of many biological membranes. Applications of these methods to understand the properties of biological membranes in homogeneous and inhomogeneous environments of proteins, whose underlying curvature fields are either isotropic or anisotropic, are discussed. The diversity in the curvature fields elicits a rich variety of morphological states, including tubes, discs, branched tubes, and caveola. Mapping the thermodynamic stability of these states as a function of tuning parameters such as concentration and strength of curvature induction of the proteins is discussed. The relative stabilities of these self-organized shapes are examined through free-energy calculations. The suite of methods discussed here can be tailored to applications in specific cellular settings such as endocytosis during cargo trafficking and tubulation of filopodial structures in migrating cells, which makes these methods a powerful complement to experimental studies.

α-helical structures drive early stages of self-assembly of amyloidogenic amyloid polypeptide aggregate formation in membranes

The human islet amyloid polypeptide (hIAPP) is the primary component in the toxic islet amyloid deposits in type-2 diabetes. hIAPP self-assembles to aggregates that permeabilize membranes and constitutes amyloid plaques. Uncovering the mechanisms of amyloid self-assembly is the key to understanding amyloid toxicity and treatment. Although structurally similar, hIAPP's rat counterpart, the rat islet amyloid polypeptide (rIAPP), is non-toxic. It has been a puzzle why these peptides behave so differently. We combined multiscale modelling and theory to explain the drastically different dynamics of hIAPP and rIAPP: The differences stem from electrostatic dipolar interactions. hIAPP forms pentameric aggregates with the hydrophobic residues facing the membrane core and stabilizing water-conducting pores. We give predictions for pore sizes, the number of hIAPP peptides, and aggregate morphology. We show the importance of curvature-induced stress at the early stages of hIAPP assembly and the α-helical structures over β-sheets. This agrees with recent fluorescence spectroscopy experiments.

Stability of membranous nanostructures: a possible key mechanism in cancer progression

Membranous nanostructures, such as nanovesicles and nanotubules, are an important pool of biological membranes. Recent results indicate that they constitute cell-cell communication systems and that cancer development is influenced by these systems. Nanovesicles that are pinched off from cancer cells can move within the circulation and interact with distant cells. It has been suggested and indicated by experimental evidence that nanovesicles can induce metastases from the primary tumor in this way. Therefore, it is of importance to understand better the mechanisms of membrane budding and vesiculation. Here, a theoretical description is presented concerning consistently related lateral membrane composition, orientational ordering of membrane constituents, and a stable shape of nanovesicles and nanotubules. It is shown that the character of stable nanostructures reflects the composition of the membrane and the intrinsic shape of its constituents. An extension of the fluid mosaic model of biological membranes is suggested by taking into account curvature-mediated orientational ordering of the membrane constituents on strongly anisotropically curved regions. Based on experimental data for artificial membranes, a possible antimetastatic effect of plasma constituents via mediation of attractive interaction between membranous structures is suggested. This mediated attractive interaction hypothetically suppresses nanovesiculation by causing adhesion of buds to the mother membrane and preventing them from being pinched off from the membrane.

The transport along membrane nanotubes driven by the spontaneous curvature of membrane components

Intercellular membrane nanotubes (ICNs) serve as a very specific transport system between neighboring cells. The underlying mechanisms responsible for the transport of membrane components and vesicular dilations along the ICNs are not clearly understood. The present study investigated the spatial distribution of anisotropic membrane components of tubular shapes and isotropic membrane components of spherical shapes. Experimental results revealed the preferential distribution of CTB (cholera toxin B)-GM1 complexes mainly on the spherical cell membrane, and cholesterol-sphingomyelin at the membrane leading edge and ICNs. In agreement with previous studies, we here propose that the spatial distribution of CTB-GM1 complexes and cholesterol-sphingomyelin rafts were due to their isotropic and anisotropic shapes, respectively. To elucidate the relationship between a membrane component shape and its spatial distribution, a two-component computational model was constructed. The minimization of the membrane bending (free) energy revealed the enrichment of the anisotropic component along the ICN and the isotropic component in the parent cell membrane, which was due to the curvature mismatch between the ICN curvature and the spontaneous curvature of the isotropic component. The equations of motion, derived from the differentiation of the membrane free energy, revealed a curvature-dependent flux of the isotropic component and a curvature-dependent force exerted on a vesicular dilation along the ICN. Finally, the effects of possible changes in the orientational ordering of the anisotropic component attendant to the transport of the vesicular dilation were discussed with connection to the propagation of electrical and chemical signals.

Fusion pore diameter regulation by cations modulating local membrane anisotropy

The fusion pore is an aqueous channel that is formed upon the fusion of the vesicle membrane with the plasma membrane. Once the pore is open, it may close again (transient fusion) or widen completely (full fusion) to permit vesicle cargo discharge. While repetitive transient fusion pore openings of the vesicle with the plasma membrane have been observed in the absence of stimulation, their frequency can be further increased using a cAMP-increasing agent that drives the opening of nonspecific cation channels. Our model hypothesis is that the openings and closings of the fusion pore are driven by changes in the local concentration of cations in the connected vesicle. The proposed mechanism of fusion pore dynamics is considered as follows: when the fusion pore is closed or is extremely narrow, the accumulation of cations in the vesicle (increased cation concentration) likely leads to lipid demixing at the fusion pore. This process may affect local membrane anisotropy, which reduces the spontaneous curvature and thus leads to the opening of the fusion pore. Based on the theory of membrane elasticity, we used a continuum model to explain the rhythmic opening and closing of the fusion pore.

On the role of membrane anisotropy and BAR proteins in the stability of tubular membrane structures

Recent studies have demonstrated that actin filaments are not crucial for the short-term stability of tubular membrane protrusions originating from the cell surface. It has also been demonstrated that prominin nanodomains and curvature inducing I-BAR proteins could account for the stability of the membrane protrusion. Here we constructed an axisymmetric model of a membrane protrusion that excludes actin filaments in order to investigate the contributions of prominin nanodomains (rafts) and I-BAR proteins to the membrane protrusion stability. It was demonstrated that prominin nanodomains and I-BAR proteins can stabilize the membrane protrusion only over a specific range of spontaneous curvature. On the other hand, high spontaneous curvature and/or high density of I-BAR proteins could lead to system instability and to non-uniform contraction in the radial direction of the membrane protrusion. In agreement with previous studies, it was also shown that the isotropic bending energy of lipids is not sufficient to explain the stability of the observed tubular membrane protrusion without actin filaments.

Systems biology and physical biology of clathrin-mediated endocytosis

In this review, we describe the application of experimental data and modeling of intracellular endocytic trafficking mechanisms with a focus on the process of clathrin-mediated endocytosis. A detailed parts-list for the protein-protein interactions in clathrin-mediated endocytosis has been available for some time. However, recent experimental, theoretical, and computational tools have proved to be critical in establishing a sequence of events, cooperative dynamics, and energetics of the intracellular process. On the experimental front, total internal reflection fluorescence microscopy, photo-activated localization microscopy, and spinning-disk confocal microscopy have focused on assembly and patterning of endocytic proteins at the membrane, while on the theory front, minimal theoretical models for clathrin nucleation, biophysical models for membrane curvature and bending elasticity, as well as methods from computational structural and systems biology, have proved insightful in describing membrane topologies, curvature mechanisms, and energetics.

Phospholipid demixing and the birth of a lipid droplet

The biogenesis of lipid droplets (LD) in the yeast Saccharomyces cerevisiae was theoretically investigated on basis of a biophysical model. In accordance with the prevailing model of LD formation, we assumed that neutral lipids oil-out between the membrane leaflets of the endoplasmic reticulum (ER), resulting in LD that bud-off when a critical size is reached. Mathematically, LD were modeled as spherical protuberances in an otherwise planar ER membrane. We estimated the local phospholipid composition, and calculated the change in elastic free energy of the membrane caused by nascent LD. Based on this model calculation, we found a gradual demixing of lipids in the membrane leaflet that goes along with an increase in surface curvature at the site of LD formation. During demixing, the phospholipid monolayer was able to gain energy during LD growth, which suggested that the formation of curved interfaces was supported by or even driven by lipid demixing. In addition, we show that demixing is thermodynamically necessary as LD cannot bud-off otherwise. In the case of Saccharomyces cerevisiae our model predicts a LD bud-off diameter of about 12 nm. This diameter is far below the experimentally determined size of typical yeast LD. Thus, we concluded that if the standard model of LD formation is valid, LD biogenesis is a two step process. Small LD are produced from the ER, which subsequently ripe within the cytosol through a series of fusions.

New insights into BAR domain-induced membrane remodeling

Mesoscopic simulations and electron microscopy of N-BAR domain-induced liposome remodeling are used to characterize the process of liposome tubulation and vesiculation. The overall process of membrane remodeling is found to involve complex couplings among the N-BAR protein density, the degree of N-BAR oligomerization, and the membrane density. A comparison of complex remodeled liposome structures from mesoscopic simulations with those measured by electron microscopy experiments suggests that the process of membrane remodeling can be described via an appropriate mesoscopic free energy framework. Liposome remodeling more representative of F-BAR domains is also presented within the mesoscopic simulation framework.

Multiscale simulation of protein mediated membrane remodeling

Proteins interacting with membranes can result in substantial membrane deformations and curvatures. This effect is known in its broadest terms as membrane remodeling. This review article will survey current multiscale simulation methodologies that have been employed to examine protein mediated membrane remodeling.

Mechanisms for the formation of membranous nanostructures in cell-to-cell communication

Cells interact by exchanging material and information. Two methods of cell-to-cell communication are by means of microvesicles and by means of nanotubes. Both microvesicles and nanotubes derive from the cell membrane and are able to transport the contents of the inner solution. In this review, we describe two physical mechanisms involved in the formation of microvesicles and nanotubes: curvature-mediated lateral redistribution of membrane components with the formation of membrane nanodomains; and plasmamediated attractive forces between membranes. These mechanisms are clinically relevant since they can be affected by drugs. In particular, the underlying mechanism of heparin's role as an anticoagulant and tumor suppressor is the suppression of microvesicluation due to plasma-mediated attractive interaction between membranes.

Conformational and hydrational properties during the L(beta)- to L(alpha)- and L(alpha)- to H(II)-phase transition in phosphatidylethanolamine

Differential scanning calorimetry (DSC) measurements have been carried out simultaneously with small- and wide-angle X-ray scattering recordings on liposomal dispersions of stearoyl-oleoyl-phosphatidylethanolamine (PE) in a temperature range from 20 to 80 degrees C. The main transition temperature, T(m), was determined at 30.9 degrees C with an enthalpy of 28.5 kJ/mol and the lamellar-to-inverse hexagonal phase transition temperature, T(hex), at 61.6 degrees C with an enthalpy of 3.8 kJ/mol. Additionally highly resolved small angle X-ray diffraction experiments performed at equilibrium conditions allowed a reliable decomposition of the lattice spacings into hydrophobic and hydrophilic structure elements as well as the determination of the lipid interface area of the lamellar gel-phase (L(beta)), the fluid lamellar phase (L(alpha)) and of the inverse hexagonal phase (H(II)). The rearrangement of the lipid matrix and the coincident change of free water per lipid is illustrated for both transitions. Last, possible transition mechanisms are discussed on a molecular level.

Attachment of beta 2-glycoprotein I to negatively charged liposomes may prevent the release of daughter vesicles from the parent membrane

The temperature-induced budding of POPC-cardiolipin-cholesterol, POPC-POPS-cholesterol and POPC-POPG-cholesterol giant lipid vesicles in the presence of beta 2-glycoprotein I (beta 2-GPI) in the outer solution was studied experimentally and theoretically. The observed budding transition of vesicles was continuous which can be explained by taking into account the orientational ordering and direct interactions between oriented lipids. The attachment of positively charged beta 2-GPI to the negatively charged outer surface of POPC-cardiolipin-cholesterol, POPC-POPS-cholesterol and POPC-POPG-cholesterol giant vesicles caused coalescence of the spheroidal membrane bud with the parent vesicle before the bud could detach from the parent vesicle, i.e. vesiculate. Theoretically, the protein-mediated attraction between the membrane of a bud and the parent membrane was described as an interaction between two electric double layers. It was shown that the specific spatial distribution of charge within beta 2-GPI molecules attached to the negatively charged membrane surface may explain the observed attraction between like-charged membrane surfaces.

Physical model of contractile ring initiation in dividing cells

We present a physical mechanism to describe initiation of the contractile ring during cell division. The model couples the membrane curvature with the contractile forces produced by protein clusters attached to the membrane. These protein clusters are mobile on the membrane and possess either an isotropic or an anisotropic spontaneous curvature. Our results show that under these conditions the contraction force gives rise to an instability that corresponds in a closed cellular system to the initiation of the contractile ring. We find a quantization of this process at distinct length-scales, which we compare to available data for different types of eukaryote cells.