Vesicle deformation by draining: geometrical and topological shape changes

Shocker─A Molecular Dynamics Protocol and Tool for Accelerating and Analyzing the Effects of Osmotic Shocks

The process of osmosis, a fundamental phenomenon in life, drives water through a semipermeable membrane in response to a solute concentration gradient across this membrane. In vitro, osmotic shocks are often used to drive shape changes in lipid vesicles, for instance, to study fission events in the context of artificial cells. While experimental techniques provide a macroscopic picture of large-scale membrane remodeling processes, molecular dynamics (MD) simulations are a powerful tool to study membrane deformations at the molecular level. However, simulating an osmotic shock is a time-consuming process due to slow water diffusion across the membrane, making it practically impossible to examine its effects in classic MD simulations. In this article, we present Shocker, a Python-based MD tool for simulating the effects of an osmotic shock by selecting and relocating water particles across a membrane over the course of several pumping cycles. Although this method is primarily aimed at efficiently simulating volume changes in vesicles, it can also handle membrane tubes and double bilayer systems. Additionally, Shocker is force field-independent and compatible with both coarse-grained and all-atom systems. We demonstrate that our tool is applicable to simulate both hypertonic and hypotonic osmotic shocks for a range of vesicular and bilamellar setups, including complex multicomponent systems containing membrane proteins or crowded internal solutions.

Passive endocytosis in model protocells

Semipermeable membranes are a key feature of all living organisms. While specialized membrane transporters in cells can import otherwise impermeable nutrients, the earliest cells would have lacked a mechanism to import nutrients rapidly under nutrient-rich circumstances. Using both experiments and simulations, we find that a process akin to passive endocytosis can be recreated in model primitive cells. Molecules that are too impermeable to be absorbed can be taken up in a matter of seconds in an endocytic vesicle. The internalized cargo can then be slowly released over hours, into the main lumen or putative cytoplasm. This work demonstrates a way by which primitive life could have broken the symmetry of passive permeation prior to the evolution of protein transporters.

Passive endocytosis in model protocells

Semipermeable membranes are a key feature of all living organisms. While specialized membrane transporters in cells can import otherwise impermeable nutrients, the earliest cells would have lacked a mechanism to import nutrients rapidly under nutrient-rich circumstances. Using both experiments and simulations, we find that a process akin to passive endocytosis can be recreated in model primitive cells. Molecules that are too impermeable to be absorbed can be taken up in a matter of seconds in an endocytic vesicle. The internalized cargo can then be slowly released over hours, into the main lumen or putative cytoplasm. This work demonstrates a way by which primitive life could have broken the symmetry of passive permeation prior to the evolution of protein transporters.

On the role of membrane embedding, protein rigidity and transmembrane length in lipid membrane fusion

The fusion of biological membranes is ubiquitous in natural processes like exo- and endocytosis, intracellular trafficking and viral entry. Membrane fusion is also utilized in artificial biomimetic fusion systems, e.g. for drug delivery. Both the natural and the biomimetic fusion systems rely on a wide range of (artificial) proteins mediating the fusion process. Although the exact mechanisms of these proteins differ, clear analogies in their general behavior can be observed in bringing the membranes in close proximity and mediating the fusion reaction. In our study, we use molecular dynamics simulations with coarse grained models, mimicking the general behavior of fusion proteins (spikes), to systematically examine the effects of specific characteristics of these proteins on the fusion process. The protein characteristics considered are (i) the type of membrane embedding, i.e., either transmembrane or not, (ii) the rigidity, and (iii) the transmembrane domain (TMD) length. The results show essential differences in fusion pathway between monotopic and transmembrane spikes, in which transmembrane spikes seem to inhibit the formation of hemifusion diaphragms, leading to a faster fusion development. Furthermore, we observed that an increased rigidity and a decreased TMD length both proved to contribute to a faster fusion development. Finally, we show that a single spike may suffice to successfully induce a fusion reaction, provided that the spike is sufficiently rigid and attractive. Not only does this shed light on biological fusion of membranes, it also provides clear design rules for artificial membrane fusion systems.

Compartmentalizing and sculpting nanovesicles by phase-separated aqueous nanodroplets

Phase-separated liquid droplets inside giant vesicles have been intensely studied as biomimetic model systems to understand cellular microcompartmentation and molecular crowding and sorting. On the nanoscale, however, how aqueous nanodroplets interact with and shape nanovesicles is poorly understood. We perform coarse-grained molecular simulations to explore the architecture of compartmentalized nanovesicles by phase-separated aqueous nanodroplets, and their morphological evolution under osmotic deflation. We show that phase separation of a biphasic liquid mixture can form both stable two-compartment and meta-stable multi-compartment nanovesicles. We identify morphological transitions of stable two-compartment nanovesicles between tube, sheet and cup morphologies, characterized by membrane asymmetry and phase-separation propensity between the aqueous phases. We demonstrate that the formation of local sheets and in turn cup-shaped nanovesicles is promoted by negative line tensions resulting from large separation propensities, an exclusive nanoscale phenomenon which is not expected for larger vesicles where energetic contributions of the line tensions are dominated by those of the membrane tensions. Despite their instability, we observe long-lived multi-compartment nanovesicles, such as nanotubules and branched tubules, whose prolonged lifetime is attributed to interfacial tensions and membrane asymmetry. Aqueous nanodroplets can thus form novel membrane nanostructures, crucial for cellular processes and forming cellular organelles on the nanoscale.

Shape Deformation, Budding and Division of Giant Vesicles and Artificial Cells: A Review

The understanding of the shape-change dynamics leading to the budding and division of artificial cells has gained much attention in the past few decades due to an increased interest in designing stimuli-responsive synthetic systems and minimal models of biological self-reproduction. In this respect, membranes and their composition play a fundamental role in many aspects related to the stability of the vesicles: permeability, elasticity, rigidity, tunability and response to external changes. In this review, we summarise recent experimental and theoretical work dealing with shape deformation and division of (giant) vesicles made of phospholipids and/or fatty acids membranes. Following a classic approach, we divide the strategies used to destabilise the membranes into two different types, physical (osmotic stress, temperature and light) and chemical (addition of amphiphiles, the addition of reactive molecules and pH changes) even though they often act in synergy when leading to a complete division process. Finally, we review the most important theoretical methods employed to describe the equilibrium shapes of giant vesicles and how they provide ways to explain and control the morphological changes leading from one equilibrium structure to another.

Remodeling of Membrane Shape and Topology by Curvature Elasticity and Membrane Tension

Cellular membranes exhibit a fascinating variety of different morphologies, which are continuously remodeled by transformations of membrane shape and topology. This remodeling is essential for important biological processes (cell division, intracellular vesicle trafficking, endocytosis) and can be elucidated in a systematic and quantitative manner using synthetic membrane systems. Here, recent insights obtained from such synthetic systems are reviewed, integrating experimental observations and molecular dynamics simulations with the theory of membrane elasticity. The study starts from the polymorphism of biomembranes as observed for giant vesicles by optical microscopy and small nanovesicles in simulations. This polymorphism reflects the unusual elasticity of fluid membranes and includes the formation of membrane necks or fluid 'worm holes'. The proliferation of membrane necks generates stable multi-spherical shapes, which can form tubules and tubular junctions. Membrane necks are also essential for the remodeling of membrane topology via membrane fission and fusion. Neck fission can be induced by fine-tuning of membrane curvature, which leads to the controlled division of giant vesicles, and by adhesion-induced membrane tension as observed for small nanovesicles. Challenges for future research include the interplay of curvature elasticity and membrane tension during membrane fusion and the localization of fission and fusion processes within intramembrane domains.

Budding and Fission of Nanovesicles Induced by Membrane Adsorption of Small Solutes

Membrane budding and fission are essential cellular processes that produce new membrane compartments during cell and organelle division, for intracellular vesicle trafficking as well as during endo- and exocytosis. Such morphological transformations have also been observed for giant lipid vesicles with a size of many micrometers. Here, we report budding and fission processes of lipid nanovesicles with a size below 50 nm. We use coarse-grained molecular dynamics simulations, by which we can visualize the morphological transformations of individual vesicles. The budding and fission processes are induced by low concentrations of small solutes that absorb onto the outer leaflets of the vesicle membranes. In addition to the solute concentration, we identify the solvent conditions as a second key parameter for these processes. For good solvent conditions, the budding of a nanovesicle can be controlled by reducing the vesicle volume for constant solute concentration or by increasing the solute concentration for constant vesicle volume. After the budding process is completed, the budded vesicle consists of two membrane subcompartments which are connected by a closed membrane neck. The budding process is reversible as we demonstrate explicitly by reopening the closed neck. For poor solvent conditions, on the other hand, we observe two unexpected morphological transformations of nanovesicles. Close to the binodal line, at which the aqueous solution undergoes phase separation, the vesicle exhibits recurrent shape changes with closed and open membrane necks, reminiscent of flickering fusion pores (kiss-and-run) as observed for synaptic vesicles. As we approach the binodal line even closer, the recurrent shape changes are truncated by the fission of the membrane neck which leads to the division of the nanovesicle into two daughter vesicles. In this way, our simulations reveal a nanoscale mechanism for the budding and fission of nanovesicles, a mechanism that arises from the interplay between membrane elasticity and solute-mediated membrane adhesion.

Pulsed Electric Fields Promote Liposome Buddings

Background: Liposomes have been a useful tool to analyze membrane behavior. Various studies have attempted to induce biological activities, for example, buddings, divisions, and endocytosis, on liposomes, focusing on lipid rafts that move along electric fields. Materials and Methods: Liposomes consisting of soybean lecithin, phosphatidylcholine, and cholesterol were prepared, with inner and outer liquid conductivities of 0.595 and 1.564 S/m, respectively. Results: We tried to induce buddings by pulsed electric fields (PEFs) on liposomes. Results demonstrated that 1.248 kV/cm, 400 μs PEF promoted postpulse liposome buddings, which were preceded by a membrane relaxation. Although a transient thick area (a lipid raft-like area) on the membrane just after PEF application preceded buddings, it was not the sufficient factor for buddings. Conclusion: We established a brief model as follows: 1.248 kV/cm, 400 μs PEF induced the lipid membrane relaxation without electroporation to trigger buddings. The current results could be a new frontier in bioelectrics.

Interaction Mechanisms of Giant Unilamellar Vesicles with Hydrophobic Glass Surfaces and Silicone Oil-Water Interfaces: Adsorption, Deformation, Rupture, Dynamic Shape Changes, Internal Vesicle Formation, and Desorption

Phospholipid monolayers at oil-water interfaces are often obtained via vesicle adsorption. However, the interaction mechanisms of vesicles with these oil-water interfaces remain unclear. Herein, we studied the adsorption of giant unilamellar vesicles (GUVs) of approximately 2-5 μm diameter onto silicone oil-water interfaces and glass surfaces modified with hexamethyldisilazane (HMDS) and octadecyltrimethoxysilane (ODTMS) using fluorescence microscopy. The GUVs exhibited various modes of interaction, adsorbing on the silanized glass surfaces without sizable deformation, whereas GUVs bound to the silicone oil-water interface exhibited large deformation. After adsorption, GUV rupture occurred within 350, 110, and 3 ms on HMDS-modified glass, ODTMS-modified glass, and silicone oil-water interface, respectively. On glass surfaces, GUV rupture was often initiated and proceeded with pore formation near the surface. The monolayer patches formed by GUV rupture on HMDS-modified glass remained for at least 1 h over an area approximately twice of that estimated from the original GUV. On the ODTMS-modified glass and silicone oil surfaces, the monolayer patch structures disappeared in milliseconds owing to lipid diffusion across the interface. When adsorbed on the oil-water interface, the GUVs spontaneously underwent dynamic shape changes, internal vesicle formation, and desorption without rupture. Thus, it can be concluded that these different pathways arose from different lipid-surface affinities.

A Multi-Scale Approach to Membrane Remodeling Processes

We present a multi-scale simulation procedure to describe membrane-related biological processes that span over a wide range of length scales. At macroscopic length-scale, a membrane is described as a flexible thin film modeled by a dynamic triangulated surface with its spatial conformations governed by an elastic energy containing only a few model parameters. An implicit protein model allows us to include complex effects of membrane-protein interactions in the macroscopic description. The gist of this multi-scale approach is a scheme to calibrate the implicit protein model using finer scale simulation techniques e.g., all atom and coarse grain molecular dynamics. We previously used this approach and properly described the formation of membrane tubular invaginations upon binding of B-subunit of Shiga toxin. Here, we provide a perspective of our multi-scale approach, summarizing its main features and sketching possible routes for future development.

Dynamics of Growth and Form in Prebiotic Vesicles

The growth, form, and division of prebiotic vesicles, membraneous bags of fluid of varying components and shapes is hypothesized to have served as the substrate for the origin of life. The dynamics of these out-of-equilibrium structures is controlled by physicochemical processes that include the intercalation of amphiphiles into the membrane, fluid flow across the membrane, and elastic deformations of the membrane. To understand prebiotic vesicular forms and their dynamics, we construct a minimal model that couples membrane growth, deformation, and fluid permeation, ultimately couched in terms of two dimensionless parameters that characterize the relative rate of membrane growth and the membrane permeability. Numerical simulations show that our model captures the morphological diversity seen in extant precursor mimics of cellular life, and might provide simple guidelines for the synthesis of these complex shapes from simple ingredients.

Shape Transformations of Vesicles Self-Assembled from Amphiphilic Hyperbranched Multiarm Copolymers via Simulation

The understanding of shape transformations of vesicles is of fundamental importance in biological and clinical sciences. Hyperbranched polymer vesicles (branched polymersomes) are newly emerging polymer vesicles with special structure and property. They have also been regarded as a good model for biomembranes. However, the shape transformations of hyperbranched polymer vesicles have not been studied from either an experimental or theoretical level. Herein, the shape transformations of vesicles self-assembled from amphiphilic hyperbranched multiarm copolymers (HMCs) in response to the interaction parameters between the hydrophobic core and hydrophilic arms and the polymer concentrations are investigated carefully through dissipative particle dynamics (DPD) simulations. In the morphological phase diagram, two types of vesicles are obtained: one type corresponds to vesicles without holes formed at low concentrations including unilamellar vesicles, double-lamellar vesicles, discocyte-shaped vesicles, and tubular vesicles, and the other type corresponds to vesicles with holes formed at high concentrations including stomatocyte-shaped vesicles, toroidal vesicles, genus-3 (G-3) toroidal vesicles with three holes, and genus-4 (G-4) toroidal vesicles with four holes. In addition, both the self-assembly mechanisms and the dynamics for the formation of these vesicles have been systematically studied. The current work will offer theoretical support for fabricating novel vesicles with various shapes from hyperbranched polymers.

Multivalency in a Dendritic Host-Guest System

Multivalency is an important instrument in the supramolecular chemistry toolkit for the creation of strong specific interactions. In this paper we investigate the multivalency effect in a dendritic host–guest system using molecular dynamics simulations. Specifically, we consider urea–adamantyl decorated poly(propyleneimine) dendrimers that together with compatible mono-, bi-, and tetravalent ureidoacetic acid guests can form dynamic patchy nanoparticles. First, we simulate the self-assembly of these particles into macromolecular nanostructures, showing guest-controlled reduction of dendrimer aggregation. Subsequently, we systematically study guest concentration dependent multivalent binding. At low guest concentrations multivalency of the guests clearly increases relative binding as tethered headgroups bind more often than free guests’ headgroups. We find that despite an abundance of binding sites, most of the tethered headgroups bind in close proximity, irrespective of the spacer length; nevertheless, longer spacers do increase binding. At high guest concentrations the dendrimer becomes saturated with bound headgroups, independent of guest valency. However, in direct competition the tetravalent guests prevail over the monovalent ones. This demonstrates the benefit of multivalency at high as well as low concentrations.

Polymersomes: Breaking the Glass Ceiling?

Polymer vesicles, also known as polymersomes, have garnered a lot of interest even before the first report of their fabrication in the mid-1990s. These capsules have found applications in areas such as drug delivery, diagnostics and cellular models, and are made via the self-assembly of amphiphilic block copolymers, predominantly with soft, rubbery hydrophobic segments. Comparatively, and despite their remarkable impermeability, glassy polymersomes (GPs) have been less pervasive due to their rigidity, lack of biodegradability and more restricted fabrication strategies. GPs are now becoming more prominent, thanks to their ability to undergo stable shape-change (e.g., into non-spherical morphologies) as a response to a predetermined trigger (e.g., light, solvent). The basics of block copolymer self-assembly with an emphasis on polymersomes and GPs in particular are reviewed here. The principles and advantages of shape transformation of GPs as well as their general usefulness are also discussed, together with some of the challenges and opportunities currently facing this area.

In Silico Investigations of Calcium Phosphate Mineralization in Extracellular Vesicles

Calcification in bone, cartilage, and cardiovascular tissues involves the release of specialized extracellular vesicles (EVs) that promote mineral nucleation. The small size of the EVs, however, makes molecular level studies difficult, and consequently uncertainty exists on the role and function of these structures in directing mineralization. The lack of mechanistic understanding associated with the initiators of ectopic mineral deposition has severely hindered the development of potential therapeutic options. Here, we used multiscale molecular dynamics simulations to investigate the calcification within the EVs. Results show that Ca²⁺-HPO₄^2- and phosphatidylserine complexes facilitate the early nucleation. Use of coarse-grained simulations allows investigations of Ca²⁺-PO₄^3- nucleation and crystallization in the EVs. Systematic variation in the ion-to-water ratio shows that the crystallization and growth strongly depend on the enrichment of the ions and dehydration inside the EVs. Our investigations provide insights into the role of EVs on calcium phosphate mineral nucleation and growth in both physiological and pathological mineralization.

Lateral Diffusion of a Submicrometer Particle on a Lipid Bilayer Membrane

In past decades, nanoparticles and nanomaterials have been actively used for applications such as visualizing nano/submicrometer cell structure, killing cancer cells, and using drug delivery systems. It is important to understand the physicochemical mechanisms that govern the motion of nanoparticles on a plasma membrane surface. However, the motion of small particles of <1000 nm on lipid membranes is poorly understood. In this study, we investigated the diffusion of particles with a diameter of 200-800 nm on a lipid membrane using cell-sized liposomes. Particle-associated liposomes were obtained by applying centrifugal force to a mixture of liposomes and particle solutions. We measured the thermal motion of the particles by phase-contrast microscopy. We found that (i) the particle-size dependence of the diffusion of particles adhering to membranes was better described by the DADL model rather than the Einstein-Stokes model, (ii) the diffusion coefficient of a particle strongly depends on the adsorption state of the particle, such as fully or partially wrapped by the membrane, and (iii) anomalous diffusion was induced by the localization of particles on the neck of budded vesicles.

Exploring the shape deformation of biomembrane tubes with theoretical analysis and computer simulation

The shape deformation of membrane nanotubes is studied by a combination of theoretical analysis and molecular simulation. First we perform free energy analysis to demonstrate the effects of various factors on two ideal states for the pearling transition, and then we carry out dissipative particle dynamics simulations, through which various types of membrane tube deformation are found, including membrane pearling, buckling, and bulging. Different models for inducing tube deformation, including the osmotic pressure, area difference and spontaneous curvature models, are considered to investigate tubular instabilities. Combined with free energy analysis, our simulations show that the origin of the deformation of membrane tubes in different models can be classified into two categories: effective spontaneous curvature and membrane tension. We further demonstrate that for different models, a positive membrane tension is required for the pearling transition. Finally we show that different models can be coupled to effectively deform the membrane tube.

Coarse-grained molecular dynamics simulation of binary charged lipid membranes: Phase separation and morphological dynamics

Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and morphological dynamics in charged lipid bilayer vesicles. The screened long-range electrostatic repulsion among charged head groups delays or inhibits the lateral phase separation in charged vesicles compared with neutral vesicles, suggesting the transition of the phase-separation mechanism from spinodal decomposition to nucleation or homogeneous dispersion. Moreover, the electrostatic repulsion causes morphological changes, such as pore formation, and further transformations into disk, string, and bicelle structures, which are spatiotemporally coupled to the lateral segregation of charged lipids. Based on our coarse-grained MD simulation, we propose a plausible mechanism of pore formation at the molecular level. The pore formation in a charged-lipid-rich domain is initiated by the prior disturbance of the local molecular orientation in the domain.

Vesicle Geometries Enabled by Dynamically Trapped States

Understanding and controlling vesicle shapes is a fundamental challenge in biophysics and materials design. In this paper, we design dynamic protocols for enlarging the shape space of both fluid and crystalline vesicles beyond the equilibrium zone. By removing water from within the vesicle at different rates, we numerically produced a series of dynamically trapped stable vesicle shapes for both fluid and crystalline vesicles in a highly controllable fashion. In crystalline vesicles that are continuously dehydrated, simulations show the initial appearance of small flat areas over the surface of the vesicles that ultimately merge to form fewer flat faces. In this way, the vesicles transform from a fullerene-like shape into various faceted polyhedrons. We perform analytical elasticity analysis to show that these salient features are attributable to the crystalline nature of the vesicle. The potential to use dynamic protocols, such as those used in this study, to engineer vesicle shape transformations is helpful for exploiting the richness of vesicle geometries for desired applications.

Surface Density-Induced Pleating of a Lipid Monolayer Drives Nascent High-Density Lipoprotein Assembly

Biogenesis of high-density lipoproteins (HDL) is coupled to the transmembrane protein, ATP-binding cassette transporter A1 (ABCA1), which transports phospholipid (PL) from the inner to the outer membrane monolayer. Using a combination of computational and experimental approaches, we show that increased outer lipid monolayer surface density, driven by excess PL or membrane insertion of amphipathic helices, results in pleating of the outer monolayer to form membrane-attached discoidal bilayers. Apolipoprotein (apo)A-I accelerates and stabilizes the pleats. In the absence of apoA-I, pleats collapse to form vesicles. These results mimic cells overexpressing ABCA1 that, in the absence of apoA-I, form and release vesicles. We conclude that the basic driving force for nascent discoidal HDL assembly is a PL pump-induced surface density increase that produces lipid monolayer pleating. We then argue that ABCA1 forms an extracellular reservoir containing an isolated pressurized lipid monolayer decoupled from the transbilayer density buffering of cholesterol.

Design and synthesis of periodic mesoporous organosilica materials with a multi-compartment structure

Multi-compartment periodic mesoporous organosilica materials show desirable properties as anticancer drug carrier with high loading capacity and slow release rate.

Free energy landscape of rim-pore expansion in membrane fusion

The productive fusion pore in membrane fusion is generally thought to be toroidally shaped. Theoretical studies and recent experiments suggest that its formation, in some scenarios, may be preceded by an initial pore formed near the rim of the extended hemifusion diaphragm (HD), a rim-pore. This rim-pore is characterized by a nontoroidal shape that changes with size. To determine this shape as well as the free energy along the pathway of rim-pore expansion, we derived a simple analytical free energy model. We argue that dilation of HD material via expansion of a rim-pore is favored over a regular, circular pore. Further, the expanding rim-pore faces a free energy barrier that linearly increases with HD size. In contrast, the tension required to expand the rim-pore decreases with HD size. Pore flickering, followed by sudden opening, occurs when the tension in the HD competes with the line energy of the rim-pore, and the rim-pore reaches its equilibrium size before reaching the critical pore size. The experimental observation of flickering and closing fusion pores (kiss-and-run) is very well explained by the observed behavior of rim-pores. Finally, the free energy landscape of rim-pore expansion/HD dilation may very well explain why some cellular fusion reactions, in their attempt to minimize energetic costs, progress via alternative formation and dilation of microscopic hemifusion intermediates.

Influence of osmotic pressure on adhesion of lipid vesicles to solid supports

The adhesion of lipid vesicles to solid supports represents an important step in the molecular self-assembly of model membrane platforms. A wide range of experimental parameters are involved in controlling this process, including substrate material and topology, lipid composition, vesicle size, solution pH, ionic strength, and osmotic pressure. At present, it is not well understood how the magnitude and direction of the osmotic pressure exerted on a vesicle influence the corresponding adsorption kinetics. In this work, using quartz crystal microbalance with dissipation (QCM-D) monitoring, we have experimentally studied the role of osmotic pressure in the adsorption of zwitterionic vesicles onto silicon oxide. The osmotic pressure was induced by changing the ionic strength of the solvent across an appreciably wider range (from 25 to 1000 mM NaCl outside of the vesicle, and 125 mM NaCl inside of the vesicle, unless otherwise noted) compared to that used in earlier works. Our key finding is demonstration that, by changing osmotic pressure, all three generic types of the kinetics of vesicle adsorption and rupture can be observed in one system, including (i) adsorption of intact vesicles, (ii) adsorption and rupture after reaching a critical vesicle coverage, and (iii) rupture just after adsorption. Furthermore, theoretical analysis of pressure-induced deformation of adsorbed vesicles and a DLVO-type analysis of the vesicle-substrate interaction qualitatively support our observations. Taken together, the findings in this work demonstrate that osmotic pressure can either promote or impede the rupture of adsorbed vesicles on silicon oxide, and offer experimental evidence to support adhesion energy-based models that describe the adsorption and spontaneous rupture of vesicles on solid supports.

On protein crowding and bilayer bulging in spontaneous vesicle formation

Spontaneous aggregation of lipids into bilayers and vesicles is a key property for the formation of biological membranes. Understanding the compartmentalization achieved by vesicle formation is an important step toward understanding the origin of life, and is crucial in current efforts to develop artificial life. Spontaneously formed vesicles may be applied as artificial cells if they can efficiently encapsulate biomacromolecules. Recent studies report an enhanced concentration of encapsulated proteins during vesicle formation. In order to obtain more insight into this encapsulation process, here we simulate the spontaneous transition of flat bilayers to vesicles in the presence of solvated model proteins using molecular dynamics simulations. In the bilayer-vesicle transition, which is found to be unaffected by the presence of the solvated proteins, the bilayer edge remains at almost the same height, while the center of the membrane bulges out, a molecular pathway we denominate "bilayer bulging". This bulging results in an interior protein concentration that is significantly lower than that of the solution. By means of an increased protein-membrane interaction, enhanced encapsulation of proteins inside the vesicles could be achieved in our simulations.

Size-dependent properties of small unilamellar vesicles formed by model lipids

The size-dependent behavior of small unilamellar vesicles is explored by dissipative particle dynamics, including the membrane characteristics and mechanical properties. The spontaneously formed vesicles are in the metastable state and the vesicle size is controlled by the concentration of model lipids. As the vesicle size decreases, the bilayer gets thinner and the area density of heads declines. Nonetheless, the area density in the inner leaflet is higher than that in the outer. The packing parameters are calculated for both leaflets. The result indicates that the shape of lipid in the outer leaflet is like a truncated cone but that in the inner leaflet resembles an inverted truncated cone. Based on a local order parameter, our simulations indication that the orientation order of lipid molecules decreases as the size of the vesicle reduces and this fact reveals that the bilayer becoming thinner for smaller vesicle is mainly attributed to the orientation disorder of the lipids. The membrane tension can be obtained through the Young-Laplace equation. The tension is found to grow with reducing vesicle size. Therefore, small vesicles are less stable against fusion. Using the inflation method, the area stretching and bending moduli can be determined and those moduli are found to grow with reducing size. Nonetheless, a general equation with a single numerical constant can relate bending modulus, area stretching modulus, and bilayer thickness irrespective of the vesicle size. Finally, a simple metastable model is proposed to explain the size-dependent behavior of bilayer thickness, orientation, and tension.

Self-reproduction of fatty acid vesicles: a combined experimental and simulation study

Dilution of a fatty acid micellar solution at basic pH toward neutrality results in spontaneous formation of vesicles with a broad size distribution. However, when vesicles of a defined size are present before dilution, the size distribution of the newly formed vesicles is strongly biased toward that of the seed vesicles. This so-called matrix effect is believed to be a key feature of early life. Here we reproduced this effect for oleate micelles and seed vesicles of either oleate or dioleoylphosphatidylcholine. Fluorescence measurements showed that the vesicle contents do not leak out during the replication process. We hypothesized that the matrix effect results from vesicle fission induced by an imbalance of material across both leaflets of the vesicle upon initial insertion of fatty acids into the outer leaflet of the seed vesicle. This was supported by experiments that showed a significant increase in vesicle size when the equilibration of oleate over both leaflets was enhanced by either slowing down the rate of fatty acid addition or increasing the rate of fatty acid transbilayer movement. Coarse-grained molecular-dynamics simulations showed excellent agreement with the experimental results and provided further mechanistic details of the replication process.

Coarse grained molecular dynamics simulations of transmembrane protein-lipid systems

Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG) can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide.