Examination of membrane fusion by dissipative particle dynamics simulation and comparison with continuum elastic models

Continuum Models of Membrane Fusion: Evolution of the Theory

Starting from fertilization, through tissue growth, hormone secretion, synaptic transmission, and sometimes morbid events of carcinogenesis and viral infections, membrane fusion regulates the whole life of high organisms. Despite that, a lot of fusion processes still lack well-established models and even a list of main actors. A merger of membranes requires their topological rearrangements controlled by elastic properties of a lipid bilayer. That is why continuum models based on theories of membrane elasticity are actively applied for the construction of physical models of membrane fusion. Started from the view on the membrane as a structureless film with postulated geometry of fusion intermediates, they developed along with experimental and computational techniques to a powerful tool for prediction of the whole process with molecular accuracy. In the present review, focusing on fusion processes occurring in eukaryotic cells, we scrutinize the history of these models, their evolution and complication, as well as open questions and remaining theoretical problems. We show that modern approaches in this field allow continuum models of membrane fusion to stand shoulder to shoulder with molecular dynamics simulations, and provide the deepest understanding of this process in multiple biological systems.

Elucidation of the mechanism and energy barrier for anesthetic triggered membrane fusion in model membranes

Membrane fusion is vital for cellular function and is generally mediated via fusogenic proteins and peptides. The mechanistic details and subsequently the transition state dynamics of membrane fusion will be dependent on the type of the fusogenic agent. We have previously established the potential of general anesthetics as a new class of fusion triggering agents in model membranes. We employed two-photon excitation fluorescence cross-correlation spectroscopy (TPE-FCCS) to report on vesicle association kinetics and steady-state fluorescence dequenching assays to monitor lipid mixing kinetics. Using halothane to trigger fusion in 110 nm diameter dioleoylphosphatidylcholine (DOPC) liposomes, we found that lipid rearrangement towards the formation of the fusion stalk was rate limiting. The activation barrier for halothane induced membrane fusion in 110 nm vesicles was found to be ∼40 kJ mol−1. We calculated the enthalpy and entropy of the transition state to be ∼40 kJ mol−1and ∼180 J mol−1K−1, respectively. We have found that the addition of halothane effectively lowers the energy barrier for membrane fusion in less curved vesicles largely due to entropic advantages.

Partner-facilitating transmembrane penetration of nanoparticles: a biological test in silico

Transmembrane penetration of nanoparticles (NPs) promises an effective pathway for cargo delivery into cells, and offers the possibility of organelle-specific targeting for biomedical applications. However, a full understanding of the underlying NP-membrane interaction mechanism is still lacking. In this work, the membrane penetration behavior of NPs is statistically analyzed based on the simulations of over 2.2 ms, which are performed with dissipative particle dynamics (DPD). Influences from multiple factors including the NP concentration, shape and surface chemistry are taken into account. It is interesting to find that, the introduction of a partner NP would greatly facilitate the transmembrane penetration of a host spherical NP. This is probably due to the membrane-mediated cooperation between the NPs. Moreover, the proper selection of a partner NP with specific surface chemistry is of great significance. For example, the best partner for a hydrophilic NP to achieve transmembrane penetration is a Janus-like one, in comparison with the hydrophilic, hydrophobic or randomly surface-decorated NPs. Furthermore, such a partner-facilitating effect in NP translocation also works for a shaped NP although less pronounced. Our results are helpful for a better understanding of the complicated nano-bio interactions, and offer a practical guide to the NP-based drug delivery strategy with high efficiency.

Pulling force and surface tension drive membrane fusion

Despite catalyzed by fusion proteins of quite different molecular architectures, intracellular, viral, and cell-to-cell fusions are found to have the essential common features and the nearly same nature of transition states. The similarity inspires us to find a more general catalysis mechanism for membrane fusion that minimally depends on the specific structures of fusion proteins. In this work, we built a minimal model for membrane fusion, and by using dissipative particle dynamics simulations, we propose a mechanism that the pulling force generated by fusion proteins initiates the fusion process and the membrane tension regulates the subsequent fusion stages. The model shows different features compared to previous computer simulation studies: the pulling force catalyzes membrane fusion through lipid head overcrowding in the contacting region, leading to an increase in the head-head repulsion and/or the unfavorable head-tail contacts from opposing membranes, both of which destabilize the contacting leaflets and thus promote membrane fusion or vesicle rupture. Our simulations produce a variety of shapes and intermediates, closely resembling cases seen experimentally. Our work strongly supports the view that the tight pulling mechanism is a conserved feature of fusion protein-mediated fusion and that the membrane tension plays an essential role in fusion.

Multiscale simulation of ideal mixtures using smoothed dissipative particle dynamics

Smoothed dissipative particle dynamics (SDPD) [P. Español and M. Revenga, Phys. Rev. E 67, 026705 (2003)] is a thermodynamically consistent particle-based continuum hydrodynamics solver that features scale-dependent thermal fluctuations. We obtain a new formulation of this stochastic method for ideal two-component mixtures through a discretization of the advection-diffusion equation with thermal noise in the concentration field. The resulting multicomponent approach is consistent with the interpretation of the SDPD particles as moving volumes of fluid and reproduces the correct fluctuations and diffusion dynamics. Subsequently, we provide a general multiscale multicomponent SDPD framework for simulations of molecularly miscible systems spanning length scales from nanometers to the non-fluctuating continuum limit. This approach reproduces appropriate equilibrium properties and is validated with simulation of simple one-dimensional diffusion across multiple length scales.

Effect of Receptor Structure and Length on the Wrapping of a Nanoparticle by a Lipid Membrane

Nanoparticles have been considered as a type of powerful tool to deliver drugs and genes into cells for disease diagnosis and therapies. It has been generally accepted that the internalization of nanoparticles into cells is mostly realized by receptor-mediated endocytosis. However, for the influence of structural factors of receptors on endocytosis, this is still largely unknown. In this paper, computer simulations are applied to investigate the effects of structure (i.e., the number of constituent chains of the receptor) and the length of the receptor on the wrapping behavior of nanoparticles by the lipid membrane, which is a key step of receptor-medicated endocytosis. It is found that these structural factors of receptors have strong effects on the nanoparticle’s final interaction configuration with the membrane in the simulations, such as adhering on the membrane surface or being partly or fully wrapped by the membrane. Furthermore, in some cases, the rupture of the lipid membrane occurs. These results are helpful for the understanding of endocytosis and the preparation of advanced nanoscale drug-delivery vectors.

Lipid nanotechnology

Nanotechnology is a multidisciplinary field that covers a vast and diverse array of devices and machines derived from engineering, physics, materials science, chemistry and biology. These devices have found applications in biomedical sciences, such as targeted drug delivery, bio-imaging, sensing and diagnosis of pathologies at early stages. In these applications, nano-devices typically interface with the plasma membrane of cells. On the other hand, naturally occurring nanostructures in biology have been a source of inspiration for new nanotechnological designs and hybrid nanostructures made of biological and non-biological, organic and inorganic building blocks. Lipids, with their amphiphilicity, diversity of head and tail chemistry, and antifouling properties that block nonspecific binding to lipid-coated surfaces, provide a powerful toolbox for nanotechnology. This review discusses the progress in the emerging field of lipid nanotechnology.

Molecular response and cooperative behavior during the interactions of melittin with a membrane: dissipative quartz crystal microbalance experiments and simulations

The molecular-level interactions of an antimicrobial peptide melittin with supported membrane were studied by the combination of dissipative quartz crystal microbalance (QCM-D) experiments and computer simulations. We found the response behavior of lipids upon peptide adsorption greatly influence their interactions. The perturbance and reorientation of the lipid in liquid phase facilitate the insertion of melittin in a trans-membrane way, but in solid phase, asymmetrical membrane disruption happens. Apart from the lipid state, the local peptide-to-lipid ratio also affects the insertion capacity of melittin. When the local peptide number density is high, adjacent peptides can cooperatively penetrate into the membrane. This observation explains the occurrence of the conventional "carpet" mechanism.

Hydrogen-bond-directed giant unilamellar vesicles of guanosine derivative: preparation, properties, and fusion

By mixing a small volume of THF containing guanosine derivative 1 and tetraethylenegrycol dodecyl ether (TEGDE) with water and subsequently removing TEGDE by gel permeation chromatography, micrometer-sized giant unilamellar vesicles (GUV) of 1 were successfully prepared. The vesicle membrane was a 2-D sheet assembly of thickness 2.5 nm, composed of a 2-D inter-guanine hydrogen-bond network. The GUV dispersion showed high stability because of a large negative zeta potential, which allowed repeated sedimentation and redispersion by centrifugation and subsequent gentle agitation. TEGDE-triggered fusion of GUVs took place within 350 ms, which proceeded by fusion of the vesicle membranes in contact. These unique static and dynamic properties of the GUV membrane assembled by the 2-D hydrogen-bond network are discussed.

Wrapping and Internalization of Nanoparticles by Lipid Bilayers: a Computer Simulation Study

Endocytosis is a basic pathway for nanoparticles to enter or leave cells. However, because of the complexity of the cell membrane, the mechanism of endocytosis is largely elusive. By dissipative particle dynamics (DPD), we investigate the wrapping and internalization processes of different particles (e.g., spheres and ellipsoids) by a lipid vesicle. It is found that rotation is possibly an important mechanism in the particle internalization process under a strong adhesive interaction, which can adjust the configuration of the nanoparticle to the lipid bilayer and facilitate the progress of the wrapping. Furthermore, the fission behaviour of the vesicle and the wrapped particle is also observed when the lipid domain is considered in the system. These simulation results give an insight into the nature of endocytosis.

Effect of polymer grafting on the bilayer gel to liquid-crystalline transition

Grafted polymers on the surface of lipid membranes have potential applications in liposome-based drug delivery and supported membrane systems. The effect of polymer grafting on the phase behavior of bilayers made up of single-tail lipids is investigated using dissipative particle dynamics. The bilayer is maintained in a tensionless state using a barostat. Simulations are carried out by varying the grafting fraction, G(f), defined as the ratio of the number of polymer molecules to the number of lipid molecules, and the length of the lipid tails. At low G(f), the bilayer shows a sharp transition from the gel (L(beta)) to the liquid-crystalline (L(alpha)) phase. This main melting transition temperature is lowered as G(f) is increased, and above a critical value of G(f), the interdigitated L(betaI) phase is observed prior to the main transition. The temperature range over which the intermediate phases are observed is a function of the lipid tail length and G(f). At higher grafting fractions, the presence of the L(betaI) phase is attributed to the increase in the area per head group due to the lateral pressure exerted by the polymer brush. The areal expansion and decrease in the melting temperatures as a function of G(f) were found to follow the scalings predicted by the self-consistent mean field theories for grafted polymer membranes. Our study shows that the grafted polymer density can be used to effectively control the temperature range and occurrence of a given bilayer phase.

Spatially resolved simulations of membrane reactions and dynamics: multipolar reaction DPD

Biophysical chemistry of mesoscale systems and quantitative modeling in systems biology now require a simulation methodology unifying chemical reaction kinetics with essential collective physics. This will enable the study of the collective dynamics of complex chemical and structural systems in a spatially resolved manner with a combinatorially complex variety of different system constituents. In order to allow a direct link-up with experimental data (e.g. high-throughput fluorescence images) the simulations must be constructed locally, i.e. mesoscale phenomena have to emerge from local composition and interactions that can be extracted from experimental data. Under suitable conditions, the simulation of such local interactions must lead to processes such as vesicle budding, transport of membrane-bounded compartments and protein sorting, all of which result from a sophisticated interplay between chemical and mechanical processes and require the link-up of different length scales. In this work, we show that introducing multipolar interactions between particles in dissipative particle dynamics (DPD) leads to extended membrane structures emerging in a self-organized manner and exhibiting the necessary mechanical stability for transport, correct scaling behavior, and membrane fluidity so as to provide a two-dimensional self-organizing dynamic reaction environment for kinetic studies in the context of cell biology.

Statistical thermodynamics of biomembranes

An overview of the major issues involved in the statistical thermodynamic treatment of phospholipid membranes at the atomistic level is summarized: thermodynamic ensembles, initial configuration (or the physical system being modeled), force field representation as well as the representation of long-range interactions. This is followed by a description of the various ways that the simulated ensembles can be analyzed: area of the lipid, mass density profiles, radial distribution functions (RDFs), water orientation profile, deuterium order parameter, free energy profiles and void (pore) formation; with particular focus on the results obtained from our recent molecular dynamic (MD) simulations of phospholipids interacting with dimethylsulfoxide (Me(2)SO), a commonly used cryoprotective agent (CPA).

Shape deformation and fission route of the lipid domain in a multicomponent vesicle

In this paper, the curvature changes and fission routes of the lipid domains in a multicomponent vesicle are studied by dissipative particle dynamics. Under different conditions of asymmetric distribution of lipids in two leaflets of lipid bilayer and area-to-volume ratio of the vesicle, we obtained different configurations of the domain in the vesicle: three typical curvature characters of the lipid domain, namely, positive, negative, and invariable curvatures compared to the vesicle are observed. Furthermore, some other morphologies of the domain and two vesicle fission routes (i.e., exocytic and endocytic fissions) are also obtained in our simulations. Particular emphasis is put on the formation of the negative curvature domain and on the behavior of endocytic fission. Based on our simulations, it is indicated that water plays an important role in the invagination and endocytic fission processes of the domain in a vesicle. For endocytic fission, domains of different sizes are evolved according to different routes under the effect of the water. Additionally, we find that both the spontaneous curvature of lipid molecules and area-to-volume ratio can promote or restrain the shape deformation of the lipid domain. Under the competition of these two factors, another possible route of endocytic fission is observed in our simulations, in that only a part of the lipid domain invaginates into the interior of the vesicle to complete the endocytic fission. Our study is helpful for understanding the possible mechanism of the shape transformation of the cellular membrane and the difference of several kinds of routes of vesicle fission.

The fusion of membranes and vesicles: pathway and energy barriers from dissipative particle dynamics

The fusion of lipid bilayers is studied with dissipative particle dynamics simulations. First, to achieve control over membrane properties, the effects of individual simulation parameters are studied and optimized. Then, a large number of fusion events for a vesicle and a planar bilayer are simulated using the optimized parameter set. In the observed fusion pathway, configurations of individual lipids play an important role. Fusion starts with individual lipids assuming a splayed tail configuration with one tail inserted in each membrane. To determine the corresponding energy barrier, we measure the average work for interbilayer flips of a lipid tail, i.e., the average work to displace one lipid tail from one bilayer to the other. This energy barrier is found to depend strongly on a certain dissipative particle dynamics parameter, and, thus, can be adjusted in the simulations. Overall, three subprocesses have been identified in the fusion pathway. Their energy barriers are estimated to lie in the range 8-15 k(B)T. The fusion probability is found to possess a maximum at intermediate tension values. As one decreases the tension, the fusion probability seems to vanish before the tensionless membrane state is attained. This would imply that the tension has to exceed a certain threshold value to induce fusion.

Lipids on the move: simulations of membrane pores, domains, stalks and curves

In this review we describe the state-of-the-art of computer simulation studies of lipid membranes. We focus on collective lipid-lipid and lipid-protein interactions that trigger deformations of the natural lamellar membrane state, showing that many important biological processes including self-aggregation of membrane components into domains, the formation of non-lamellar phases, and membrane poration and curving, are now amenable to detailed simulation studies.

Tension-induced vesicle fusion: pathways and pore dynamics

The dynamics of tension-induced fusion of two vesicles is studied using dissipative particle dynamics (DPD) simulations. The vesicle membranes use an improved DPD parameter set that results in their sustaining only a 10-30% relative area stretch before rupturing on the microsecond timescale of the simulations. Two distinct fusion pathways are observed depending on the initial vesicle tensions. In pathway I, at low membrane tension, a flattened adhesion zone is formed between the vesicles, and one vesicle subsequently ruptures in this contact zone to form a hemifusion state. This state is unstable and eventually opens a pore to complete the fusion process. In pathway II, at higher tension, a stalk is formed during the fusion process that is then transformed by transmembrane pore formation into a fusion pore. Whereas the latter pathway II resembles stalk pathways as observed in other simulation studies, fusion pathway I, which does not involve any stalk formation, has not been described previously to the best of our knowledge. A statistical analysis of the various processes shows that fusion is the dominant pathway for releasing the tension of the vesicles. The functional dependence of the observed fusion time on membrane tension implies that the fusion process is completed by overcoming two energy barriers with scales of 13kBT and 11kBT. The fusion pore radius as a function of time has also been extracted from the simulations, and provides a quantitative measure of the fusion dynamics which are in agreement with recent experiments.

Coarse-grained molecular dynamics simulations of phase transitions in mixed lipid systems containing LPA, DOPA, and DOPE lipids

The mechanisms that mediate biomembrane shape transformations are of considerable interest in cell biology. Recent in vitro experiments show that the chemical transformation of minor membrane lipids can induce dramatic shape changes in biomembranes. Specifically, it was observed that the addition of DOPA to DOPE has no effect on the stability of the bilayer structure of the membrane. In contrast, the addition of LPA to DOPE stabilizes the bilayer phase of DOPE, increasing the temperature of a phase transition from the bilayer to the inverted hexagonal phase. This result suggests that the chemical conversion of DOPA to LPA is sufficient for triggering a dramatic change in the shape of biomembranes. The LPA/DOPA/DOPE mixture of lipids provides a simple model system for understanding the molecular events driving the shape change. In this work, we used coarse-grained molecular dynamics simulations to study the phase transitions of this lipid mixture. We show that despite the simplicity of the coarse-grained model, it reproduces the experimentally observed phase changes of: 1), pure LPA and DOPA with respect to changes in the concentration of cations; and 2), LPA/DOPE and DOPA/DOPE mixtures with respect to temperature. The good agreement between the model and experiments suggests that the computationally inexpensive coarse-grained approach can be used to infer macroscopic membrane properties. Furthermore, analysis of the shape of the lipid molecules demonstrates that the phase behavior of single-lipid systems is consistent with molecular packing theory. However, the phase stability of mixed lipid systems exhibits significant deviations from this theory, which suggests that the elastic energy of the lipids, neglected in the packing theory, plays an important role.

A detailed look at vesicle fusion

Many different hypotheses on the molecular mechanisms of vesicle fusion exist. Because these mechanisms cannot be readily asserted experimentally, we address the problem by a coarse-grained molecular dynamics simulations study and compare the results with the results of other techniques. The simulations performed include the fusion of small and large vesicles and exocytosis, i.e., the fusion of small vesicles with flat bilayers. We demonstrate that the stalk, the initial contact between two fusing vesicles, is initiated by lipid tails that extend spontaneously. The stalk is revealed to be composed of the contacting monolayers only, yet without hydrophobic voids. Anisotropic and radial expansion of the stalk have been theorized; we show that stalk evolution can proceed via both pathways starting from similar setups and that water triggers the transition from elongated stalk to hemifusion diaphragm.

Pathway of membrane fusion with two tension-dependent energy barriers

Fusion of bilayer membranes is studied via dissipative particle dynamics (DPD) simulations. A new set of DPD parameters is introduced which leads to an energy barrier for flips of lipid molecules between adhering membranes. A large number of fusion events is monitored for a vesicle in contact with a planar membrane. Several time scales of the fusion process are found to depend exponentially on the membrane tension. This implies an energy barrier of about 10k(B)T for intermembrane flips and a second size-dependent barrier for the nucleation of a small hemifused membrane patch.

Budding Dynamics of Individual Domains in Multicomponent Membranes Simulated by N-Varied Dissipative Particle Dynamics

We study the budding dynamics of individual domains in flat, multicomponent membranes using dissipative particle dynamics (DPD) simulations with varied bead number N, in which addition and deletion of beads based on their density at the membrane boundary is introduced. The budding process of a tubular bud, accompanied by a dynamical transition reflected in the energy and morphology evolutions, is investigated. The simulations show that budding duration is shortened with increasing line tension and depends on the domain size quadratically. At low line tension, increasing bending modulus accelerates budding at first, but suppresses the process as it increases further. In addition, the controlling role of the surface tension in the budding process is also explored. Finally, we use the N-varied DPD to simulate the experimentally observed multicomponent tubular vesicles, and the three bud growth modes are confirmed.