Coarse Grained Molecular Dynamics Simulations of the Fusion of Vesicles Incorporating Water Channels

As the dynamics of the cell membrane and the working mechanisms of proteins cannot be readily asserted at a molecular level, many different hypotheses exist that try to predict and explain these processes, for instance vesicle fusion. Therefore, we use coarse grained molecular dynamics simulations to elucidate the fusion mechanism of vesicles. The implementation of this method with hydrophilic and hydrophobic particles is known for its valid representation of bilayers. With a minimalistic approach, using only 3 atom types, 12 atoms per two-tailed phospholipids and incorporating only a bond potential and Lennard-Jones potential, phospholipid bilayers and vesicles can be simulated exhibiting authentic dynamics. We have simulated the spontaneous full fusion of both tiny (6 nm diameter) and larger (13 nm diameter) vesicles. We showed that, without applying constraints to the vesicles, the initial contact between two fusing vesicles, the stalk, is initiated by a bridging lipid tail that extends from the membrane spontaneously. Subsequently it is observed that the evolution of the stalk can proceed via two pathways, anisotropic and radial expansion, which is in accordance with literature. Contrary to the spherical vesicles of in vitro experiments, the fused vesicles remain tubular since the internal volume of these vesicles is too small compared to their membrane area. While the lipid bilayer has some permeability for water, it is not high enough to allow for the large flux required to equilibrate the vesicle content in the time accessible to our simulations. To increase the membrane permeability, we incorporate proteinaceous water channels, by applying the coarse grained technique to aquaporin. Even though incorporating water channels in the vesicles does significantly increase water permeability, the vesicles do not become spherical. Presumably the lipids have to be redistributed as well

Coarse-grained modelling of urea-adamantyl functionalized poly(propylene imine) dendrimers

To investigate the behaviour of poly(propylene imine) dendrimers -- and urea-adamantyl functionalized ones -- in solution using molecular dynamics simulations, we developed a coarse grained model to tackle the relatively large system sizes and time scales needed. Harmonic bond and angle potentials were derived from atomistic simulations using an iterative Boltzmann inversion scheme, modified to incorporate Gaussian fits of the bond and angle distributions. With the coarse grained model and accompanying force field simulations of generations 1 to 7 of both dendrimer types in water were performed. They compare favourably with atomistic simulations and experimental results on the basis of size, shape, monomer density, spacer back-folding and atomic form factor measurements. These results show that the structural dynamics of these dendrimers originate from flexible chains constrained by configurational and spatial requirements. Large dendrimers are more rigid and spherical, while small ones are flexible, alternatively rod-like and globular

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

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

Coarse-grained transmembrane proteins : hydrophobic matching, aggregation, and their effect on fusion

Molecular transport between organelles is predominantly governed by vesicle fission and fusion. Unlike experimental vesicles, the fused vesicles in molecular dynamics simulations do not become spherical readily, because the lipid and water distribution is inappropriate for the fused state and spontaneous amendment is slow. Here, we study the hypothesis that enhanced transport across the membrane of water, lipids, or both is required to produce spherical vesicles. This is done by adding several kinds of model proteins to fusing vesicles. The results show that equilibration of both water and lipid content is a requirement for spherical vesicles. In addition, the effect of these transmembrane proteins is studied in bilayers and vesicles, including investigations into hydrophobic matching and aggregation. Our simulations show that the level of aggregation does not only depend on hydrophobic mismatch, but also on protein shape. Additionally, one of the proteins promotes fusion by inducing pore formation. Incorporation of these proteins allows even flat membranes to fuse spontaneously. Moreover, we encountered a novel spontaneous vesicle enlargement mechanism we call the engulfing lobe, which may explain how lipids added to a vesicle solution are quickly incorporated into the inner monolayer

Vesicle deformation by draining : geometrical and topological shape changes

A variety of factors, including changes in temperature or osmotic pressure, can trigger morphological transitions of vesicles. Upon osmotic upshift, water diffuses across the membrane in response to the osmotic difference, resulting in a decreased vesicle volume to membrane area ratio and, consequently, a different shape. In this paper, we study the vesicle deformations on osmotic deflation using coarse grained molecular dynamics simulations. Simple deflation of a spontaneously formed spherical vesicle results in oblate ellipsoid and discous vesicles. However, when the hydration of the lipids in the outer membrane leaflet is increased, which can be the result of a changed pH or ion concentration, prolate ellipsoid, pear-shaped and budded vesicles are formed. Under certain conditions the deflation even results in vesicle fission. The simulations also show that vesicles formed by a bilayer to vesicle transition are, although spontaneously formed, not immediately stress-free. Instead, the membrane is stretched during the final stage of the transition and only reaches equilibrium once the excess interior water has diffused across the membrane. This suggests the presence of residual membrane stress immediately after vesicle closure in experimental vesicle formation and is especially important for MD simulations of vesicles where the time scale to reach equilibrium is out of reach