Kristian Dimitrievski

Simulations of Lipid Vesicle Adsorption for Different Lipid Mixtures

Numerous experimental studies of lipid vesicle adsorption on solid surfaces show that electrostatic interactions play an important role for the kinetics and end result. The latter can, e.g., be intact vesicles or supported lipid bilayers (SLB). Despite an accumulated quite large experimental data base, the understanding of the underlying processes is still poor, and mathematical models are scarce. We have developed a phenomenological model of a vesicle adsorbing on a substrate, where the charge of the surface and the charge and polar state of the lipid headgroup can be varied. With physically reasonable assumptions and input parameters, we reproduce many key experimental observations, clarify the details of some experiments, and give predictions and suggestions for future experiments. Specifically, we have investigated the influence of different lipid mixtures (different charges of the headgroups) in the vesicle on the outcome of a vesicle adsorption event. For different mixtures of zwitterionic lipids with positive and negative lipids, we investigated whether the vesicle adsorbs or not, and--if it adsorbs--to what extent it gets deformed and when it ruptures spontaneously. Diffusion of neutral vesicles on different types of negatively charged substrates was also simulated. The mean surface charge density of the substrate was varied, including or excluding local fluctuations in the surface charge density. The simulations are compared to available experiments. A consistent picture of the influence of different lipid mixtures in the vesicle on adsorption, and the influence of different types of substrates on vesicle diffusion, appear as a result of the simulation data.

Deformation of adsorbed lipid vesicles as a function of vesicle size.

Experimental indications that adsorbed lipid vesicles are deformed on the surface (e.g., on SiO(2)) and that the deformation seems to be more pronounced for larger vesicles have been reported. In general, it has been assumed that larger vesicles should show a stronger tendency for spontaneous rupture, which is also backed up by thermodynamic considerations (Seifert, U.; Lipowsky, R. Phys. Rev. A 1990, 42, 4768; Seifert, U. Adv. Phys. 1997, 46, 13). However, using a newly developed model of a lipid bilayer, simulations were performed to study the shape of adsorbed lipid vesicles for different vesicle sizes, with the observation that larger vesicles indeed are more deformed on the surface, but that there is no additional tendency for larger vesicles to rupture spontaneously. It is shown here that the radius of curvature, on the portions of the vesicle membrane that are most strained, is practically independent of the vesicle size. A kinetic barrier for vesicle rupture is proposed to be the reason for the observed disagreement with thermodynamic theory.

Interaction of virions with membrane glycolipids.

Cellular membranes contain various lipids including glycolipids (GLs). The hydrophilic head groups of GLs extend from the membrane into the aqueous environment outside the cell where they act as recognition sites for specific interactions. The first steps of interaction of virions with cells often include contacts with GLs. To clarify the details of such contacts, we have used the total internal reflection fluorescence microscopy to explore the interaction of individual unlabelled virus-like particles (or, more specifically, norovirus protein capsids), which are firmly bound to a lipid bilayer, and fluorescent vesicles containing glycosphingolipids (these lipids form a subclass of GLs). The corresponding binding kinetics were earlier found to be kinetically limited, while the detachment kinetics were logarithmic over a wide range of time. Here, the detachment rate is observed to dramatically decrease with increasing concentration of glycosphingolipids from 1% to 8%. This effect has been analytically explained by using a generic model describing the statistics of bonds in the contact area between a virion and a lipid membrane. Among other factors, the model takes the formation of GL domains into account. Our analysis indicates that in the system under consideration, such domains, if present, have a characteristic size smaller than the contact area between the vesicle and the virus-like particle.

Influence of Lipid-Bilayer-Associated Molecules on Lipid-Vesicle Adsorption

Supported lipid bilayers (SLBs) containing different types of bilayer-associated molecules (membrane-bound molecules) where one part of the molecule resides inside the lipid bilayer and another part of the molecule sticks out of the bilayer (e.g., membrane proteins) are important biophysical model systems. SLBs are commonly formed via lipid vesicle adsorption on certain surfaces (e.g., SiO(2)). However, vesicles doped with different types of (bio)molecules often do not form an SLB on the surface, and the reasons for this are not clear. Using a newly developed model of a lipid bilayer, simulations were performed to clarify the influence of the bilayer-associated molecules on vesicle adsorption and rupture. It is shown that by increasing the concentration of membrane-bound molecules in the vesicles the tendency for vesicle rupture decreases markedly and for a certain concentration rupture does not happen. The reason for this is that vesicles containing significant concentrations of such molecules tend to deform less on the surface (lower vesicle strain), especially for a significantly corrugated bilayer-surface potential. After vesicle rupture, membrane-bound molecules face either the surface or the solution in the resulting bilayer patch on the surface, depending on whether the molecules point outward or inward in the original vesicle, respectively. Vesicle surface diffusion is also studied for weak and strong surface corrugation, where vesicles are found to be almost immobile in the latter case.

Influence of surface pinning points on diffusion of adsorbed lipid vesicles

Using a simple model of a vesicle and a substrate, we have studied the surface diffusion of an adsorbed vesicle. We show that the experimentally observed but unexplained fact, that a neutral (POPC) vesicle adsorbed to a SiO(2) or mica surface does not diffuse but can be moved laterally by an atomic force microscope (AFM) tip, without rupture, can be explained by transient (i.e., temporary) pinning of lipid head groups to surface charges. We studied the surface diffusion for different vesicle adsorption strengths (without any pinning taking place), with the observation that a stronger vesicle-surface attraction leads to slower surface diffusion. However, the surface diffusion was still significant and too high to explain the experimentally observed immobility. When allowing transient lipid pinning between the vesicle and the surface, a 1-2 orders of magnitude decrease in the surface diffusion coefficient was observed. For a lipid adsorption potential of around 20 k(B)T and a lipid pinning potential of about 25 k(B)T, the vesicle is found to be practically immobile on the surface.

Chain length scaling of protein folding time: Beta sheet structures

We present comprehensive 3D lattice Monte Carlo simulations of the folding kinetics of two-turn antiparallel β sheets. The model employed takes into account isotropic nonspecific interactions as in previous flexible heteropolymer models and also orientation-dependent monomer–monomer interactions, mimicking the formation of hydrogen bonds and chain rigidity. The chain length is varied from N=15 to 33. For each chain length, we calculate the fastest folding temperature, Tfast, folding temperature, Tfold, and glass-transition temperature, Tg. The time-averaged occupation probability of the native state is found to be nearly independent of N at all temperatures. The dependence of Tfast and Tfold on N is accordingly relatively weak. The temperature interval where the folding is fast rapidly decreases with increasing N. For the chain lengths chosen, Tfold slightly exceeds Tg. The dependence of the folding time τf on N is well fitted by using the power law, τf∝Nλ. The exponent λ is found to depend on temperature...

Simulations of lipid vesicle rupture induced by an adjacent supported lipid bilayer patch.

Using a simple phenomenological model of a lipid bilayer and a surface, simulations were performed to study the bilayer-induced vesicle rupture probability as a vesicle adsorbs adjacently to a bilayer patch already adsorbed on the surface. The vesicle rupture probability was studied as a function of temperature, vesicle size, and surface-bilayer interaction strength. From the simulation data, estimates of the apparent activation energy for bilayer-induced vesicle rupture were calculated, both for different vesicle sizes and for different surface-bilayer interaction strengths.

Rate-determining moves in protein folding

We present lattice Monte Carlo simulations of protein folding for the three main types of 3-D native protein conformations, including globular structures, bundles of α helices, and β sheets. Scrutinizing the relative role of the end, crankshaft, and corner monomer moves, we show that the latter moves are rate-determining in all the cases.