Tomasz Róg

Significance of Sterol Structural Specificity DESMOSTEROL CANNOT REPLACE CHOLESTEROL IN LIPID RAFTS

Desmosterol is an immediate precursor of cholesterol in the Bloch pathway of sterol synthesis and an abundant membrane lipid in specific cell types. The significance of the difference between the two sterols, an additional double bond at position C24 in the tail of desmosterol, is not known. Here, we provide evidence that the biophysical and functional characteristics of the two sterols differ and that this is because the double bond at C24 significantly weakens the sterol ordering potential. In model membranes, desmosterol was significantly weaker than cholesterol in promoting the formation or stability of ordered domains, and in mammalian cell membranes, desmosterol associated less avidly than cholesterol with detergent-resistant membranes. Atomic scale molecular dynamics simulations showed that the double bond gives rise to additional stress in the tail, creating a rigid structure between C24 and C27 and favoring tilting of desmosterol distinct from cholesterol. Functional effects of desmosterol in cell membranes were assessed upon acutely exchanging ∼70% of cholesterol to desmosterol. This led to impaired raft-dependent signaling via the insulin receptor, whereas non-raft-dependent protein secretion was not affected. We suggest that the choice of cholesterol synthesis route may provide a physiological mechanism to modulate raft-dependent functions in cells.

Lateral sorting in model membranes by cholesterol-mediated hydrophobic matching

Theoretical studies predict hydrophobic matching between transmembrane domains of proteins and bilayer lipids to be a physical mechanism by which membranes laterally self-organize. We now experimentally study the direct consequences of mismatching of transmembrane peptides of different length with bilayers of different thicknesses at the molecular level. In both model membranes and simulations we show that cholesterol critically constrains structural adaptations at the peptide-lipid interface under mismatch. These constraints translate into a sorting potential and lead to selective lateral segregation of peptides and lipids according to their hydrophobic length.

Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration.

We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM).

Study of PEGylated lipid layers as a model for PEGylated liposome surfaces: Molecular dynamics simulation and Langmuir monolayer studies

We have combined Langmuir monolayer film experiments and all-atom molecular dynamics (MD) simulation of a bilayer to study the surface structure of a PEGylated liposome and its interaction with the ionic environment present under physiological conditions. Lipids that form both gel and liquid-crystalline membranes have been used in our study. By varying the salt concentration in the Langmuir film experiment and including salt at the physiological level in the simulation, we have studied the effect of salt ions present in the blood plasma on the structure of the poly(ethylene glycol) (PEG) layer. We have also studied the interaction between the PEG layer and the lipid bilayer in both the liquid-crystalline and gel states. The MD simulation shows two clear results: (a) The Na(+) ions form close interactions with the PEG oxygens, with the PEG chains forming loops around them and (b) PEG penetrates the lipid core of the membrane for the case of a liquid-crystalline membrane but is excluded from the tighter structure of the gel membrane. The Langmuir monolayer results indicate that the salt concentration affects the PEGylated lipid system, and these results can be interpreted in a fashion that is in agreement with the results of our MD simulation. We conclude that the currently accepted picture of the PEG surface layer acting as a generic neutral hydrophilic polymer entirely outside the membrane, with its effect explained through steric interactions, is not sufficient. The phenomena we have observed may affect both the interaction between the liposome and bloodstream proteins and the liquid-crystalline-gel transition and is thus relevant to nanotechnological drug delivery device design.

Analysis of Twisting of Cellulose Nanofibrils in Atomistic Molecular Dynamics Simulations

We use atomistic molecular dynamics simulations to study the crystal structure of cellulose nanofibrils, whose sizes are comparable with the crystalline parts in commercial nanocellulose. The simulations show twisting, whose rate of relaxation is strongly temperature dependent. Meanwhile, no significant bending or stretching of nanocellulose is discovered. Considerations of atomic-scale interaction patterns bring about that the twisting arises from hydrogen bonding within and between the chains in a fibril.

Replacing the Cholesterol Hydroxyl Group with the Ketone Group Facilitates Sterol Flip-Flop and Promotes Membrane Fluidity

The 3alpha-hydroxyl group is a characteristic structural element of all membrane sterol molecules, while the 3-ketone group is more typically found in steroid hormones. In this work, we investigate the effect of substituting the hydroxyl group in cholesterol with the ketone group to produce ketosterone. Extensive atomistic molecular dynamics simulations of saturated lipid membranes with either cholesterol or ketosterone show that, like cholesterol, ketosterone increases membrane order and induces condensation. However, the effect of ketosterone on membrane properties is considerably weaker than that of cholesterol. This is largely due to the unstable positioning of ketosterone at the membrane-water interface, which gives rise to a small but significant number of flip-flop transitions, where ketosterone is exchanged between membrane leaflets. This is remarkable, as flip-flop motions of sterol molecules have not been previously reported in analogous lipid bilayer simulations. In the same context, ketosterone is found to be more tilted with respect to the membrane normal than cholesterol. The atomic level mechanism responsible for the increase of the steroid tilt and the promotion of flip-flops is the decrease in polar interactions at the membrane-water interface. Interactions between lipids or water and the ketone group are found to be weaker than in the case of the hydroxyl group, which allows ketosterone to penetrate through the hydrocarbon region of a membrane.

Effects of the Lipid Bilayer Phase State on the Water Membrane Interface

We performed 200 ns MD simulations of phosphatidylcholine (PC) bilayers in the liquid crystalline (L(α)) and gel (L(β)) states to compare the properties of the water-membrane interfaces in these two thermotropic bilayer phases. Our simulations show that the membrane phase determines the behavior of water, ions, and PC head groups. When the membrane was in the gel phase, we found partial dehydration (fewer PC-water interactions), particularly in the carbonyl groups region, as well as an almost complete lack of ionic penetration into this region as compared with the bilayer in the liquid-crystalline phase. In the latter case, there is an exchange of Na(+) ions between the water layer and the interfacial region. This is mainly due to the fact that the most stable binding of Na(+) in the liquid-crystalline bilayer is to the carbonyl groups. The lack of Na(+) binding to the carbonyl groups in the gel phase bilayer can be explained by the more compact structure of the bilayer in this phase.

Effects of phospholipid unsaturation on the bilayer nonpolar region: a molecular simulation study

Molecular dynamics simulations of two monounsaturated phosphatidylcholine (PC) bilayers made of 1-palmitoyl-2-oleoyl-PC (POPC; cis-unsaturated) and 1-palmitoyl-2-elaidoyl-PC (PEPC; trans-unsaturated) were carried out to investigate the effect of a double bond in the PC β-chain and its conformation on the bilayer core. Four nanosecond trajectories were used for analyses. A fully saturated 1,2-dimyristoyl-PC (DMPC) bilayer was used as a reference system. In agreement with experimental data, this study shows that properties of the PEPC bilayer are more similar to those of the DMPC than to the POPC bilayer. The differences between POPC and PEPC bilayers may be attributed to the different ranges of angles covered by the torsion angles β10 and β12 of the single bonds next to the double bond in the oleoyl (O) and elaidoyl (E) chains. Broader distributions of β10 and β12 in the E chain than in the O chain make the E chain more flexible. In effect, the packing of chains in the PEPC bilayer is similar to that in the DMPC bilayer, whereas that in the POPC bilayer is looser than that in the DMPC bilayer. The effect of the cis-double bond on torsions at the beginning of the O chain (β4 and β5) is similar to that of cholesterol on these torsions in a myristoyl chain.

Role of Glycolipids in Lipid Rafts: A View through Atomistic Molecular Dynamics Simulations with Galactosylceramide

Even in small amounts, glycolipids are an integral part of lipid rafts and their cellular functions. Here we employ atomistic molecular dynamics simulations to consider galactosylceramide (GalCer), one of the common glycosphingolipids, and investigate its interactions with other raft components (cholesterol, POPC, sphingomyelin) as well as the role and the effects of GalCer on the physical properties of raft-like membranes. Our results for 5 mol % GalCer indicate that whereas the thickness of raft membranes is clearly increased by the addition of GalCer, the average area per lipid and lipid conformational order remain virtually unchanged. Notable changes are observed in lateral diffusion of the raft lipids. This is found to be associated with the interdigitation of GalCer. With cholesterol, GalCer is observed to interact specifically by shielding it from the water phase.

Role of cardiolipins in the inner mitochondrial membrane : insight gained through atom-scale simulations

Mitochondrial membranes are unique in many ways. Unlike other cellular membranes, they are comprised of two membranes instead of just one, and cardiolipins, one of the abundant lipid species in mitochondrial membranes, are not found in significant amounts elsewhere in the cell. Among other aspects, the exceptional nature of cardiolipins is characterized by their small charged head group connected to typically four hydrocarbon chains. In this work, we present atomic-scale molecular dynamics simulations of the inner mitochondrial membrane modeled as a mixture of cardiolipins (CLs), phosphatidylcholines (PCs), and phosphatidylethanolamines (PEs). For comparison, we also consider pure one-component bilayers and mixed PC-PE, PC-CL, and PE-CL membranes. We find that the influence of CLs on membrane properties depends strongly on membrane composition. This is highlighted by studies of the stability of CL-containing membranes, which indicate that the interactions of CL in ternary lipid bilayers cannot be deduced from the corresponding ones in binary membranes. Moreover, while the membrane properties in the hydrocarbon region are only weakly affected by CLs, the changes at the membrane-water interface turn out to be prominent. The effects at the interface are most evident in membrane properties related to hydrogen bonding and the binding phenomena associated with electrostatic interactions.