Alteration of interleaflet coupling due to compounds displaying rapid translocation in lipid membranes

Can Urea and Trimethylamine-N-oxide Prevent the Pressure-Induced Phase Transition of Lipid Membrane?

Organisms dwelling in ocean trenches are exposed to the high hydrostatic pressure of ocean water. Increasing pressure can alter the membrane packing density and fluidity and trigger the fluid-to-gel phase transition. To combat environmental stress, the organisms synthesize small polar solutes, which are known as osmolytes. Urea and trimethylamine-N-oxide (TMAO) are two such solutes found in deep-sea creatures. While TMAO stabilizes protein, urea induces protein denaturation. These solutes strongly influence the packing density and membrane fluidity of the lipid bilayer at different conditions. But can these solutes affect the pressure-induced phase transition of the lipid membrane? In the present work, we have studied the effect of these two solutes on pressure-induced fluid-to-gel phase transition based on the all-atom molecular dynamics (MD) simulation approach. A high-pressure-stimulated fluid-to-gel phase transition of the membrane is seen at 800 bar, which is consistent with previous experiments. We have also observed that in the low-pressure region (1-400 bar), urea slightly increases the membrane fluidity where TMAO decreases the same. However, the phase transition pressure remains almost unchanged on the addition of urea while TMAO shifts the phase transition toward a lower pressure. We have found that the hydrogen (H)-bond interaction between lipid and urea plays an important role in preserving the fluidity of the membrane in the low-pressure zone. However, at a higher pressure, both water and urea are excluded from the membrane surface. TMAO is also excluded from the interfacial region of the membrane at all pressures. Exclusion from the membrane surface further triggers the phase transition of the lipid membrane from the fluid to gel phase at a high pressure.

LiPyphilic: A Python Toolkit for the Analysis of Lipid Membrane Simulations

Molecular dynamics simulations are now widely used to study emergent phenomena in lipid membranes with complex compositions. Here, we present LiPyphilic-a fast, fully tested, and easy-to-install Python package for analyzing such simulations. Analysis tools in LiPyphilic include the identification of cholesterol flip-flop events, the classification of local lipid environments, and the degree of interleaflet registration. LiPyphilic is both force field- and resolution-agnostic, and by using the powerful atom selection language of MDAnalysis, it can handle membranes with highly complex compositions. LiPyphilic also offers two on-the-fly trajectory transformations to (i) fix membranes split across periodic boundaries and (ii) perform nojump coordinate unwrapping. Our implementation of nojump unwrapping accounts for fluctuations in the box volume under the NPT ensemble-an issue that most current implementations have overlooked. The full documentation of LiPyphilic, including installation instructions and links to interactive online tutorials, is available at https://lipyphilic.readthedocs.io/en/latest.

Cryostabilization of the Cell Membrane of a Psychrotolerant Bacteria via Homeoviscous Adaptation

Homeoviscous adaptation (maintenance of a critical balance between the saturated and unsaturated lipids) of the cell membrane of psychrotolerant bacteria is essential to protect them against freeze-thaw cycle. But how does the homeoviscous adaptation protect the cell membrane during cold stress? In this Letter, we answer this question using a coarse-grained molecular dynamics simulation technique. On the basis of the reported fatty acid profiles of psychrotolerant bacteria at different temperatures, multiple lipid membranes are simulated at a wide range of temperatures between 250 and 300 K. We explicate how the homeoviscous adaptation minimizes the effect of cold stress on the structure and fluidity of the membrane. Partial freezing of the saturated lipid domain occurs with the self-aggregation of saturated and unsaturated lipids near the melting temperature of the unadapted lipid membrane. The gel-like phase provides necessary local packing density that can be sensed by sensor proteins responsible for the homeoviscous adaptation.

Computational Modeling of Realistic Cell Membranes

Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.

Cholesterol Flip-Flop Impacts Domain Registration in Plasma Membrane Models

The plasma membrane is a highly complex multicomponent system that is central to the functioning of cells. Cholesterol, a key lipid component of the plasma membrane, promotes the formation of nanodomains. These nanodomains are often correlated across the two membrane leaflets, but the underlying physical mechanism remains unclear. Using coarse-grained molecular dynamics simulations, we investigate the influence of cholesterol flip-flop on membrane properties, in particular, the interleaflet coupling of cholesterol-enriched domains. We show that the cholesterol density correlation between the leaflets of an average mammalian plasma membrane is significantly reduced by suppressing interleaflet cholesterol population. Our results suggest an amplifying role of cholesterol in signal transduction across the leaflets.

Effects of fullerene on lipid bilayers displaying different liquid ordering: a coarse-grained molecular dynamics study

BACKGROUND

The toxic effects and environmental impact of nanomaterials, and in particular of Fullerene particles, are matters of serious concern. It has been reported that fullerene molecules enter the cell membrane and occupy its hydrophobic region. Understanding the effects of carbon-based nanoparticles on biological membranes is therefore of critical importance to determine their exposure risks.

METHODS

We report on a systematic coarse-grained molecular dynamics study of the interaction of fullerene molecules with simple model cell membranes. We have analyzed bilayers consisting of lipid species with different degrees of unsaturation and a variety of cholesterol fractions. Addition of fullerene particles to phase-segregated ternary membranes is also investigated in the context of the lipid raft model for the organization of the cell membrane.

RESULTS

Fullerene addition to lipid membranes modifies their structural properties like thickness, area and internal ordering of the lipid species, as well as dynamical aspects such as molecular diffusion and cholesterol flip-flop. Interestingly, we show that phase-segregating ternary lipid membranes accumulate fullerene molecules preferentially in the liquid-disordered domains promoting phase-segregation and domain alignment across the membrane.

CONCLUSIONS

Lipid membrane internal ordering determines the behavior and distribution of fullerene particle, and this, in turn, determines the influence of fullerene on the membrane. Lipid membranes are good solvents of fullerene molecules, and in particular those with low internal ordering.

GENERAL SIGNIFICANCE

Preference of fullerene molecules to be dissolved in the more disordered hydrophobic regions of a lipid bilayer and the consequent alteration of its phase behavior may have important consequences on the activity of biological cell membranes and on the bioconcentration of fullerene in living organisms.