Molecular Dynamics Simulation Studies of Lipid Flip-Flop in Different Membrane Environments


Student thesis: Doctoral Thesis

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Awarding Institution
Award date27 Jul 2021


In most mammalian cells, the plasma membranes are heterogeneous in composition and structure because of the flipping of lipid molecules from one leaflet to another. Moreover, the asymmetric partitioning of lipids is vital for cellular functions and plays a significant role in membrane mechanical stability, modulation of the activity of membrane proteins, and even apoptosis. Thus, understanding the molecular mechanism behind them and finding new methodologies to control or repair lipid scrambling activity in the plasma membrane are of significant medical interest.

Previous studies have demonstrated that lipid flip-flop can be tremendously affected by membrane-ion interactions, transmembrane potentials, antimicrobial peptides (AMPs), and DNA nanostructures. Two-Dimensional (2D) nanomaterials such as graphene nanosheets (GNs) and graphene oxide nanosheets (GOs) could attach or embed into the cell membranes, thus leading to the change of membrane properties and biological activities. Though numerous studies have been done to learn about the interactions between nanosheets and the cell membranes as well as the cytotoxicity of nanomaterials, the effects of how and to what extent the lipid flip-flop will be affected by nanomaterials have been seldomly studies. Therefore, in this thesis, molecular dynamics (MD) simulation has been taken as a “computational microscope” to systematically study the difference in the rate of lipid transfer under different membrane environments and design stable biomimetic nanodevices to control lipid translocation.

To thoroughly understand the membrane properties affected by nanomaterials, and to carefully investigate the molecular mechanism, all-atom (AA) MD models were used in our simulations. In this thesis, we first investigated the nature and the extent of the local perturbation of the lipid bilayers by GN. Two typical interaction states of GN-membrane systems were observed: GN adhering or inserting to the membrane. Both states have different effects on the cell membranes (lipid density, membrane thickness, and the mobility of phospholipids). Of great interest is that we found that the perpendicular insertion of GN and the parallel adhesion of GN, both could reduce the rates of lipid flip flop, particularly for the inserted GN, which could generate a liquid ordering domain around it.

Different hydrophobic and hydrophilic nanomaterials can have different impacts on membrane properties. Based on the preliminary results, we supposed that unlike the hydrophobic nanosheet GN, the hydrophilic nanosheet GO might have a different influence on the rates of lipid molecules migration. Different interaction states were firstly compared. Four characteristic interaction states were observed, namely: “adhesion,” “insertion,” “corrugated sandwich,” and “pore formation.” Membrane properties (lipid density, membrane thickness, the bending rigidity of the lipid bilayers, and the mobility of phospholipids) are affected differently by various interaction patterns. In addition, the cytotoxicity of nanosheets is not only related to the interaction states between nanosheets and cell membranes but also related to the size of nanosheets. Therefore, we also considered the membrane perturbation caused by varying the nanosheet sizes.

Furthermore, the free energy barrier and the rates of lipid flip-flop were calculated to tailor the interleaflet lipid transfer affected by GN and GO. Interestingly, GN and GO work in opposite directions. On one hand, the hydrophobic GN significantly increased the free energy barrier for lipid flip-flop near the inserted GN, thus leading to the decrease of lipid flip-flip rates. On the other hand, due to the hydrophilic functional groups on GO’s surface, the free energy of lipid transfer near the embedded GO dramatically decreased, which could increase the rates of lipid flip-flop between two lipid leaflets. These two opposite results provide new strategies for us to control the rates of the interleaflet lipid transfer. It also opens a new avenue for medical applications of nanomaterials, like controlling the composition of cell membranes and lipid homeostasis.

Taken together, a comprehensive investigation of the lipid flip-flop affected in different membrane environments was performed. Both dynamic and thermodynamics analyses were investigated to provide molecular views and implications for the mitigation of phospholipids. Our results revealed that different nanomaterials have different influences on the interleaflet lipid transfer as well as membrane properties under different interaction states. Moreover, controlling the size and the orientation of nanosheets are significant for the controlling of cytotoxicity of nanomaterials because nanosheets of different sizes and rotations have varying degrees of destructive damage to the structure of the cell membrane. Last but not least, the distinct roles of the GN and the GO on regulating the lipid flip-flop provide implications for designing stable biomimetic nanomaterials.

In one word, our works are expected to help future studies on bridging different interaction states and the perturbation on membrane properties. Besides, these interesting molecular details also can facilitate alleviating the cytotoxic of nanomaterials and make nanomaterials to be suitable for biomedical applications.