Studying the lateral chain packing in a ceramide bilayer with molecular dynamics simulations

3rd International Conference on Mathematical Modeling in Physical Sciences

物理学;数学

Papadimitriou, N.I.^1 ; Karozis, S.N.^1 ; Kainourgiakis, M.E.^1 ; Charalambopoulou, G. Ch.^1

Environmental Research Laboratory, National Center for Scientific Research Demokritos, Agia Paraskevi

15310, Greece^1

关键词: Barrier functions;    Degree of mobility;    Lateral chains;    Lipid domains;    Molecular dynamics simulations;    Novel techniques;    Radial distribution functions;    Separation distances;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/574/1/012014/pdf
DOI  :  10.1088/1742-6596/574/1/012014

来源: IOP

【 摘 要 】

In this work, we present a novel technique, based on molecular dynamics simulations, that allows the study of the lateral chain packing in a lipid bilayer. It utilizes the radial distribution function of the alkyl chains to determine the arrangement of the chains along the bilayer plane. The positions of the mass centres of the chains are projected onto the bilayer plane and a 2D radial distribution function is calculated for these projections. The proposed technique can be particularly useful for lipid bilayers in the gel (solid) phase where the chains present a limited degree of mobility. As a case study, we have examined a bilayer that consists of ceramide NS 24:0. Ceramide bilayers can be found in the lipid domain of the skin where they have a significant role in its barrier function. The specific bilayer was found (at 300 K) to adopt a strictly hexagonal chain packing with a separation distance between the chains of 0.466 nm, in good agreement with the available experimental data.