ABSTRACT Structural and transport properties of lipid bilayers consisting of pure ceramides are investigated through molecular dynamics simulations. Two different initial configurations are used: one where the lipids already form a pre-constructed bilayer and one obtained from the self-assemblage of lipids randomly distributed in an aqueous phase. The latter is created using the MARTINI coarse-grained forcefield followed by back-mapping to atomistic description using the CHARMM forcefield. It is found that the pre-constructed and the self-assembled bilayers have in general comparable structural properties. Nevertheless they exhibit certain differences with respect to the packing and conformation of the aliphatic chains, leading to a different energy barrier that a drug molecule such as ibuprofen must overcome in order to move along the bilayer normal. These results show that the choice of the initial lipids setup for molecular dynamics simulations of a lipid bilayer may have a significant impact on the simulation outcome and thus, the respective calculated structure and transport properties.

中文翻译：

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自组装神经酰胺双层的分子模拟：结构和阻隔性能的比较

摘要通过分子动力学模拟研究了由纯神经酰胺组成的脂质双层的结构和运输特性。使用了两种不同的初始配置：一种是脂质已经形成预先构建的双层，另一种是从随机分布在水相中的脂质的自组装中获得的。后者是使用 MARTINI 粗粒度力场创建的，然后使用 CHARMM 力场反向映射到原子描述。发现预构建的和自组装的双层通常具有相当的结构特性。然而，它们在脂肪链的堆积和构象方面表现出某些差异，导致药物分子（如布洛芬）必须克服的不同能量屏障才能沿双层法线移动。这些结果表明，选择用于脂质双层分子动力学模拟的初始脂质设置可能对模拟结果产生重大影响，从而对相应的计算结构和传输特性产生重大影响。