M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , ul. Miklukho-Maklaya, 16/10, Moscow 117997, Russia.
ACS Nano. 2013 Oct 22;7(10):9428-42. doi: 10.1021/nn4042392. Epub 2013 Sep 30.
The atomic-scale diffusion of water in the presence of several lipid bilayers mimicking biomembranes is characterized via unconstrained molecular dynamics (MD) simulations. Although the overall water dynamics corresponds well to literature data, namely, the efficient braking near polar head groups of lipids, a number of interesting and biologically relevant details observed in this work have not been sufficiently discussed so far; for instance, the fact that waters "sense" the membrane unexpectedly early, before water density begins to decrease. In this "transitional zone" the velocity distributions of water and their H-bonding patterns deviate from those in the bulk solution. The boundaries of this zone are well preserved even despite the local (<1 nm size) perturbation of the lipid bilayer, thus indicating a decoupling of the surface and bulk dynamics of water. This is in excellent agreement with recent experimental data. Near the membrane surface, water movement becomes anisotropic, that is, solvent molecules preferentially move outward the bilayer. Deep in the membrane interior, the velocities can even exceed those in the bulk solvent and undergo large-scale fluctuations. The analysis of MD trajectories of individual waters in the middle part of the acyl chain region of lipids reveals a number of interesting rare phenomena, such as the fast (ca. 50 ps) breakthrough across the membrane or long-time (up to 750 ps) "roaming" between lipid leaflets. The analysis of these events was accomplished to delineate the mechanisms of spontaneous water permeation inside the hydrophobic membrane core. It was shown that such nontrivial dynamics of water in an "alien" environment is driven by the dynamic heterogeneities of the local bilayer structure and the formation of transient atomic-scale "defects" in it. The picture observed in lipid bilayers is drastically different from that in a primitive membrane mimic, a hydrated cyclohexane slab. The possible biological impact of such phenomena in equilibrated lipid bilayers is discussed.
通过无约束分子动力学（MD）模拟，研究了模拟生物膜的多层脂双层中水分子的原子尺度扩散。尽管整体水动力学与文献数据非常吻合，即脂类极性头部附近的水的有效制动，但到目前为止，该工作中观察到的许多有趣和与生物学相关的细节尚未得到充分讨论；例如，水在密度开始降低之前就出乎意料地提前“感知”到膜的事实。在这个“过渡区”，水的速度分布及其氢键模式与本体溶液中的不同。即使脂质双层受到局部（<1nm 大小）扰动，该区域的边界也能很好地保持，这表明水的表面和体相动力学解耦。这与最近的实验数据非常吻合。在靠近膜表面处，水的运动变得各向异性，即溶剂分子优先从双层向外移动。在膜内部深处，速度甚至可以超过体相溶剂的速度，并经历大规模波动。对脂质酰链区域中间部分单个水分子的 MD 轨迹进行分析，揭示了一些有趣的罕见现象，例如快速（约 50ps）穿过膜或在脂质双层之间长时间（长达 750ps）“漫游”。完成了对这些事件的分析，以描绘在疏水分子核心内自发水渗透的机制。结果表明，在“陌生”环境中，水的这种非平凡动力学是由局部双层结构的动态非均质性和其中瞬态原子尺度“缺陷”的形成所驱动的。在脂双层中观察到的图像与水合环己烷片这种原始膜模拟物中的图像截然不同。讨论了在平衡脂双层中这些现象的可能生物学影响。
