Yang J, Calero C, Martí J
Department of Physics and Nuclear Engineering, Technical University of Catalonia-Barcelona Tech, B4-B5 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain.
J Chem Phys. 2014 Mar 14;140(10):104901. doi: 10.1063/1.4867385.
Microscopic structure and dynamics of water and lipids in a fully hydrated dimyristoylphosphatidylcholine phospholipid lipid bilayer membrane in the liquid-crystalline phase have been analyzed with all-atom molecular dynamics simulations based on the recently parameterized CHARMM36 force field. The diffusive dynamics of the membrane lipids and of its hydration water, their reorientational motions as well as their corresponding spectral densities, related to the absorption of radiation, have been considered for the first time using the present force field. In addition, structural properties such as density and pressure profiles, a deuterium-order parameter, surface tension, and the extent of water penetration in the membrane have been analyzed. Molecular self-diffusion, reorientational motions, and spectral densities of atomic species reveal a variety of time scales playing a role in membrane dynamics. The mechanisms of lipid motion strongly depend on the time scale considered, from fast ballistic translation at the scale of picoseconds (effective diffusion coefficients of the order of 10(-5) cm(2)/s) to diffusive flow of a few lipids forming nanodomains at the scale of hundreds of nanoseconds (diffusion coefficients of the order of 10(-8) cm(2)/s). In the intermediate regime of sub-diffusion, collisions with nearest neighbors prevent the lipids to achieve full diffusion. Lipid reorientations along selected directions agree well with reported nuclear magnetic resonance data and indicate two different time scales, one about 1 ns and a second one in the range of 2-8 ns. We associated the two time scales of reorientational motions with angular distributions of selected vectors. Calculated spectral densities corresponding to lipid and water reveal an overall good qualitative agreement with Fourier transform infrared spectroscopy experiments. Our simulations indicate a blue-shift of the low frequency spectral bands of hydration water as a result of its interaction with lipids. We have thoroughly analyzed the physical meaning of all spectral features from lipid atomic sites and correlated them with experimental data. Our findings include a "wagging of the tails" frequency around 30 cm(-1), which essentially corresponds to motions of the tail-group along the instantaneous plane formed by the two lipid tails, i.e., in-plane oscillations are clearly of bigger importance than those along the normal-to-the plane direction.
基于最近参数化的CHARMM36力场，通过全原子分子动力学模拟分析了处于液晶相的完全水合二肉豆蔻酰磷脂酰胆碱磷脂双层膜中水和脂质的微观结构及动力学。首次使用当前力场考虑了膜脂质及其水化水的扩散动力学、它们的重取向运动以及与辐射吸收相关的相应谱密度。此外，还分析了诸如密度和压力分布、氘序参数、表面张力以及水在膜中的渗透程度等结构性质。分子自扩散、重取向运动以及原子种类的谱密度揭示了在膜动力学中起作用的各种时间尺度。脂质运动的机制强烈依赖于所考虑的时间尺度，从皮秒尺度的快速弹道平移（有效扩散系数约为10^(-5) cm²/s）到数百纳秒尺度上少数脂质形成纳米域的扩散流（扩散系数约为10^(-8) cm²/s）。在亚扩散的中间区域，与最近邻的碰撞阻止脂质实现完全扩散。沿选定方向的脂质重取向与报道的核磁共振数据吻合良好，并表明存在两个不同的时间尺度，一个约为1 ns，另一个在2 - 8 ns范围内。我们将重取向运动的两个时间尺度与选定矢量的角分布相关联。计算得到的对应脂质和水的谱密度与傅里叶变换红外光谱实验总体上具有良好的定性一致性。我们的模拟表明，由于水化水与脂质的相互作用，其低频谱带发生蓝移。我们深入分析了脂质原子位点所有谱特征的物理意义，并将它们与实验数据相关联。我们的发现包括约30 cm^(-1) 的“尾部摆动”频率，这基本上对应于尾基团沿由两条脂质尾部形成的瞬时平面的运动，即面内振荡显然比沿垂直于平面方向的振荡更重要。
