Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.
Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands.
J Phys Chem B. 2017 Apr 20;121(15):3443-3457. doi: 10.1021/acs.jpcb.6b09111. Epub 2017 Jan 6.
The periodic Saffman-Delbrück (PSD) model, an extension of the Saffman-Delbrück model developed to describe the effects of periodic boundary conditions on the diffusion constants of lipids and proteins obtained from simulation, is tested using the coarse-grained Martini and all-atom CHARMM36 (C36) force fields. Simulations of pure Martini dipalmitoylphosphatidylcholine (DPPC) bilayers and those with one embedded gramicidin A (gA) dimer or one gA monomer with sizes ranging from 512 to 2048 lipids support the PSD model. Underestimates of D (the value of the diffusion constant for an infinite system) from the 512-lipid system are 35% for DPPC, 45% for the gA monomer, and 70% for the gA dimer. Simulations of all-atom DPPC and dioleoylphosphatidylcholine (DOPC) bilayers yield diffusion constants not far from experiment. However, the PSD model predicts that diffusion constants at the sizes of the simulation should underestimate experiment by approximately a factor of 3 for DPPC and 2 for DOPC. This likely implies a deficiency in the C36 force field. A Bayesian method for extrapolating diffusion constants of lipids and proteins in membranes obtained from simulation to infinite system size is provided.
周期性 Saffman-Delbrück（PSD）模型是 Saffman-Delbrück 模型的扩展，用于描述模拟中周期性边界条件对脂质和蛋白质扩散常数的影响，该模型使用粗粒度 Martini 和全原子 CHARMM36（C36）力场进行了测试。纯 Martini 二棕榈酰磷脂酰胆碱（DPPC）双层膜以及嵌入一个革兰氏菌素 A（gA）二聚体或一个大小从 512 到 2048 个脂质的 gA 单体的模拟支持 PSD 模型。对于 512 个脂质的系统，从扩散常数（无限系统的值）的低估值为 DPPC 的 35%，gA 单体的 45%，gA 二聚体的 70%。全原子 DPPC 和二油酰基磷脂酰胆碱（DOPC）双层膜的模拟得到的扩散常数与实验值相差不远。然而，PSD 模型预测，对于 DPPC 和 DOPC，模拟大小的扩散常数应该比实验值低估约 3 倍和 2 倍。这可能意味着 C36 力场存在缺陷。提供了一种从模拟中提取膜中脂质和蛋白质的扩散常数并将其外推到无限系统大小的贝叶斯方法。
