Martini Force Field Parameters for Glycolipids
Martini Force Field Parameters for Glycolipids
复制标题
DOI：
10.1021/ct3009655
复制
发表时间：
2013-03-01
影响因子：
5.5
通讯作者：
Marrink, Siewert J.
中科院分区：
文献类型：
--
作者：
Lopez, Cesar A.;Sovova, Zofie;Marrink, Siewert J.
我们提出了Martini粗粒力场的扩展到糖脂。这里考虑的糖脂是单半乳糖二酰甘油(MGDG)、磺基喹诺酮二酰甘油(SQDG)、二半乳糖二酰甘油(DGDG)、磷脂酰肌醇(PI)及其磷酸化形式(PIP、PIP2)，以及糖鞘糖脂半乳糖神经酰胺(GCER)和单唾液酸四己糖神经节苷脂(GM1)。该对映体遵循与先前用于脂类、蛋白质和碳水化合物的相同的原理，侧重于在极性和非极性溶剂之间复制小化合物的分配自由能。通过与原子力场采样的脂类构象进行比较，特别是相对于糖苷键周围填充最多的状态的表示，来优化成键参数。粗粒糖脂模型膜的模拟结果与原子模拟和实验数据符合得很好，特别是在电子密度、每脂面积和膜厚度等结构性质方面。我们的粗粒度模型为大规模模拟生物过程开辟了道路，其中糖脂是重要的，包括识别、分类和聚集外部和膜结合的蛋白质。
We present an extension of the Martini coarse-grained force field to glycolipids. The glycolipids considered here are the glycoglycerolipids monogalactosyldiacylglycerol (MGDG), sulfoquinovosyldiacylglycerol (SQDG), digalactosyldiacylglycerol (DGDG), and phosphatidylinositol (PI) and its phosphorylated forms (PIP, PIP2), as well as the glycosphingolipids galactosylceramide (GCER) and monosialotetrahexosylganglioside (GM1). The parametrization follows the same philosophy as was used previously for lipids, proteins, and carbohydrates focusing on the reproduction of partitioning free energies of small compounds between polar and nonpolar solvents. Bonded parameters are optimized by comparison to lipid conformations sampled with an atomistic force field, in particular with respect to the representation of the most populated states around the glycosidic linkage. Simulations of coarse-grained glycolipid model membranes show good agreement with atomistic simulations as well as experimental data available, especially concerning structural properties such as electron densities, area per lipid, and membrane thickness. Our coarse grained model opens the way to large scale simulations of biological processes in which glycolipids are important, including recognition, sorting, and clustering of both external and membrane bound proteins.