Miguel Virginia, Perillo Maria A, Villarreal Marcos A
Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT), CONICET - Cátedra de Química Biológica, Departamento de Química-ICTA, Facultad de Ciencias Exactas Físicas, Universidad Nacional de Córdoba, Argentina.
Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT), CONICET - Cátedra de Química Biológica, Departamento de Química-ICTA, Facultad de Ciencias Exactas Físicas, Universidad Nacional de Córdoba, Argentina.
Biochim Biophys Acta. 2016 Nov;1858(11):2903-2910. doi: 10.1016/j.bbamem.2016.08.016. Epub 2016 Aug 31.
Coarse-grained (CG) models allow enlarging the size and time scales that are reachable by atomistic molecular dynamics simulations. A CG force field (FF) for lipids and amino acids that possesses a polarizable water model has been developed following the MARTINI parametrization strategy, the BMW-MARTINI [1]. We tested the BMW-MARTINI FF capability to describe some structural and thermodynamical properties of lipid monolayers and bilayers. We found that, since the surface tension values of oil/water interfaces calculated with the model are not correct, compression isotherms of lipid monolayers present artifacts. Also, this FF predicts DPPC and DAPC bilayers to remain in the L phase at temperatures as low as 283K, contrary to the expected from their experimental Tm values. Finally, simulations at constant temperature of bilayers of saturated lipids belonging to PC homologous, showed an increase in the mean molecular area (Mma) upon increasing the chain length, inversely to the experimental observation. We refined BMW-MARTINI FF by modifying as few parameters as possible in order to bring simulated and experimental measurements closer. We have also modified structural parameters of the lipid geometry that do not have direct influence in global properties of the bilayer membranes or monolayers, but serve to approach the obtained CG geometry to atomistic reference values. The refined FF is able to better reproduce phase transition temperatures and Mma for saturated PC bilayers than BMW-MARTINI and MARTINI FF. Finally, the simulated surface pressure-Mma isotherms of PC monolayers resemble the experimental ones and eliminate serious artifacts of previous models.
粗粒度(CG)模型能够扩大原子分子动力学模拟可触及的尺寸和时间尺度。遵循MARTINI参数化策略(即BMW-MARTINI [1]),已开发出一种用于脂质和氨基酸的具有可极化水模型的CG力场(FF)。我们测试了BMW-MARTINI FF描述脂质单层和双层的一些结构和热力学性质的能力。我们发现,由于用该模型计算的油/水界面的表面张力值不正确,脂质单层的压缩等温线存在伪影。此外,该FF预测二棕榈酰磷脂酰胆碱(DPPC)和二花生酰磷脂酰胆碱(DAPC)双层在低至283K的温度下仍处于L相,这与根据它们的实验熔点(Tm)值所预期的情况相反。最后,对属于磷脂酰胆碱(PC)同系物的饱和脂质双层进行恒温模拟时,结果显示平均分子面积(Mma)随链长增加而增大,这与实验观察结果相反。我们尽可能少地修改参数来优化BMW-MARTINI FF,以使模拟测量值和实验测量值更接近。我们还修改了脂质几何结构的参数,这些参数对双层膜或单层的整体性质没有直接影响,但有助于使获得的CG几何结构接近原子参考值。优化后的FF比BMW-MARTINI和MARTINI FF能够更好地再现饱和PC双层的相变温度和Mma。最后,PC单层的模拟表面压力-Mma等温线与实验等温线相似,并消除了先前模型中的严重伪影。