Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA.
Biophys J. 2010 Nov 3;99(9):2896-905. doi: 10.1016/j.bpj.2010.08.044.
Detailed atomistic computer simulations are now widely used to study biological membranes, including increasingly mixed lipid systems that involve, for example, cholesterol, which is a key membrane lipid. Typically, simulations of these systems start from a preassembled bilayer because the timescale on which self-assembly occurs in mixed lipid systems is beyond the practical abilities of fully atomistic simulations. To overcome this limitation and study bilayer self-assembly, coarse-grained models have been developed. Although there are several coarse-grained models for cholesterol reported in the literature, these generally fail to account explicitly for the unique molecular features of cholesterol that relate to its function and role as a membrane lipid. In this work, we propose a new coarse-grained model for cholesterol that retains the molecule's unique features and, as a result, can be used to study crystalline structures of cholesterol. In the development of the model, two levels of coarse-graining are explored and the importance of retaining key molecular features in the coarse-grained model that are relevant to structural properties is investigated.
详细的原子级计算机模拟现在被广泛用于研究生物膜,包括越来越多的混合脂质系统,例如胆固醇,胆固醇是一种关键的膜脂质。通常,这些系统的模拟从预先组装的双层开始,因为在混合脂质系统中发生自组装的时间尺度超出了全原子模拟的实际能力。为了克服这一限制并研究双层自组装,已经开发了粗粒化模型。尽管文献中有几种报道的胆固醇粗粒化模型,但这些模型通常没有明确考虑胆固醇的独特分子特征,这些特征与其功能和作为膜脂质的作用有关。在这项工作中,我们提出了一种新的胆固醇粗粒化模型,该模型保留了分子的独特特征,因此可用于研究胆固醇的晶体结构。在模型的开发过程中,探索了两个层次的粗粒化,并研究了在与结构性质相关的粗粒化模型中保留关键分子特征的重要性。