Abstract：
Cholesterol (CHL) plays an integral role in modulating the function and activity of various mammalian membrane proteins. Due to the slow dynamics of lipids, conventional computational studies of protein-CHL interactions rely on either long-time scale atomistic simulations or coarse-grained approximations to sample the process. A highly mobile membrane mimetic (HMMM) has been developed to enhance lipid diffusion and thus used to facilitate the investigation of lipid interactions with peripheral membrane proteins and, with customized in silico solvents to replace phospholipid tails, with integral membrane proteins. Here, we report an updated HMMM model that is able to include CHL, a nonphospholipid component of the membrane, henceforth called HMMM-CHL. To this end, we had to optimize the effect of the customized solvents on CHL behavior in the membrane. Furthermore, the new solvent is compatible with simulations using force-based switching protocols. In the HMMM-CHL, both improved CHL dynamics and accelerated lipid diffusion are integrated. To test the updated model, we have applied it to the characterization of protein-CHL interactions in two membrane protein systems, the human β2-adrenergic receptor (β2AR) and the mitochondrial voltage-dependent anion channel 1 (VDAC-1). Our HMMM-CHL simulations successfully identified CHL binding sites and captured detailed CHL interactions in excellent consistency with experimental data as well as other simulation results, indicating the utility of the improved model in applications where an enhanced sampling of protein-CHL interactions is desired.
摘要：
胆固醇（CHL）在调节各种哺乳动物膜蛋白的功能和活性中起着不可或缺的作用。由于脂质的缓慢动力学，蛋白质-CHL相互作用的常规计算研究依赖于长时间尺度原子模拟或粗粒度近似来采样过程。已经开发了一种高度移动的膜模拟物（HMMM）来增强脂质扩散，因此用于促进脂质与外周膜蛋白相互作用的研究，用定制的硅溶剂代替磷脂尾巴，与完整的膜蛋白。这里,我们报告了一个更新的HMMM模型，该模型能够包括CHL，膜的非磷脂成分，此后称为HMMM-CHL。为此,我们必须优化定制溶剂对膜中CHL行为的影响。此外，新溶剂与使用基于力的切换协议的模拟兼容。在HMMM-CHL中，两者改善CHL动力学和加速脂质扩散整合。要测试更新的模型，我们已经将其应用于表征两个膜蛋白系统中的蛋白质-CHL相互作用，人β2-肾上腺素能受体（β2AR）和线粒体电压依赖性阴离子通道1（VDAC-1）。我们的HMMM-CHL模拟成功地识别了CHL结合位点，并捕获了详细的CHL相互作用，与实验数据以及其他模拟结果非常一致。表明改进模型在需要增强蛋白质-CHL相互作用采样的应用中的实用性。
