多尺度分子动力学模拟研究BAR-PH蛋白重塑细胞膜的微观机制

Membrane remodeling, including change of membrane curvature, membrane fission and fusion, is involved in various important cellular processes, such as, cell division, cell motility, endocytosis and signal transduction. It is essential that the cell can accurately remodel membrane to maintain its regular functions. Proteins with BAR domain participate in the membrane remodeling processes and play essential roles. The molecular mechanisms of these processes are not fully understood yet. Recently, it is found that the ACAP1 protein containing BAR-PH domain could remodel liposome and induce the tubule formation. Experimental results suggest that the membrane remodeling mechanism through BAR-PH domain is a novel mechanism, different from previous ones, scaffolding and wedging. Since it is very difficult to observe the remodeling process via experiments, we propose to explore the remodeling mechanism through multi-scale simulations. Systematical molecular dynamics simulations will be performed under the hierarchy targeting different problems. First of all, interactions between important residues in proteins will be screened out and evaluated using all-atom molecular dynamics simulations. Moreover, simulations results will be further employed to construct coarse-grained models through robust coarse-graining methodologies. Finally, large-scale simulations will be performed to explore the remodeling mechanism, including multiple BAR-PH domain proteins interacting with the membrane, as well as multiple PH domain proteins interacting with the membrane. Simulation results will elucidate how BAR-PH domains interact with lipid bilayer and induce curvature, as well as the role of PH domains. Besides, the newly developed coarse-graining method will be applicable to other BAR family proteins, which induce different curvature formation on lipid bilayers. We will investigate the fundamental principles behind these phenomena，and hopefully draw a general, or universal conclusion on the membrane remodeling mechanism through BAR family proteins. These studies will facilitate our further investigations on cellular activities related to membrane deformation and remodeling.

细胞分裂、细胞内外的物质和信号传输等细胞生理过程都涉及到细胞膜的曲率变化、开裂和融合。这些细胞膜的重塑过程影响着细胞维持其正常生命活动。为了深入研究这些过程，我们首先需要透彻了解细胞膜重塑的微观机制。在很多细胞膜重塑过程中一类含有BAR结构域的蛋白质家族起着关键性作用，他们通过脚手架或者楔入机制令细胞膜变形。但最新实验结果显示我们对重塑的微观机制的了解得并不全面，一种含有BAR-PH结构域的蛋白质是通过新的未知机制重塑细胞膜的。由于直接从实验观察这一重塑过程非常困难，所以本项目将针对该蛋白质开发一套粗粒化模型，并结合不同尺度的分子动力学模拟研究细胞膜的重塑过程：全原子分子动力学模拟确定蛋白质与细胞膜结合的关键位点；粗粒化分子动力学模拟研究细胞膜变形的过程。本项目开发的多尺度模拟方法可适用于研究其他BAR蛋白质家族成员与细胞膜的相互作用，从而完善BAR蛋白重塑细胞膜的微观机制。

细胞膜的重组包括细胞膜的弯曲、细胞膜分裂和细胞膜的融合。上述重组牵涉到诸多重要的细胞活动，如 细胞分裂，细胞迁移，内吞以及信号转导。细胞膜的精确重组对细胞维持其正常功能至关重要。含有BAR结构域的蛋白质参与了细胞膜的重组过程并在其中发挥重要作用。该过程的分子机制至今仍未完全为人所了解。最近有研究发现含有BAR-PH结构域的ACAP1蛋白能重组脂质体并引发小管的形成。实验结果表明BAR-PH结构域参与的细胞膜重组机制与以往的皆不相同。由于实验上直接观测到重组过程非常困难，所以本项目采用了分子动力学模拟来研究蛋白质与细胞膜的相互作用。首先，我们将单个蛋白质放置膜的上方，观察到对称的蛋白质只有一端结合到膜上，最重要的氨基酸包括R147，R148和F280，实验合作者也验证了它们的重要性。其次，我们采用伞状采样方法研究了PH结构域对PIP磷脂的选择特异性。通过对比PH结构域与PIP2和PS的结合自由能，我们发现前者是后者的2-3倍，这就解释了PIP族磷脂的重要性。接下来，我们把多个蛋白质搭成一个点阵，结合冷冻电镜云密度分布数据，我们使用分子动力学柔性拟合来优化蛋白质点阵的结构用以研究蛋白质之间的相互作用，并在蛋白质之间的界面上预测了7个带电的氨基酸和数个其他重要的氨基酸，突变试验也进一步确认它们对细胞膜变形所起的决定性作用。本课题成功的理解了BAR-PH蛋白质重塑膜的分子机制。