论文标题
使用多尺度分子动力学模拟，以获取对形成毒素机制的孔的见解
Using Multiscale Molecular Dynamics Simulations to Obtain Insights into Pore Forming Toxin Mechanisms
论文作者
论文摘要
形成毒素（PFT）的毛孔是由多种物种释放的有毒蛋白质，包括许多细菌菌株，以攻击和杀死宿主细胞。在本文中，我们关注分子动力学（MD）模拟的效用以及从这些技术收集到PFT的孔隙途径上的分子见解。除了广泛使用的全原子模拟外，粗粒状的马提尼酒模型和基于结构的模型也已用于研究PFT。在这里，重点是在设置，监视和评估膜环境中PFT的MD模拟的属性时所涉及的方法和技术。我们从几个案例研究中得出，以说明MD模拟如何为蛋白质蛋白质和蛋白质 - 脂质相互作用，脂质动力学，构象动力学，构象转变和结构提供了分子见解。
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the molecular insights gleaned from these techniques on the pore forming pathways of PFTs. In addition to all-atom simulations which are widely used, coarse grained MARTINI models and structure based models have also been used to study PFTs. Here, the emphasis is on methods and techniques involved while setting up, monitoring, and evaluating properties from MD simulations of PFTs in a membrane environment. We draw from several case studies to illustrate how MD simulations have provided molecular insights into protein-protein and protein-lipid interactions, lipid dynamics, conformational transitions and structures of both the oligomeric intermediates and assembled pore structures.
