Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, Berkeley, California, USA.
PLoS Comput Biol. 2013 Apr;9(4):e1002995. doi: 10.1371/journal.pcbi.1002995. Epub 2013 Apr 25.
Vinculin can interact with F-actin both in recruitment of actin filaments to the growing focal adhesions and also in capping of actin filaments to regulate actin dynamics. Using molecular dynamics, both interactions are simulated using different vinculin conformations. Vinculin is simulated either with only its vinculin tail domain (Vt), with all residues in its closed conformation, with all residues in an open I conformation, and with all residues in an open II conformation. The open I conformation results from movement of domain 1 away from Vt; the open II conformation results from complete dissociation of Vt from the vinculin head domains. Simulation of vinculin binding along the actin filament showed that Vt alone can bind along the actin filaments, that vinculin in its closed conformation cannot bind along the actin filaments, and that vinculin in its open I conformation can bind along the actin filaments. The simulations confirm that movement of domain 1 away from Vt in formation of vinculin 1 is sufficient for allowing Vt to bind along the actin filament. Simulation of Vt capping actin filaments probe six possible bound structures and suggest that vinculin would cap actin filaments by interacting with both S1 and S3 of the barbed-end, using the surface of Vt normally occluded by D4 and nearby vinculin head domain residues. Simulation of D4 separation from Vt after D1 separation formed the open II conformation. Binding of open II vinculin to the barbed-end suggests this conformation allows for vinculin capping. Three binding sites on F-actin are suggested as regions that could link to vinculin. Vinculin is suggested to function as a variable switch at the focal adhesions. The conformation of vinculin and the precise F-actin binding conformation is dependent on the level of mechanical load on the focal adhesion.
纽蛋白可以与 F-肌动蛋白相互作用,既能将肌动蛋白丝募集到不断增长的黏着斑,又能通过帽化肌动蛋白丝来调节肌动蛋白动力学。使用分子动力学,模拟了不同纽蛋白构象的这两种相互作用。纽蛋白模拟要么只有其纽蛋白尾部结构域(Vt),要么所有残基都处于关闭构象,要么所有残基都处于开放 I 构象,要么所有残基都处于开放 II 构象。开放 I 构象是由结构域 1 远离 Vt 运动产生的;开放 II 构象是由 Vt 从纽蛋白头部结构域完全解离产生的。沿着肌动蛋白丝模拟纽蛋白结合显示,只有 Vt 本身可以沿着肌动蛋白丝结合,处于关闭构象的纽蛋白不能沿着肌动蛋白丝结合,而处于开放 I 构象的纽蛋白可以沿着肌动蛋白丝结合。模拟证实,结构域 1 远离 Vt 的运动在纽蛋白 1 的形成中足以允许 Vt 沿着肌动蛋白丝结合。Vt 帽化肌动蛋白丝的模拟探测了六个可能的结合结构,并表明纽蛋白通过与丝氨酸 1 和丝氨酸 3 的结合来帽化肌动蛋白丝,利用通常被 D4 和附近纽蛋白头部结构域残基阻塞的 Vt 表面。D1 分离后 D4 与 Vt 的分离形成了开放 II 构象。开放 II 纽蛋白与丝氨酸 3 的结合表明这种构象允许纽蛋白帽化。在 F-肌动蛋白上建议有三个结合位点作为可以与纽蛋白连接的区域。建议纽蛋白在黏着斑处作为一个可变开关发挥作用。纽蛋白的构象和确切的 F-肌动蛋白结合构象取决于黏着斑上的机械负荷水平。