Department of Chemical Engineering, University of Washington, Seattle, WA 98195-1750, USA.
J Mol Biol. 2012 Feb 10;416(1):148-61. doi: 10.1016/j.jmb.2011.12.025. Epub 2011 Dec 17.
We investigated the structure, properties and dynamics of the actin filament branch junction formed by actin-related protein (Arp) 2/3 complex using all-atom molecular dynamics (MD) simulations based on a model fit to a reconstruction from electron tomograms. Simulations of the entire structure consisting of 31 protein subunits together with solvent molecules containing ∼3 million atoms were performed for an aggregate time of 175 ns. One 75-ns simulation of the original reconstruction was compared to two 50-ns simulations of alternate structures, showing that the hypothesized branch junction structure is very stable. Our simulations revealed that the interface between Arp2/3 complex and the mother actin filament features a large number of salt bridges and hydrophobic contacts, many of which are dynamic and formed/broken on the timescale of the simulation. The simulations suggest that the DNase binding loops in Arp3, and possibly Arp2, form stabilizing contacts with the mother filament. Unbiased comparison of models sampled from the MD simulation trajectory with the primary experimental electron tomography data identified regions were snapshots from the simulation provide atomic details of the model structures and also pinpoints regions where the initial modeling based on the electron tomogram reconstruction may be suboptimal.
我们使用基于电子断层扫描重建拟合模型的全原子分子动力学 (MD) 模拟研究了肌动蛋白相关蛋白 (Arp) 2/3 复合物形成的肌动蛋白丝分支连接的结构、性质和动力学。对包含约 300 万个原子的溶剂分子和 31 个蛋白质亚基的整个结构进行了总计 175 纳秒的模拟。将原始重建的一个 75 纳秒模拟与两个替代结构的 50 纳秒模拟进行了比较，结果表明假设的分支连接结构非常稳定。我们的模拟表明，Arp2/3 复合物与母肌动蛋白丝之间的界面具有大量盐桥和疏水接触，其中许多是动态的，并且在模拟时间尺度上形成/断裂。模拟表明，Arp3 中的 DNase 结合环，可能还有 Arp2，与母丝形成稳定的接触。从 MD 模拟轨迹中采样的模型与原始电子断层扫描数据的无偏比较确定了一些区域，模拟快照提供了模型结构的原子细节，还指出了基于电子断层扫描重建的初始建模可能不太理想的区域。
