We studied actin filament polymerization and nucleation with molecular dynamics simulations and a previously established coarse-grained model having each residue represented by a single interaction site located at the Cα atom. We approximate each actin protein as a fully or partially rigid unit to identify the equilibrium structural ensemble of interprotein complexes. Monomers in the F-actin configuration bound to both barbed and pointed ends of a short F-actin filament at the anticipated locations for polymerization. Binding at both ends occurred with similar affinity. Contacts between residues of the incoming subunit and the short filament were consistent with expectation from models based on crystallography, x-ray diffraction, and cryo-electron microscopy. Binding at the barbed and pointed end also occurred at an angle with respect to the polymerizable bound structure, and the angle range depended on the flexibility of the D-loop. Additional barbed end bound states were seen when the incoming subunit was in the G-actin form. Consistent with an activation barrier for pointed end polymerization, G-actin did not bind at an F-actin pointed end. In all cases, binding at the barbed end also occurred in a configuration similar to the antiparallel (lower) dimer. Individual monomers bound each other in a short-pitch helix complex in addition to other configurations, with several of them apparently nonproductive for polymerization. Simulations with multiple monomers in the F-actin form show assembly into filaments as well as transient aggregates at the barbed end. We discuss the implications of these observations on the kinetic pathway of actin filament nucleation and polymerization and possibilities for future improvements of the coarse-grained model.

中文翻译：

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使用粗粒度模型深入了解肌动蛋白聚合和成核

我们通过分子动力学模拟和先前建立的粗粒度模型研究了肌动蛋白丝聚合和成核，每个残基由位于 Cα 原子的单个相互作用位点表示。我们将每个肌动蛋白近似为一个完全或部分刚性单元，以识别蛋白质间复合物的平衡结构集合。F-肌动蛋白构型中的单体在聚合的预期位置与短 F-肌动蛋白丝的带倒钩和尖端结合。两端的结合以相似的亲和力发生。传入亚基的残基与短丝之间的接触与基于晶体学、X 射线衍射和低温电子显微镜的模型的预期一致。倒钩和尖端的结合也相对于可聚合的结合结构以一定角度发生，角度范围取决于 D 环的柔韧性。当传入的亚基处于 G-肌动蛋白形式时，可以看到额外的带倒钩的末端结合状态。与尖端聚合的激活屏障一致，G-肌动蛋白在 F-肌动蛋白尖端不结合。在所有情况下，倒钩末端的结合也发生在类似于反平行（下部）二聚体的配置中。除了其他构型外，单个单体在短螺距螺旋复合物中相互结合，其中一些显然对聚合无效。F-肌动蛋白形式的多个单体的模拟显示组装成细丝以及带刺末端的瞬态聚集体。