Approach behavior of binding proteins toward actin filament (brownian dynamics simulation)

Actin filament, the most abundant component of the cytoskeleton, plays important roles in fundamental cellular activities by dynamically changing its structure by elongation, branching, and bundling. These dynamic structural changes are regulated by various types of actin-binding proteins, whose binding is primarily determined by their approach behavior toward the filament. These molecular-level phenomena occur on spatial and temporal scales, relevant to diffusions of the molecules as well as filaments by thermal fluctuations in the cytoplasm. Therefore, to better understand the actin filament dynamics, this study narrowed down a target on this spatiotemporal scale with the aim of modeling and simulating the approach behavior of binding proteins toward the actin filament in the solvent. As a representative binding protein, we focused on the Arp2/3 complex ; one of the binding proteins known to initiate filament branching. In the model based on Brownian dynamics, the actin monomers and the Arp2/3 complex were considered globular particles governed by the Langeven equation, and the solvent was described as a continuum. In the case of shorter filaments, simulation results revealed that the frequency of the Arp2/3 complex approaching the filament ends was significantly higher compared with the middle portion. Contrary to this, as the filament length increases, the frequency ratio of the filament ends decreases. These results indicate that the fluctuations enhance binding to the ends of shorter filaments, but when the filaments become longer, the frequency of binding to the middle of the filament increases, such as observed in the branching phenomena.