Relative Affinity of VCA Domain of Wave to Actin, Arp3, and Arp2 using Molecular Dynamics Simulations

Abstract

Initiation of branching in actin cytoskeletal filaments requires an Arp2/3 complex bind to the side of an existing actin filament. Arp2 and Arp3, the major subunits of the Arp2/3 complex, nucleate actin branches by forming the first short pitch dimer of the daughter actin filament. Nucleation promoting factors like Wiskott-Aldrich (WA) family proteins are thought to activate the Arp2/3 complex and promote the elongation process by orienting and enhancing actin monomer binding to the daughter actin filament. Previous kinetics and cross-linking studies have established the importance of binding the VCA/WH2 domains of WA proteins in Arp2/3 complex activation, but the quaternary interactions are not well understood. We hypothesize that as in actin binding, the VCA domain of the WA protein WAVE also binds the hydrophobic cleft present between subdomain 1 and subdomain 3 of either Arp3 or Arp2, displacing the relative C-terminal extension of each present in the cleft. Binding and displacement allows conformational changes in the Arps to occur that result in the formation of a short-pitch Arp3:Arp2 dimer. We suggest that the binding of a VCA domain and ATP thus facilitates the activation of the Arp2/3 complex for branching. Here, we use molecular dynamics simulations to study complexes of V and C fragments of VCA domains individually with actin and both Arps in different nucleotide bound states in order to assess the relative energetics and conformational variation of different binding orientations.