Computational Modeling of Ena/VASP Interacting with Actin Filament to Understand its Processivity

Abstract

Ena/VASP proteins enhance formation of filopodia in the cell membrane, which is composed of long and straight actin filaments. These proteins processively bind to the barbed end of actin filaments and increase actin elongation rate by two to three times. In this work, we first built an all-atom model of Ena/VASP interacting with actin filament (F-actin) by using computational protein design techniques since a complete structure of Ena/VASP interacting with F-actin is currently not available. We assessed the correct binding site of F-actin binding domain (FAB) of Ena/VASP on the F-actin by using well-tempered metadynamics (WTMetaD) simulations. The WTMetaD simulations demonstrated that FAB domain favors to interact with the cleft between subdomain (SD) 1 and SD 3 of the actin subunits, which is in a good agreement with a previous hypothesis. To understand the factors affecting the processivity of Ena/VASP at the barbed end of crosslinked filaments, we generated coarse-grained (CG) model of this structure by using a bottom-up approach, and then elaborated this CG structure to include four arms and two actin filaments connected with a cross-linker. We varied the number of arms in the CG model and investigated differences between their behaviors to understand the underlying mechanism of decreasing processivity with reduced number of arms as observed in the experiments. Our results showed that Ena/VASP becomes less stable on the filament when the number of arms decrease, which might be one of the factors that causes reduced processivity of Ena/VASP. The findings of this work can be used to resolve the underlying molecular mechanisms of actin network assembly/disassembly interacting with Ena/VASP.