Particle-based modeling of living actin filaments in an optical trap

Abstract

We report a coarse-grained molecular dynamics simulation study of a bundle of parallelactin filaments under supercritical conditions pressing against a loaded mobile wall using aparticle-based approach where each particle represents an actin unit. The filaments are graftedto a fixed wall at one end and are reactive at the other end, where they can perform singlemonomer (de)polymerization steps and push on a mobile obstacle. We simulate a reactive grandcanonical ensemble in a box of fixed transverse area A, with a fixed number of grafted filaments Nf ,at temperature T and monomer chemical potential μ1. For a single filament case (Nf=1) and fora bundle of Nf = 8 filaments, we analyze the structural and dynamical properties at equilibriumwhere the external load compensates the average force exerted by the bundle. The dynamics of thebundle-moving-wall unit are characteristic of an over-damped Brownian oscillator in agreementwith recent in vitro experiments by an optical trap setup. We analyze the influence of thepressing wall on the kinetic rates of (de)polymerization events for the filaments. Both static anddynamic results compare reasonably well with recent theoretical treatments of the same system.Thus, we consider the proposed model as a good tool to investigate the properties of a bundle ofliving filaments.