An Agent-Based Model of Protein Polymerization Dynamics: Focus on the Actin System
Actin polymerization is a critical cellular process involved in a wide range of activities, from cell motility to cytokinesis. The complex behavior of this molecular system, resulting in three different phases (i.e., nucleation, elongation, and steady state) is clear by looking at the way these dynamics emerge from a large number of interactions between different proteins, regulatory elements, and signaling pathways. In this article, we present an agent-based model of actin polymerization dynamics implemented with the NetLogo simulation platform and focus on the time evolution of actin filaments length distribution in two dimensions starting from a pool of free G-actin monomers. Stochastic simulations were able to reproduce all main steps of the polymerization process in vitro, as well as two emerging patterns which have been previously discovered using alternative approaches, namely global treadmilling of F-actin filaments and competition between nucleation and elongation. The ability of the model to replicate relevant theoretical and experimental findings makes this new tool suitable for simulating complex molecular mechanisms by manipulating a limited set of parameters.