We develop an efficient stochastic simulation algorithm for analyzing actin filament growth and decay in the presence of various actin-binding proteins. The evolution of nucleotide profiles of filaments can be tracked and the resulting feedback to actin-binding proteins is incorporated. The computational efficiency of the new method enables us to focus on experimentally realistic problems, and as one example we use it to analyze the experimental data of Helfer et al. [(2006). Mammalian twinfilin sequesters ADP-G-actin and caps filament barbed ends: implications in motility. EMBO J. 25, 1184-1195] on the capping and G-actin sequestering activity of twinfilin. We show that the binding specificity of twinfilin for ADP-G-actin is crucial for the observed biphasic evolution of the filament length distribution in the presence of twinfilin, and we demonstrate that twinfilin can be an essential part of the molecular machinery for regulating filament lengths after a short burst of polymerization. Significantly, our simulations indicate that the pyrenyl-actin fluorescence experiments would fail to report the emergence of large filaments under certain experimental conditions.
- Capping protein
- Stochastic simulation algorithm