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ARTICLE

Coarse-grained Modeling and Simulation of Actin Filament Behavior Based on Brownian Dynamics Method

Yoshitaka Shimada^∗,†, Taiji Adachi^∗,†,‡, Yasuhiro Inoue^∗,†, Masaki Hojo^∗

∗ Department of Mechanical Engineering and Science, Kyoto University
† Computational Cell Biomechanics Team, VCAD System Research Program, RIKEN
‡ Corresponding author. Department of Mechanical Engineering and Science, Kyoto University, Yoshida-Honmachi, Sakyo, Kyoto 606-8501, Japan. E-mail: adachi@me.kyoto-u.ac.jp

Molecular & Cellular Biomechanics 2009, 6(3), 161-174. https://doi.org/10.3970/mcb.2009.006.161

Abstract

The actin filament, which is the most abundant component of the cytoskeleton, plays important roles in fundamental cellular activities such as shape determination, cell motility, and mechanosensing. In each activity, the actin filament dynamically changes its structure by polymerization, depolymerization, and severing. These phenomena occur on the scales ranging from the dynamics of actin molecules to filament structural changes with its deformation due to the various forces, for example, by the membrane and solvent. To better understand the actin filament dynamics, it is important to focus on these scales and develop its mathematical model. Thus, the objectives of this study were to model and simulate actin filament polymerization, depolymerization, and severing based on the Brownian dynamics method. In the model, the actin monomers and the solvent were considered as globular particles and a continuum, respectively. The motion of the actin molecules was assumed to follow the Langevin equation. The polymerization, which increases the filament length, was determined by the distance between the center of the actin particle at the barbed end and actin particles in the solvent. The depolymerization, which decreases the filament length, was modeled such that the number of dissociation particles from the filament end per unit time was constant. In addition, the filament severing, in which one filament divides into two, was modeled to occur at an equal rate along the filament. Then, we simulated the actin filament dynamics using the developed model, and analyzed the filament elongation rate, its turnover, and the effects of filament severing on the polymerization and depolymerization. Results indicated that the model reproduced the linear dependence of the filament elongation on time, filament turnover process by polymerization and depolymerization, and acceleration of the polymerization and depolymerization by severing, which qualitatively agreed with those observed in experiments.

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