Molecular dynamics assessment of the mechanical properties of fibrillar actin

Koubassova N.A., Tsaturyan A.K.
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Actin is a conserved structural protein that is expressed in all eukaryotic cells. When polymerized, it forms long filaments of fibrillar actin, or F-actin, which are involved in the formation of the cytoskeleton, in muscle contraction and its regulation, and in many other processes. The dynamic and mechanical properties of actin are important for interaction with other proteins and the realization of its numerous functions in the cell. We performed 204.8 ns long molecular dynamics (MD) simulations of an actin filament segment consisting of 24 monomers in the absence and the presence of MgADP at 300 K in the presence of a solvent and at physiological ionic strength using the AMBER99SBILDN and CHARMM36 force fields in the GROMACS software environment, using modern structural models as the initial structure obtained by high-resolution cryoelectron microscopy. MD calculations have shown that the stationary regime of fluctuations in the structure of the F-actin long segment is developed 80–100 ns after the start of the MD trajectory. Based on the results of MD calculations, the main parameters of the actin helix and its bending, longitudinal, and torsional stiffness were estimated using a section of the calculation model that is far enough away from its ends. The estimated subunit axial (2.72–2.75 nm) and angular (165–168◦) translation of the F-actin helix, its bending (2.8–4.7 · 10−26 N·m2), longitudinal (36–47·10−9 N), and torsional (2.6–3.1·10−26 N·m2) stiffness are in good agreement with the results of the most reliable experiments. The results of MD calculations have shown that modern structural models of F-actin make it possible to accurately describe its dynamics and mechanical properties, provided that computational models contain a sufficiently large number of monomers, modern force fields, and relatively long MD trajectories are used. The inclusion of actin partner proteins, in particular, tropomyosin and troponin, in the MD model can help to understand the molecular mechanisms of such important processes as the regulation of muscle contraction.

Keywords: F-actin, MgADP, mathematical modeling, molecular dynamics, flexural, longitudinal, and torsional stiffness
Citation in English: Koubassova N.A., Tsaturyan A.K. Molecular dynamics assessment of the mechanical properties of fibrillar actin // Computer Research and Modeling, 2022, vol. 14, no. 5, pp. 1081-1092
Citation in English: Koubassova N.A., Tsaturyan A.K. Molecular dynamics assessment of the mechanical properties of fibrillar actin // Computer Research and Modeling, 2022, vol. 14, no. 5, pp. 1081-1092
DOI: 10.20537/2076-7633-2022-14-5-1081-1092
URL: http://crm-en.ics.org.ru/journal/article/3253/
Creative Commons License This work is licensed under a Creative Commons Attribution-NoDerivs 3.0 Unported License.

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