Mechanical Unfolding of Proteins - A Comparative Nonequilibrium Molecular 
Dynamics Study

Mykuliak, Vasyl V.; Sikora, Mateusz; Booth, Jonathan J.; Cieplak, Marek; Shalashilin, Dmitrii V.; Hytönen, Vesa P.

doi:10.1016/j.bpj.2020.07.030

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Mechanical Unfolding of Proteins - A Comparative Nonequilibrium Molecular Dynamics Study

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Sikora, Mateusz
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;

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Citation

Mykuliak, V. V., Sikora, M., Booth, J. J., Cieplak, M., Shalashilin, D. V., & Hytönen, V. P. (2020). Mechanical Unfolding of Proteins - A Comparative Nonequilibrium Molecular Dynamics Study. Biophysical Journal, 119, 939-949. doi:10.1016/j.bpj.2020.07.030.

Cite as: https://hdl.handle.net/21.11116/0000-0006-E3E5-7

Abstract

Mechanical signals regulate functions of mechanosensitive proteins by inducing structural changes that are determinant for force-dependent interactions. Talin is a focal adhesion protein that is known to extend under mechanical load, and it has been shown to unfold via intermediate states. Here, we compared different nonequilibrium molecular dynamics (MD) simulations to study unfolding of the talin rod. We combined boxed MD (BXD), steered MD, and umbrella sampling (US) techniques and provide free energy profiles for unfolding of talin rod subdomains. We conducted BXD, steered MD, and US simulations at different detail levels and demonstrate how these different techniques can be used to study protein unfolding under tension. Unfolding free energy profiles determined by BXD suggest that the intermediate states in talin rod subdomains are stabilized by force during unfolding, and US confirmed these results.