An efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation

Abstract The alpha-helix coiled-coils within talin’s rod domain have mechanical and signalling functions through their unfolding and refolding dynamics. A better understanding of talin unfolding events and the forces that are involved should allow better prediction of talin signalling. To overcome t...

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Autores principales:	Guy G. Butcher, William S. Harwin, Chris I. Jones
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/96d7a3dd6b0c44e88ec57b54524e450a
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spelling	oai:doaj.org-article:96d7a3dd6b0c44e88ec57b54524e450a2021-12-02T14:53:42ZAn efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation10.1038/s41598-021-88369-32045-2322https://doaj.org/article/96d7a3dd6b0c44e88ec57b54524e450a2021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-88369-3https://doaj.org/toc/2045-2322Abstract The alpha-helix coiled-coils within talin’s rod domain have mechanical and signalling functions through their unfolding and refolding dynamics. A better understanding of talin unfolding events and the forces that are involved should allow better prediction of talin signalling. To overcome the current limitations of force measuring in molecular dynamics simulations, a new simulation framework was developed which operated directly within the force domain. Along with a corresponding alpha-helix modelling method, the simulation framework was developed drawing on robotic kinematics to specifically target force interactions. Coordinate frames were used efficiently to compartmentalise the simulation structures and static analysis was applied to determine the propagation of forces and torques through the protein structure. The results of the electrostatic approximation using Coulomb’s law shows a simulated force interaction within the physiological relevant range of 5–40 pN for the rod sub-domains of talin. This covers the range of forces talin operates in and is 2–3 orders of magnitude closer to experimentally measured values than the compared all-atom and coarse-grained molecular dynamics. This targeted, force-based simulation is, therefore, able to produce more realistic forces values than previous simulation methods.Guy G. ButcherWilliam S. HarwinChris I. JonesNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Guy G. Butcher William S. Harwin Chris I. Jones An efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation
description	Abstract The alpha-helix coiled-coils within talin’s rod domain have mechanical and signalling functions through their unfolding and refolding dynamics. A better understanding of talin unfolding events and the forces that are involved should allow better prediction of talin signalling. To overcome the current limitations of force measuring in molecular dynamics simulations, a new simulation framework was developed which operated directly within the force domain. Along with a corresponding alpha-helix modelling method, the simulation framework was developed drawing on robotic kinematics to specifically target force interactions. Coordinate frames were used efficiently to compartmentalise the simulation structures and static analysis was applied to determine the propagation of forces and torques through the protein structure. The results of the electrostatic approximation using Coulomb’s law shows a simulated force interaction within the physiological relevant range of 5–40 pN for the rod sub-domains of talin. This covers the range of forces talin operates in and is 2–3 orders of magnitude closer to experimentally measured values than the compared all-atom and coarse-grained molecular dynamics. This targeted, force-based simulation is, therefore, able to produce more realistic forces values than previous simulation methods.
format	article
author	Guy G. Butcher William S. Harwin Chris I. Jones
author_facet	Guy G. Butcher William S. Harwin Chris I. Jones
author_sort	Guy G. Butcher
title	An efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation
title_short	An efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation
title_full	An efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation
title_fullStr	An efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation
title_full_unstemmed	An efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation
title_sort	efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/96d7a3dd6b0c44e88ec57b54524e450a
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_version_	1718389399832494080

An efficient alpha helix model and simulation framework for stationary electrostatic interaction force estimation

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