Mapplebeck, S orcid.org/0000-0002-8223-186X, Booth, J and Shalashilin, D orcid.org/0000-0001-6104-1277 (2021) Simulation of protein pulling dynamics on second time scale with boxed molecular dynamics. The Journal of Chemical Physics, 155 (8). 085101. ISSN 0021-9606
Abstract
We demonstrate how recently developed Boxed Molecular Dynamics (BXD) and kinetics [D. V. Shalashilin et al., J. Chem. Phys. 137, 165102 (2012)] can provide a kinetic description of protein pulling experiments, allowing for a connection to be made between experiment and the atomistic protein structure. BXD theory applied to atomic force microscopy unfolding is similar in spirit to the kinetic two-state model [A. Noy and R. W. Friddle, Methods 60, 142 (2013)] but with some differences. First, BXD uses a large number of boxes, and therefore, it is not a two-state model. Second, BXD rate coefficients are obtained from atomistic molecular dynamics simulations. BXD can describe the dependence of the pulling force on pulling speed. Similar to Shalashilin et al. [J. Chem. Phys. 137, 165102 (2012)], we show that BXD is able to model the experiment at a very long time scale up to seconds, which is way out of reach for standard molecular dynamics.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | Published under an exclusive license by AIP Publishing. This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Sarah Mapplebeck, Jonathan Booth, and Dmitrii Shalashilin , "Simulation of protein pulling dynamics on second time scale with boxed molecular dynamics", J. Chem. Phys. 155, 085101 (2021) and may be found at https://doi.org/10.1063/5.0059321. Uploaded in accordance with the publisher's self-archiving policy. |
Dates: |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Engineering & Physical Sciences (Leeds) > School of Chemistry (Leeds) > Physical Chemistry (Leeds) |
Depositing User: | Symplectic Publications |
Date Deposited: | 02 Sep 2021 16:43 |
Last Modified: | 07 Oct 2021 08:23 |
Status: | Published |
Publisher: | AIP Publishing |
Identification Number: | 10.1063/5.0059321 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:177658 |