Booth, JJ and Shalashilin, DV (2016) Fully Atomistic Simulations of Protein Unfolding in Low Speed Atomic Force Microscope and Force Clamp Experiments with the Help of Boxed Molecular Dynamics. Journal of Physical Chemistry B, 120 (4). pp. 700-708. ISSN 1520-6106
Abstract
The results of Boxed Dynamics (BXD) fully atomistic simulations of protein unfolding by Atomic Force Microscope (AFM), in both force clamp (FC) and velocity clamp (VC) modes are reported. In AFM experiments the unfolding occurs on time scale which is too long for standard atomistic Molecular Dynamics (MD) simulations, which are usually performed with the addition of forces which exceed those of experiment by many orders of magnitude. BXD can reach the time scale of slow unfolding and sample the very high free energy unfolding pathway, reproducing the experimental dependence of pulling force against extension and extension against time. Calculations show the presence of the pulling force ‘humps’ previously observed in the Velocity Clamp (VC) AFM experiments and allow the identification of intermediate protein conformations responsible for them. Fully atomistic BXD simulations can estimate the rate of unfolding in the Force Clamp (FC) experiments up to the time scale of seconds.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2016 American Chemical Society. This is an open access article published under a Creative Commons Attribution (CC-BY) License, which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. |
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: | 20 Jan 2016 11:18 |
Last Modified: | 20 Apr 2016 02:33 |
Published Version: | http://dx.doi.org/10.1021/acs.jpcb.5b11519 |
Status: | Published |
Publisher: | American Chemical Society |
Identification Number: | 10.1021/acs.jpcb.5b11519 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:93765 |