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Internal protein dynamics shifts the distance to the mechanical transition state

West, D.K., Paci, E. and Olmsted, P.D. (2006) Internal protein dynamics shifts the distance to the mechanical transition state. Physical Review E : Statistical, Nonlinear and Soft Matter Physics, 74 (6). Art. No. 061912. ISSN 1550-2376

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Abstract

Mechanical unfolding of polyproteins by force spectroscopy provides valuable insight into their free energy landscapes. Most experiments of the unfolding process have been fit to two-state and/or one dimensional models, with the details of the protein and its dynamics often subsumed into a zero-force unfolding rate and a distance x(u)(1D) to the transition state. We consider the entire phase space of a model protein under a constant force, and show that x(u)(1D) contains a sizeable contribution from exploring the full multidimensional energy landscape. This effect is greater for proteins with many degrees of freedom that are affected by force; and surprisingly, we predict that externally attached flexible linkers also contribute to the measured unfolding characteristics.

Item Type: Article
Copyright, Publisher and Additional Information: © 2006 The American Physical Society. This is an author produced version of a paper subsequently published in Physical Review E.
Institution: The University of Leeds
Academic Units: The University of Leeds > Faculty of Maths and Physical Sciences (Leeds) > School of Physics and Astronomy (Leeds)
The University of Leeds > University of Leeds Research Centres and Institutes > Astbury Centre for Structural Molecular Biology (Leeds)
Depositing User: Repository Officer
Date Deposited: 08 Feb 2007
Last Modified: 09 Jun 2014 19:36
Published Version: http://link.aps.org/abstract/PRE/v74/e061912
Status: Published
Publisher: American Physical Society
Refereed: Yes
Identification Number: 10.1103/PhysRevE.74.061912
URI: http://eprints.whiterose.ac.uk/id/eprint/1957

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