Internal protein dynamics shifts the distance to the mechanical transition state

Daniel K. West, Emanuele Paci, and Peter D. Olmsted
Phys. Rev. E 74, 061912 – Published 29 December 2006

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 xu1D to the transition state. We consider the entire phase space of a model protein under a constant force, and show that xu1D 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.

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  • Received 9 May 2006

DOI:https://doi.org/10.1103/PhysRevE.74.061912

©2006 American Physical Society

Authors & Affiliations

Daniel K. West

  • School of Physics and Astronomy and School of Biochemistry and Microbiology, University of Leeds, Leeds LS2 9JT, United Kingdom

Emanuele Paci and Peter D. Olmsted*

  • School of Physics and Astronomy and Astbury Centre for Structural Biology, University of Leeds, Leeds LS2 9JT, United Kingdom

  • *Electronic address: p.d.olmsted@leeds.ac.uk

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Issue

Vol. 74, Iss. 6 — December 2006

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