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Internal protein dynamics shifts the distance to the mechanical transition state

Daniel K. West·Emanuele Paci·Peter D. Olmsted
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Abstract

Mechanical unfolding of polyproteins by force spectroscopy provides valuable insight into their free energy landscapes. Most phenomenological models of the unfolding process are two-state and/or one dimensional, with the details of the protein and its dynamics often subsumed into a zero-force unfolding rate and a single distance $x_u^{1\textrm{D}}$ to the transition state. We consider the entire phase space of a model protein under a constant force, and show that the distance $x_u^{1\textrm{D}}$ contains a sizeable contribution from exploring the full multidimensional energy landscape. Proteins with more degrees of freedom are expected to have larger values for $x_u^{1\textrm{D}}$. We show that externally attached flexible linkers also contribute to the measured unfolding characteristics.

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Daniel K. West, Emanuele Paci, Peter D. Olmsted. 2006-12-19. Internal protein dynamics shifts the distance to the mechanical transition state. https://doi.org/10.1103/physreve.74.061912

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