Internal protein dynamics shifts the distance to the mechanical transition state

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.