title: 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 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.
authors.affiliation: School of Physics and Astronomy and School of Biochemistry and Microbiology, University of Leeds, Leeds LS2 9JT, United Kingdom.
authors.forename: Daniel K
authors.initials: DK
authors.lastname: West
authors.forename: Emanuele
authors.initials: E
authors.lastname: Paci
authors.forename: Peter D
authors.initials: PD
authors.lastname: Olmsted
mesh_terms: D003198:Computer Simulation; D004548:Elasticity; D007700:Kinetics; D019563:Mechanics; D008846:Micromanipulation / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D044367:Phase Transition; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D013314:Stress, Mechanical
chemical_list: D011506:Proteins