Unfolding times for proteins in a force clamp

Summary, in English

The escape process from the native valley for proteins subjected to a constant stretching force is examined using a model for a beta barrel. For a wide range of forces, the unfolding dynamics can be treated as one-dimensional diffusion, parametrized in terms of the end-to-end distance. In particular, the escape times can be evaluated as first passage times for a Brownian particle moving on the protein free-energy landscape, using the Smoluchowski equation. At strong forces, the unfolding process can be viewed as a diffusive drift away from the native state, while at weak forces thermal activation is the relevant mechanism. An escape-time analysis within this approach reveals a crossover from an exponential to an inverse Gaussian escape-time distribution upon passing from weak to strong forces. Moreover, a single expression valid at weak and strong forces can be devised both for the average unfolding time as well as for the corresponding variance. The analysis offers a possible explanation of recent experimental findings for the proteins ddFLN4 and ubiquitin.

• Author: Stefano Luccioli; Alberto Imparato; Simon Mitternacht; Anders Irbäck; Alessandro Torcini
• Department/s: Computational Biology and Biological Physics - Has been reorganised
• Publishing year: 2010
• Language: English
• Publication/Series: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)
• Volume: 81
• Issue: 1
• Links: http://dx.doi.org/10.1103/PhysRevE.81.010902
• Document type: Journal article
• Publisher: American Physical Society
• Topic: Biophysics
• Status: Published
• ISBN/ISSN/Other: ISSN: 1539-3755