Unfolding times for proteins in a force clamp.
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.
Luccioli
Stefano
S
Istituto dei Sistemi Complessi, CNR, via Madonna del Piano, Sesto Fiorentino, Italy.
Imparato
Alberto
A
Mitternacht
Simon
S
Irbäck
Anders
A
Torcini
Alessandro
A
D000465:Algorithms; D003285:Contractile Proteins / Q000737:chemistry; D004023:Dictyostelium; D064448:Filamins; D008840:Microfilament Proteins / Q000737:chemistry; D008956:Models, Chemical; D016011:Normal Distribution; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D015800:Protozoan Proteins / Q000737:chemistry; D013997:Time Factors; D025801:Ubiquitin / Q000737:chemistry
D003285:Contractile Proteins; D064448:Filamins; D008840:Microfilament Proteins; D011506:Proteins; D015800:Protozoan Proteins; D025801:Ubiquitin