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Unfolding times for proteins in a force clamp

Luccioli, Stefano; Imparato, Alberto; Mitternacht, Simon LU ; Irbäck, Anders LU and Torcini, Alessandro (2010) In Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)2001-01-01+01:002016-01-01+01:00 81(1).
Abstract
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... (More)
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. (Less)
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Contribution to journal
publication status
published
subject
in
Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)2001-01-01+01:002016-01-01+01:00
volume
81
issue
1
publisher
American Physical Society
external identifiers
  • wos:000277186100003
  • scopus:76349091603
ISSN
1539-3755
DOI
10.1103/PhysRevE.81.010902
language
English
LU publication?
yes
id
fbe58c02-4b1d-48c3-8403-ac9f5b9ac5ed (old id 1601083)
date added to LUP
2010-05-20 10:51:07
date last changed
2018-05-29 10:30:28
@article{fbe58c02-4b1d-48c3-8403-ac9f5b9ac5ed,
  abstract     = {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.},
  articleno    = {010902},
  author       = {Luccioli, Stefano and Imparato, Alberto and Mitternacht, Simon and Irbäck, Anders and Torcini, Alessandro},
  issn         = {1539-3755},
  language     = {eng},
  number       = {1},
  publisher    = {American Physical Society},
  series       = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)2001-01-01+01:002016-01-01+01:00},
  title        = {Unfolding times for proteins in a force clamp},
  url          = {http://dx.doi.org/10.1103/PhysRevE.81.010902},
  volume       = {81},
  year         = {2010},
}