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Dissecting the mechanical unfolding of ubiquitin

Irbäck, Anders LU ; Mitternacht, Simon LU and Mohanty, Sandipan LU (2005) In Proceedings of the National Academy of Sciences 102(38). p.13427-13432
Abstract
The unfolding behavior of ubiquitin under the influence of a stretching force recently was investigated experimentally by single-molecule constant-force methods. Many observed unfolding traces had a simple two-state character, whereas others showed clear evidence of intermediate states. Here, we use Monte Carlo simulations to investigate the force-induced unfolding of ubiquitin at the atomic level. In agreement with experimental data, we find that the unfolding process can occur either in a single step or through intermediate states. In addition to this randomness, we find that many quantities, such as the frequency of occurrence of intermediates, show a clear systematic dependence on the strength of the applied force. Despite this... (More)
The unfolding behavior of ubiquitin under the influence of a stretching force recently was investigated experimentally by single-molecule constant-force methods. Many observed unfolding traces had a simple two-state character, whereas others showed clear evidence of intermediate states. Here, we use Monte Carlo simulations to investigate the force-induced unfolding of ubiquitin at the atomic level. In agreement with experimental data, we find that the unfolding process can occur either in a single step or through intermediate states. In addition to this randomness, we find that many quantities, such as the frequency of occurrence of intermediates, show a clear systematic dependence on the strength of the applied force. Despite this diversity, one common feature can be identified in the simulated unfolding events, which is the order in which the secondary-structure elements break. This order is the same in two and three-state events and at the different forces studied. The observed order remains to be verified experimentally but appears physically reasonable. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Monte Carlo simulation, all-atom model, force-induced unfolding
in
Proceedings of the National Academy of Sciences
volume
102
issue
38
pages
13427 - 13432
publisher
National Acad Sciences
external identifiers
  • wos:000232115100015
  • scopus:26444577856
ISSN
1091-6490
DOI
10.1073/pnas.0501581102
language
English
LU publication?
yes
id
8fb6382e-759e-44fc-bd67-0c6f3a941383 (old id 222472)
date added to LUP
2007-08-08 15:47:21
date last changed
2017-09-24 03:27:40
@article{8fb6382e-759e-44fc-bd67-0c6f3a941383,
  abstract     = {The unfolding behavior of ubiquitin under the influence of a stretching force recently was investigated experimentally by single-molecule constant-force methods. Many observed unfolding traces had a simple two-state character, whereas others showed clear evidence of intermediate states. Here, we use Monte Carlo simulations to investigate the force-induced unfolding of ubiquitin at the atomic level. In agreement with experimental data, we find that the unfolding process can occur either in a single step or through intermediate states. In addition to this randomness, we find that many quantities, such as the frequency of occurrence of intermediates, show a clear systematic dependence on the strength of the applied force. Despite this diversity, one common feature can be identified in the simulated unfolding events, which is the order in which the secondary-structure elements break. This order is the same in two and three-state events and at the different forces studied. The observed order remains to be verified experimentally but appears physically reasonable.},
  author       = {Irbäck, Anders and Mitternacht, Simon and Mohanty, Sandipan},
  issn         = {1091-6490},
  keyword      = {Monte Carlo simulation,all-atom model,force-induced unfolding},
  language     = {eng},
  number       = {38},
  pages        = {13427--13432},
  publisher    = {National Acad Sciences},
  series       = {Proceedings of the National Academy of Sciences},
  title        = {Dissecting the mechanical unfolding of ubiquitin},
  url          = {http://dx.doi.org/10.1073/pnas.0501581102},
  volume       = {102},
  year         = {2005},
}