Anders Irbäck, Simon Mitternacht and Sandipan Mohanty
Dissecting the Mechanical Unfolding of Ubiquitin
Proceedings of the National Academy of Sciences USA 102, 13427-13432 (2005)

Abstract
The unfolding behavior of ubiquitin under the influence of a stretching force was recently 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 (MC) 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 via 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.

LU TP 05-06