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Thermal versus mechanical unfolding of ubiquitin
Author(s) -
Irbäck Anders,
Mitternacht Simon
Publication year - 2006
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21145
Subject(s) - thermal , monte carlo method , physics , molecular dynamics , thermal fluctuations , event (particle physics) , ubiquitin , atom (system on chip) , statistical physics , crystallography , chemistry , thermodynamics , computer science , mathematics , biochemistry , statistics , quantum mechanics , gene , embedded system
The authors studied the temperature‐induced unfolding of ubiquitin by all‐atom Monte Carlo simulations. The unfolding behavior is compared with that seen in previous simulations of the mechanical unfolding of this protein, based on the same model. In mechanical unfolding, secondary‐structure elements were found to break in a quite well‐defined order. In thermal unfolding, the authors saw somewhat larger event‐to‐event fluctuations, but the unfolding pathway was still far from random. Two long‐lived secondary‐structure elements could be identified in the simulations. These two elements have been found experimentally to be the thermally most stable ones. Interestingly, one of these long‐lived elements, the first β‐hairpin, was found to break early in the mechanical unfolding simulations. Their combined simulation results thus enable the authors to predict in detail important differences between the thermal and mechanical unfolding behaviors of ubiquitin. Proteins 2006. © 2006 Wiley‐Liss, Inc.