The role of binding site on the mechanical unfolding mechanism of ubiquitin.
We apply novel atomistic simulations based on potential energy surface exploration to investigate the constant force-induced unfolding of ubiquitin. At the experimentally-studied force clamping level of 100 pN, we find a new unfolding mechanism starting with the detachment between β5 and β3 involving the binding site of ubiquitin, the Ile44 residue. This new unfolding pathway leads to the discovery of new intermediate configurations, which correspond to the end-to-end extensions previously seen experimentally. More importantly, it demonstrates the novel finding that the binding site of ubiquitin can be responsible not only for its biological functions, but also its unfolding dynamics. We also report in contrast to previous single molecule constant force experiments that when the clamping force becomes smaller than about 300 pN, the number of intermediate configurations increases dramatically, where almost all unfolding events at 100 pN involve an intermediate configuration. By directly calculating the life times of the intermediate configurations from the height of the barriers that were crossed on the potential energy surface, we demonstrate that these intermediate states were likely not observed experimentally due to their lifetimes typically being about two orders of magnitude smaller than the experimental temporal resolution.
Department of Mechanical Engineering, Boston University, Boston, MA 02215.
Penghui
P
Cao
1] Department of Mechanical Engineering, Boston University, Boston, MA 02215 [2] Department of Mechanical Engineering, Korea University, Seoul 136-701, South Korea.
Gwonchan
G
Yoon
Department of Mechanical Engineering, Boston University, Boston, MA 02215.
Weiwei
W
Tao
Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University, Suwon 440-746, South Korea.
Kilho
K
Eom
Department of Mechanical Engineering, Boston University, Boston, MA 02215.
Harold S
HS
Park
D001665:Binding Sites; D007532:Isoleucine / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D058767:Protein Unfolding; D013314:Stress, Mechanical; D025801:Ubiquitin / Q000737:chemistry* / Q000378:metabolism
D025801:Ubiquitin; D007532:Isoleucine