Stretching of single poly-ubiquitin molecules revisited: dynamic disorder in the non-exponential unfolding kinetics.
A theoretical framework based on a generalized Langevin equation (GLE) with fractional Gaussian noise (fGn) and a power-law memory kernel is presented to describe the non-exponential kinetics of the unfolding of a single poly-ubiquitin molecule under a constant force [T.-L. Kuo, S. Garcia-Manyes, J. Li, I. Barel, H. Lu, B. J. Berne, M. Urbakh, J. Klafter, and J. M. Fernández, Proc. Natl. Acad. Sci. U.S.A. 107, 11336 (2010)]. Such a GLE-fGn strategy is made on the basis that the pulling coordinate variable x undergoes subdiffusion, usually resulting from conformational fluctuations, over a one-dimensional force-modified free-energy surface U(x, F). By using the Kramers' rate theory, we have obtained analytical formulae for the time-dependent rate coefficient k(t, F), the survival probability S(t, F) as well as the waiting time distribution function f(t, F) as functions of time t and force F. We find that our results can fit the experimental data of f(t, F) perfectly in the whole time range with a power-law exponent γ = 1/2, the characteristic of typical anomalous subdiffusion. In addition, the fitting of the survival probabilities for different forces facilitates us to reach rather reasonable estimations for intrinsic properties of the system, such as the free-energy barrier and the distance between the native conformation and the transition state conformation along the reaction coordinate, which are in good agreements with molecular dynamics simulations in the literatures. Although static disorder has been implicated in the original work of Kuo et al., our work suggests a sound and plausible alternative interpretation for the non-exponential kinetics in the stretching of poly-ubiquitin molecules, associated with dynamic disorder.
College of Chemistry, Sichuan University, Chengdu 610064, China.
Yue
Y
Zheng
Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, China.
Yukun
Y
Bian
College of Chemistry, Sichuan University, Chengdu 610064, China.
Nanrong
N
Zhao
Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China.
Zhonghuai
Z
Hou
D007700:Kinetics; D056004:Molecular Dynamics Simulation; D025821:Polyubiquitin / Q000737:chemistry*; D058767:Protein Unfolding
D025821:Polyubiquitin