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Refolding upon Force Quench and Pathways of Mechanical and Thermal Unfolding of Ubiquitin

Mai Suan Li ^*, Maksim Kouza ^* and Chin-Kun Hu 

^* Institute of Physics, Polish Academy of Sciences, Warsaw, Poland; and Institute of Physics, Academia Sinica, Nankang, Taipei, Taiwan

Correspondence: Address reprint requests to Prof. Mai Suan Li, E-mail: masli{at}ifpan.edu.pl; or Prof. Chin-Kun Hu, E-mail: huck{at}phys.sinica.edu.tw.

The refolding from stretched initial conformations of ubiquitin (PDB ID: 1ubq) under the quenched force is studied using the C-G model and the Langevin dynamics. It is shown that the refolding decouples the collapse and folding kinetics. The force-quench refolding-times scale as _F exp(f_qx_F/k_BT), where f_q is the quench force and x_F 0.96 nm is the location of the average transition state along the reaction coordinate given by the end-to-end distance. This value is close to x_F 0.8 nm obtained from the force-clamp experiments. The mechanical and thermal unfolding pathways are studied and compared with the experimental and all-atom simulation results in detail. The sequencing of thermal unfolding was found to be markedly different from the mechanical one. It is found that fixing the N-terminus of ubiquitin changes its mechanical unfolding pathways much more drastically compared to the case when the C-end is anchored. We obtained the distance between the native state and the transition state x_UF 0.24 nm, which is in reasonable agreement with the experimental data.