Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin

The refolding from stretched initial conformations of ubiquitin (PDB ID: 1ubq) under the quenched force is studied using the C-alpha-G (o) over bar model and the Langevin dynamics. It is shown that the refolding decouples the collapse and folding kinetics. The force- quench refolding- times scale as tF; exp( fqDxF/kBT), where f(q) is the quench force and Delta x(F) approximate to 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 Delta x(F) approximate to 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. xing 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 Delta x(UF) approximate to 0.24 nm, which is in reasonable agreement with the experimental data.