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)-Gō model and the Langevin dynamics. It is shown that the refolding decouples the collapse and folding kinetics. The force-quench refolding-times scale as tau(F) approximately exp(f(q)Deltax(F)/k(B)T), where f(q) is the quench force and Deltax(F) approximately 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 Deltax(F) approximately 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 Deltax(UF) approximately 0.24 nm, which is in reasonable agreement with the experimental data.
Li
Mai Suan
MS
Institute of Physics, Polish Academy of Sciences, Warsaw, Poland. masli@ifpan.edu.pl
Kouza
Maksim
M
Hu
Chin-Kun
CK
D003198:Computer Simulation; D004548:Elasticity; D019563:Mechanics; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D013314:Stress, Mechanical; D013696:Temperature; D025801:Ubiquitin / Q000737:chemistry* / Q000648:ultrastructure*
D025801:Ubiquitin