title: Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin.
abstract: 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.
authors.affiliation: Institute of Physics, Polish Academy of Sciences, Warsaw, Poland. masli@ifpan.edu.pl
authors.forename: Mai Suan
authors.initials: MS
authors.lastname: Li
authors.forename: Maksim
authors.initials: M
authors.lastname: Kouza
authors.forename: Chin-Kun
authors.initials: CK
authors.lastname: Hu
mesh_terms: 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*
chemical_list: D025801:Ubiquitin