Protein folding kinetics under force from molecular simulation.
Despite a large number of studies on the mechanical unfolding of proteins, there are still relatively few successful attempts to refold proteins in the presence of a stretching force. We explore refolding kinetics under force using simulations of a coarse-grained model of ubiquitin. The effects of force on the folding kinetics can be fitted by a one-dimensional Kramers theory of diffusive barrier crossing, resulting in physically meaningful parameters for the height and location of the folding activation barrier. By comparing parameters obtained from pulling in different directions, we find that the unfolded state plays a dominant role in the refolding kinetics. Our findings explain why refolding becomes very slow at even moderate pulling forces and suggest how it could be practically observed in experiments at higher forces.
Best
Robert B
RB
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
Hummer
Gerhard
G
D003198:Computer Simulation; D007700:Kinetics; D008956:Models, Chemical; D017510:Protein Folding; D013314:Stress, Mechanical; D025801:Ubiquitin / Q000737:chemistry*
D025801:Ubiquitin