Hopping around an entropic barrier created by force.
We use Langevin dynamics to investigate the role played by the recently discovered force-induced entropic energy barrier on the two-state hopping phenomena that has been observed in single RNA, DNA and protein molecules placed under a stretching force. Simple considerations about the free energy of a molecule readily show that the application of force introduces an entropic barrier separating the collapsed state of the molecule, from a force-driven extended conformation. A notable characteristic of the force induced barrier is its long distances to transition state, up to tens of nanometers, which renders the kinetics of crossing this barrier highly sensitive to an applied force. Langevin dynamics across such force induced barriers readily demonstrates the hopping behavior observed for a variety of single molecules placed under force. Such hopping is frequently interpreted as a manifestation of two-state folding/unfolding reactions observed in bulk experiments. However, given that such barriers do not exist at zero force these reactions do not take place at all in bulk.
Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
Ronen
R
Berkovich
Sergi
S
Garcia-Manyes
Joseph
J
Klafter
Michael
M
Urbakh
Julio M
JM
Fernández
D004247:DNA / Q000737:chemistry*; D019277:Entropy; D018625:Microscopy, Atomic Force; D008956:Models, Chemical; D011506:Proteins / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*
D011506:Proteins; D012313:RNA; D004247:DNA