Refolding dynamics of stretched biopolymers upon force quench.

Proceedings of the National Academy of Sciences of the United States of America
Changbong HyeonD Thirumalai

Abstract

Single-molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse of RNA and proteins upon force quench by using simulations of an RNA hairpin and theory based on the de Gennes model for homopolymer collapse. The folding time, tau(F), depends asymmetrically on deltaf(S) = f (S) - f (m) and deltaf (Q) = f (m) - f (Q) where f (S) (f (Q)) is the stretch (quench) force and f (m) is the transition midforce of the RNA hairpin. In accord with experiments, the relaxation kinetics of the molecular extension, R(t), occurs in three stages: A rapid initial decrease in the extension is followed by a plateau and finally, an abrupt reduction in R(t) occurs as the native state is approached. The duration of the plateau increases as lambda = tau (Q)/tau (F) decreases (where tau (Q) is the time in which the force is reduced from f (S) to f (Q)). Variations in the mechanisms of force-quench relaxation as lambda is altered are reflected in the experimentally measurable time-dependent entropy, which is computed directly from the folding trajectories. An analytical solution of ...Continue Reading

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Citations

Sep 29, 2011·Nature Communications·Changbong Hyeon, D Thirumalai
Apr 13, 2011·Proceedings of the National Academy of Sciences of the United States of America·Fei XiaFrauke Gräter
Aug 22, 2012·Proceedings of the National Academy of Sciences of the United States of America·Won Kyu KimWokyung Sung
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