eprintid: 1820
rev_number: 6
eprint_status: archive
userid: 6
dir: disk0/00/00/18/20
datestamp: 2013-10-04 09:56:41
lastmod: 2013-11-21 12:19:10
status_changed: 2013-10-04 09:56:41
type: article
metadata_visibility: show
creators_name: Hyeon, Changbong
creators_name: Morrison, Greg
creators_name: Pincus, David L.
creators_name: Thirumalai, D.
creators_id: 
creators_id: greg.morrison@imtlucca.it
creators_id: 
creators_id: 
title: Refolding dynamics of stretched biopolymers upon force quench
ispublished: pub
subjects: QC
divisions: EIC
full_text_status: none
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, τF, depends asymmetrically on δfS = f S − f m and δf 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 λ = τ Q/τ F decreases (where τ 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 λ is altered are reflected in the experimentally measurable time-dependent entropy, which is computed directly from the folding trajectories. An analytical solution of the de Gennes model under tension reproduces the multistage stage kinetics in R(t). The prediction that the initial stages of collapse should also be a generic feature of polymers is validated by simulation of the kinetics of toroid (globule) formation in semiflexible (flexible) homopolymers in poor solvents upon quenching the force from a fully stretched state. Our findings give a unified explanation for multiple disparate experimental observations of protein folding.
date: 2009-12
date_type: published
publication: Proceedings of the National Academy of Sciences
volume: 106
number: 48
publisher: National Academy of Sciences
pagerange: 20288-20293
id_number: 10.1073/pnas.0905764106 
refereed: TRUE
issn: 1091-6490
official_url: http://www.pnas.org/content/106/48/20288.abstract
related_url_url: http://arxiv.org/abs/0911.3530
citation:   Hyeon, Changbong and Morrison, Greg and Pincus, David L. and Thirumalai, D.  Refolding dynamics of stretched biopolymers upon force quench.  Proceedings of the National Academy of Sciences, 106 (48).  pp. 20288-20293.  ISSN 1091-6490      (2009)