Literature DB >> 22908254

Weak temporal signals can synchronize and accelerate the transition dynamics of biopolymers under tension.

Won Kyu Kim1, Changbong Hyeon, Wokyung Sung.   

Abstract

In addition to thermal noise, which is essential to promote conformational transitions in biopolymers, the cellular environment is replete with a spectrum of athermal fluctuations that are produced from a plethora of active processes. To understand the effect of athermal noise on biological processes, we studied how a small oscillatory force affects the thermally induced folding and unfolding transition of an RNA hairpin, whose response to constant tension had been investigated extensively in both theory and experiments. Strikingly, our molecular simulations performed under overdamped condition show that even at a high (low) tension that renders the hairpin (un)folding improbable, a weak external oscillatory force at a certain frequency can synchronously enhance the transition dynamics of RNA hairpin and increase the mean transition rate. Furthermore, the RNA dynamics can still discriminate a signal with resonance frequency even when the signal is mixed among other signals with nonresonant frequencies. In fact, our computational demonstration of thermally induced resonance in RNA hairpin dynamics is a direct realization of the phenomena called stochastic resonance and resonant activation. Our study, amenable to experimental tests using optical tweezers, is of great significance to the folding of biopolymers in vivo that are subject to the broad spectrum of cellular noises.

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Year:  2012        PMID: 22908254      PMCID: PMC3437832          DOI: 10.1073/pnas.1202952109

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  35 in total

1.  Reversible unfolding of single RNA molecules by mechanical force.

Authors:  J Liphardt; B Onoa; S B Smith; I Tinoco; C Bustamante
Journal:  Science       Date:  2001-04-27       Impact factor: 47.728

2.  Single kinesin molecules studied with a molecular force clamp.

Authors:  K Visscher; M J Schnitzer; S M Block
Journal:  Nature       Date:  1999-07-08       Impact factor: 49.962

3.  The complex folding network of single calmodulin molecules.

Authors:  Johannes Stigler; Fabian Ziegler; Anja Gieseke; J Christof M Gebhardt; Matthias Rief
Journal:  Science       Date:  2011-10-28       Impact factor: 47.728

4.  Resonant activation in polymer translocation: new insights into the escape dynamics of molecules driven by an oscillating field.

Authors:  N Pizzolato; A Fiasconaro; D Persano Adorno; B Spagnolo
Journal:  Phys Biol       Date:  2010-08-04       Impact factor: 2.583

5.  Intrinsic rates and activation free energies from single-molecule pulling experiments.

Authors:  Olga K Dudko; Gerhard Hummer; Attila Szabo
Journal:  Phys Rev Lett       Date:  2006-03-15       Impact factor: 9.161

6.  Dynamics of allosteric transitions in GroEL.

Authors:  Changbong Hyeon; George H Lorimer; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2006-11-29       Impact factor: 11.205

7.  Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins.

Authors:  Changbong Hyeon; Ruxandra I Dima; D Thirumalai
Journal:  Structure       Date:  2006-11       Impact factor: 5.006

8.  Mechanical control of the directional stepping dynamics of the kinesin motor.

Authors:  Changbong Hyeon; José N Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-24       Impact factor: 11.205

9.  Single-molecule experiments in biological physics: methods and applications.

Authors:  F Ritort
Journal:  J Phys Condens Matter       Date:  2006-07-25       Impact factor: 2.333

Review 10.  Models for the specific adhesion of cells to cells.

Authors:  G I Bell
Journal:  Science       Date:  1978-05-12       Impact factor: 47.728

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  4 in total

1.  Thermal and inertial resonances in DNA unzipping.

Authors:  A E Bergues-Pupo; J M Bergues; F Falo; A Fiasconaro
Journal:  Eur Phys J E Soft Matter       Date:  2015-05-22       Impact factor: 1.890

2.  Stochastic resonance during a polymer translocation process.

Authors:  Debasish Mondal; M Muthukumar
Journal:  J Chem Phys       Date:  2016-04-14       Impact factor: 3.488

3.  Talin folding as the tuning fork of cellular mechanotransduction.

Authors:  Rafael Tapia-Rojo; Álvaro Alonso-Caballero; Julio M Fernández
Journal:  Proc Natl Acad Sci U S A       Date:  2020-08-17       Impact factor: 11.205

Review 4.  T-cell Receptor Is a Threshold Detector: Sub- and Supra-Threshold Stochastic Resonance in TCR-MHC Clusters on the Cell Surface.

Authors:  László Bene; Miklós Bagdány; László Damjanovich
Journal:  Entropy (Basel)       Date:  2022-03-10       Impact factor: 2.524

  4 in total

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