Literature DB >> 24209869

Kinetics and energetics of biomolecular folding and binding.

Christopher A Pierse1, Olga K Dudko.   

Abstract

The ability of biomolecules to fold and to bind to other molecules is fundamental to virtually every living process. Advanced experimental techniques can now reveal how single biomolecules fold or bind against mechanical force, with the force serving as both the regulator and the probe of folding and binding transitions. Here, we present analytical expressions suitable for fitting the major experimental outputs from such experiments to enable their analysis and interpretation. The fit yields the key determinants of the folding and binding processes: the intrinsic on-rate and the location and height of the activation barrier.
Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Mesh:

Year:  2013        PMID: 24209869      PMCID: PMC3824551          DOI: 10.1016/j.bpj.2013.09.023

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  7 in total

Review 1.  Mechanical processes in biochemistry.

Authors:  Carlos Bustamante; Yann R Chemla; Nancy R Forde; David Izhaky
Journal:  Annu Rev Biochem       Date:  2004       Impact factor: 23.643

2.  A mechanically stabilized receptor-ligand flex-bond important in the vasculature.

Authors:  Jongseong Kim; Cheng-Zhong Zhang; Xiaohui Zhang; Timothy A Springer
Journal:  Nature       Date:  2010-08-19       Impact factor: 49.962

3.  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

4.  Protein folding kinetics under force from molecular simulation.

Authors:  Robert B Best; Gerhard Hummer
Journal:  J Am Chem Soc       Date:  2008-02-29       Impact factor: 15.419

5.  Exploring hysteresis and energy dissipation in single-molecule force spectroscopy.

Authors:  Zion Tshiprut; Michael Urbakh
Journal:  J Chem Phys       Date:  2009-02-28       Impact factor: 3.488

6.  Full distance-resolved folding energy landscape of one single protein molecule.

Authors:  J Christof M Gebhardt; Thomas Bornschlögl; Matthias Rief
Journal:  Proc Natl Acad Sci U S A       Date:  2010-01-19       Impact factor: 11.205

7.  Energy landscape analysis of native folding of the prion protein yields the diffusion constant, transition path time, and rates.

Authors:  Hao Yu; Amar Nath Gupta; Xia Liu; Krishna Neupane; Angela M Brigley; Iveta Sosova; Michael T Woodside
Journal:  Proc Natl Acad Sci U S A       Date:  2012-08-20       Impact factor: 11.205

  7 in total
  13 in total

1.  On artifacts in single-molecule force spectroscopy.

Authors:  Pilar Cossio; Gerhard Hummer; Attila Szabo
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-04       Impact factor: 11.205

2.  Folding and binding: when the force is against you.

Authors:  Robert B Best
Journal:  Biophys J       Date:  2013-12-17       Impact factor: 4.033

3.  Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape.

Authors:  Hao Yu; Derek R Dee; Xia Liu; Angela M Brigley; Iveta Sosova; Michael T Woodside
Journal:  Proc Natl Acad Sci U S A       Date:  2015-06-24       Impact factor: 11.205

4.  Mechanical heterogeneity favors fragmentation of strained actin filaments.

Authors:  Enrique M De La Cruz; Jean-Louis Martiel; Laurent Blanchoin
Journal:  Biophys J       Date:  2015-05-05       Impact factor: 4.033

5.  Force-Regulated Refolding of the Mechanosensory Domain in the Platelet Glycoprotein Ib-IX Complex.

Authors:  X Frank Zhang; Wei Zhang; M Edward Quach; Wei Deng; Renhao Li
Journal:  Biophys J       Date:  2019-04-08       Impact factor: 4.033

6.  Force-induced on-rate switching and modulation by mutations in gain-of-function von Willebrand diseases.

Authors:  Jongseong Kim; Nathan E Hudson; Timothy A Springer
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-25       Impact factor: 11.205

7.  Measurement of the specific and non-specific binding energies of Mg2+ to RNA.

Authors:  A Martinez-Monge; Isabel Pastor; Carlos Bustamante; Maria Manosas; Felix Ritort
Journal:  Biophys J       Date:  2022-07-21       Impact factor: 3.699

8.  Conformational dynamics of the frameshift stimulatory structure in HIV-1.

Authors:  Dustin B Ritchie; Tonia R Cappellano; Collin Tittle; Negar Rezajooei; Logan Rouleau; William K A Sikkema; Michael T Woodside
Journal:  RNA       Date:  2017-05-18       Impact factor: 4.942

9.  The energy cost of polypeptide knot formation and its folding consequences.

Authors:  Andrés Bustamante; Juan Sotelo-Campos; Daniel G Guerra; Martin Floor; Christian A M Wilson; Carlos Bustamante; Mauricio Báez
Journal:  Nat Commun       Date:  2017-11-17       Impact factor: 14.919

10.  Comparison of human and mouse E-selectin binding to Sialyl-Lewis(x).

Authors:  Anne D Rocheleau; Thong M Cao; Tait Takitani; Michael R King
Journal:  BMC Struct Biol       Date:  2016-07-02
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