Literature DB >> 22895787

Rate limit of protein elastic response is tether dependent.

Ronen Berkovich1, Rodolfo I Hermans, Ionel Popa, Guillaume Stirnemann, Sergi Garcia-Manyes, Bruce J Berne, Julio M Fernandez.   

Abstract

The elastic restoring force of tissues must be able to operate over the very wide range of loading rates experienced by living organisms. It is surprising that even the fastest events involving animal muscle tissues do not surpass a few hundred hertz. We propose that this limit is set in part by the elastic dynamics of tethered proteins extending and relaxing under a changing load. Here we study the elastic dynamics of tethered proteins using a fast force spectrometer with sub-millisecond time resolution, combined with Brownian and Molecular Dynamics simulations. We show that the act of tethering a polypeptide to an object, an inseparable part of protein elasticity in vivo and in experimental setups, greatly reduces the attempt frequency with which the protein samples its free energy. Indeed, our data shows that a tethered polypeptide can traverse its free-energy landscape with a surprisingly low effective diffusion coefficient D(eff) ~ 1,200 nm(2)/s. By contrast, our Molecular Dynamics simulations show that diffusion of an isolated protein under force occurs at D(eff) ~ 10(8) nm(2)/s. This discrepancy is attributed to the drag force caused by the tethering object. From the physiological time scales of tissue elasticity, we calculate that tethered elastic proteins equilibrate in vivo with D(eff) ~ 10(4)-10(6) nm(2)/s which is two to four orders magnitude smaller than the values measured for untethered proteins in bulk.

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Year:  2012        PMID: 22895787      PMCID: PMC3437906          DOI: 10.1073/pnas.1212167109

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


  28 in total

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Journal:  Proc Natl Acad Sci U S A       Date:  2001-08-28       Impact factor: 11.205

2.  Reverse engineering of the giant muscle protein titin.

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3.  The unfolding kinetics of ubiquitin captured with single-molecule force-clamp techniques.

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Journal:  Proc Natl Acad Sci U S A       Date:  2004-04-27       Impact factor: 11.205

4.  Locating the barrier for folding of single molecules under an external force.

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5.  Cold-blooded snipers: thermal independence of ballistic tongue projection in the salamander Hydromantes platycephalus.

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6.  Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods.

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Review 7.  Internal friction of single polypeptide chains at high stretch.

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8.  Direct quantification of the attempt frequency determining the mechanical unfolding of ubiquitin protein.

Authors:  Ionel Popa; Julio M Fernández; Sergi Garcia-Manyes
Journal:  J Biol Chem       Date:  2011-07-16       Impact factor: 5.157

9.  Muscular force in running turkeys: the economy of minimizing work.

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10.  Analyzing single-molecule manipulation experiments.

Authors:  Christopher P Calderon; Nolan C Harris; Ching-Hwa Kiang; Dennis D Cox
Journal:  J Mol Recognit       Date:  2009 Sep-Oct       Impact factor: 2.137

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  20 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.  Dynamics of equilibrium folding and unfolding transitions of titin immunoglobulin domain under constant forces.

Authors:  Hu Chen; Guohua Yuan; Ricksen S Winardhi; Mingxi Yao; Ionel Popa; Julio M Fernandez; Jie Yan
Journal:  J Am Chem Soc       Date:  2015-03-09       Impact factor: 15.419

3.  Extracting intrinsic dynamic parameters of biomolecular folding from single-molecule force spectroscopy experiments.

Authors:  Gi-Moon Nam; Dmitrii E Makarov
Journal:  Protein Sci       Date:  2015-07-14       Impact factor: 6.725

4.  Elasticity, structure, and relaxation of extended proteins under force.

Authors:  Guillaume Stirnemann; David Giganti; Julio M Fernandez; B J Berne
Journal:  Proc Natl Acad Sci U S A       Date:  2013-02-13       Impact factor: 11.205

5.  A HaloTag Anchored Ruler for Week-Long Studies of Protein Dynamics.

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Journal:  J Am Chem Soc       Date:  2016-08-09       Impact factor: 15.419

6.  How force unfolding differs from chemical denaturation.

Authors:  Guillaume Stirnemann; Seung-gu Kang; Ruhong Zhou; Bruce J Berne
Journal:  Proc Natl Acad Sci U S A       Date:  2014-02-18       Impact factor: 11.205

7.  Determining intrachain diffusion coefficients for biopolymer dynamics from single-molecule force spectroscopy measurements.

Authors:  Michael T Woodside; John Lambert; Kevin S D Beach
Journal:  Biophys J       Date:  2014-10-07       Impact factor: 4.033

Review 8.  Reconstructing folding energy landscapes by single-molecule force spectroscopy.

Authors:  Michael T Woodside; Steven M Block
Journal:  Annu Rev Biophys       Date:  2014       Impact factor: 12.981

9.  Proteins Breaking Bad: A Free Energy Perspective.

Authors:  Jessica Valle-Orero; Rafael Tapia-Rojo; Edward C Eckels; Jaime Andrés Rivas-Pardo; Ionel Popa; Julio M Fernández
Journal:  J Phys Chem Lett       Date:  2017-07-25       Impact factor: 6.475

10.  Tracking unfolding and refolding reactions of single proteins using atomic force microscopy methods.

Authors:  Paul J Bujalowski; Andres F Oberhauser
Journal:  Methods       Date:  2013-03-20       Impact factor: 3.608

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