Literature DB >> 24745458

Evidence of disorder in biological molecules from single molecule pulling experiments.

Changbong Hyeon1, Michael Hinczewski2, D Thirumalai2.   

Abstract

Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an exactly solvable model in which the unfolding rate due to mechanical force depends parametrically on an auxiliary variable representing an entropy barrier arising from fluctuations in internal dynamics. When the rate of fluctuations--a measure of dynamical disorder--is comparable to or smaller than the rate of force-induced unbinding, we show that there are two experimentally observable consequences: nonexponential survival probability at constant force, and a heavy-tailed rupture force distribution at constant loading rate. By fitting our analytical expressions to data from single molecule pulling experiments on proteins and DNA, we quantify the extent of disorder. We show that only by analyzing data over a wide range of forces and loading rates can the role of disorder due to internal dynamics be quantitatively assessed.

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Year:  2014        PMID: 24745458      PMCID: PMC5580271          DOI: 10.1103/PhysRevLett.112.138101

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  25 in total

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Authors:  T Strunz; K Oroszlan; R Schäfer; H J Güntherodt
Journal:  Proc Natl Acad Sci U S A       Date:  1999-09-28       Impact factor: 11.205

Review 2.  Probing the relation between force--lifetime--and chemistry in single molecular bonds.

Authors:  E Evans
Journal:  Annu Rev Biophys Biomol Struct       Date:  2001

3.  Nonkinetic modeling of the mechanical unfolding of multimodular proteins: theory and experiments.

Authors:  F Benedetti; C Micheletti; G Bussi; S K Sekatskii; G Dietler
Journal:  Biophys J       Date:  2011-09-20       Impact factor: 4.033

4.  Temperature softening of a protein in single-molecule experiments.

Authors:  Michael Schlierf; Matthias Rief
Journal:  J Mol Biol       Date:  2005-10-10       Impact factor: 5.469

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.  Force-clamp analysis techniques give highest rank to stretched exponential unfolding kinetics in ubiquitin.

Authors:  Herbert Lannon; Eric Vanden-Eijnden; J Brujic
Journal:  Biophys J       Date:  2012-11-20       Impact factor: 4.033

7.  Perspective: The glass transition.

Authors:  Giulio Biroli; Juan P Garrahan
Journal:  J Chem Phys       Date:  2013-03-28       Impact factor: 3.488

8.  Single-molecule enzymatic dynamics.

Authors:  H P Lu; L Xun; X S Xie
Journal:  Science       Date:  1998-12-04       Impact factor: 47.728

9.  Cell-to-cell heterogeneity in lipid droplets suggests a mechanism to reduce lipotoxicity.

Authors:  Albert Herms; Marta Bosch; Nicholas Ariotti; Babu J N Reddy; Alba Fajardo; Andrea Fernández-Vidal; Anna Alvarez-Guaita; Manuel Alejandro Fernández-Rojo; Carles Rentero; Francesc Tebar; Carlos Enrich; María-Isabel Geli; Robert G Parton; Steven P Gross; Albert Pol
Journal:  Curr Biol       Date:  2013-07-18       Impact factor: 10.834

10.  DNA unwinding heterogeneity by RecBCD results from static molecules able to equilibrate.

Authors:  Bian Liu; Ronald J Baskin; Stephen C Kowalczykowski
Journal:  Nature       Date:  2013-07-14       Impact factor: 49.962

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  9 in total

1.  Molecular investigations into the mechanics of a muscle anchoring complex.

Authors:  Nicholas K Bodmer; Kelly E Theisen; Ruxandra I Dima
Journal:  Biophys J       Date:  2015-05-05       Impact factor: 4.033

2.  Cation-induced kinetic heterogeneity of the intron-exon recognition in single group II introns.

Authors:  Danny Kowerko; Sebastian L B König; Miriam Skilandat; Daniela Kruschel; Mélodie C A S Hadzic; Lucia Cardo; Roland K O Sigel
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-03       Impact factor: 11.205

3.  Regulatory element in fibrin triggers tension-activated transition from catch to slip bonds.

Authors:  Rustem I Litvinov; Olga Kononova; Artem Zhmurov; Kenneth A Marx; Valeri Barsegov; D Thirumalai; John W Weisel
Journal:  Proc Natl Acad Sci U S A       Date:  2018-08-07       Impact factor: 11.205

4.  Contact Statistics Highlight Distinct Organizing Principles of Proteins and RNA.

Authors:  Lei Liu; Changbong Hyeon
Journal:  Biophys J       Date:  2016-06-07       Impact factor: 4.033

5.  Directly measuring single-molecule heterogeneity using force spectroscopy.

Authors:  Michael Hinczewski; Changbong Hyeon; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2016-06-17       Impact factor: 11.205

6.  Decoding Single Molecule Time Traces with Dynamic Disorder.

Authors:  Wonseok Hwang; Il-Buem Lee; Seok-Cheol Hong; Changbong Hyeon
Journal:  PLoS Comput Biol       Date:  2016-12-27       Impact factor: 4.475

7.  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

8.  Mechanical Unfolding of Single Polyubiquitin Molecules Reveals Evidence of Dynamic Disorder.

Authors:  Prasanta Kundu; Soma Saha; Gautam Gangopadhyay
Journal:  ACS Omega       Date:  2020-04-15

9.  Dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis.

Authors:  Wonseok Hwang; Jungmin Yoo; Yuno Lee; Suyeon Park; Phuong Lien Hoang; HyeokJin Cho; Jeongmin Yu; Thi Minh Hoa Vo; Minsang Shin; Mi Sun Jin; Daeho Park; Changbong Hyeon; Gwangrog Lee
Journal:  Nat Commun       Date:  2018-10-23       Impact factor: 14.919

  9 in total

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