Literature DB >> 29225374

Theory of Biopolymer Stretching at High Forces.

Ngo Minh Toan1, D Thirumalai1,2.   

Abstract

We provide a unified theory for the high force entropic elasticity of biopolymers solely in terms of the persistence length, ξp , and the monomer spacing, a. When the force f>ℱ h ~ kBTξp /a2 the biopolymers behave as freely jointed chains (FJCs) while in the range ℱ l ~ kBT/ξp <f<ℱ h the worm-like chain (WLC) is a better model. We show that ξp can be estimated from the force extension curve (FEC) at the extension x ≈ 1/2 (normalized by the contour length of the biopolymer). After validating the theory using simulations, we provide a quantitative analysis of the FECs for a diverse set of biopolymers (dsDNA, ssRNA, ssDNA, polysaccharides, and unstructured PEVK domain of titin) for x ≥ 1/2. The success of a specific polymer model (FJC or WLC) to describe the FEC of a given biopolymer is naturally explained by the theory. Only by probing the response of biopolymers over a wide range of forces can the f-dependent elasticity be fully described.

Entities:  

Year:  2010        PMID: 29225374      PMCID: PMC5722244          DOI: 10.1021/ma902008y

Source DB:  PubMed          Journal:  Macromolecules        ISSN: 0024-9297            Impact factor:   5.985


  32 in total

1.  PEVK domain of titin: an entropic spring with actin-binding properties.

Authors:  Wolfgang A Linke; Michael Kulke; Hongbin Li; Setsuko Fujita-Becker; Ciprian Neagoe; Dietmar J Manstein; Mathias Gautel; Julio M Fernandez
Journal:  J Struct Biol       Date:  2002 Jan-Feb       Impact factor: 2.867

2.  Reverse engineering of the giant muscle protein titin.

Authors:  Hongbin Li; Wolfgang A Linke; Andres F Oberhauser; Mariano Carrion-Vazquez; Jason G Kerkvliet; Hui Lu; Piotr E Marszalek; Julio M Fernandez
Journal:  Nature       Date:  2002-08-29       Impact factor: 49.962

3.  Theory of high-force DNA stretching and overstretching.

Authors:  C Storm; P C Nelson
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2003-05-09

4.  Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads.

Authors:  S B Smith; L Finzi; C Bustamante
Journal:  Science       Date:  1992-11-13       Impact factor: 47.728

5.  Elastic properties of a single-stranded charged homopolymeric ribonucleotide.

Authors:  Yeonee Seol; Gary M Skinner; Koen Visscher
Journal:  Phys Rev Lett       Date:  2004-09-10       Impact factor: 9.161

6.  Persistence length changes dramatically as RNA folds.

Authors:  G Caliskan; C Hyeon; U Perez-Salas; R M Briber; S A Woodson; D Thirumalai
Journal:  Phys Rev Lett       Date:  2005-12-29       Impact factor: 9.161

7.  Pulling self-interacting polymers in two dimensions.

Authors:  J Krawczyk; I Jensen; A L Owczarek; S Kumar
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-03-23

8.  Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules.

Authors:  S B Smith; Y Cui; C Bustamante
Journal:  Science       Date:  1996-02-09       Impact factor: 47.728

9.  Polysaccharide elasticity governed by chair-boat transitions of the glucopyranose ring.

Authors:  P E Marszalek; A F Oberhauser; Y P Pang; J M Fernandez
Journal:  Nature       Date:  1998-12-17       Impact factor: 49.962

10.  Stretching of homopolymeric RNA reveals single-stranded helices and base-stacking.

Authors:  Yeonee Seol; Gary M Skinner; Koen Visscher; Arnaud Buhot; Avraham Halperin
Journal:  Phys Rev Lett       Date:  2007-04-12       Impact factor: 9.161

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  3 in total

1.  On the origin of the unusual behavior in the stretching of single-stranded DNA.

Authors:  Ngo Minh Toan; D Thirumalai
Journal:  J Chem Phys       Date:  2012-06-21       Impact factor: 3.488

2.  Mechanochemistry in Translation.

Authors:  Sarah E Leininger; Karthik Narayan; Carol Deutsch; Edward P O'Brien
Journal:  Biochemistry       Date:  2019-06-11       Impact factor: 3.162

3.  Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis.

Authors:  Benjamin Fritch; Andrey Kosolapov; Phillip Hudson; Daniel A Nissley; H Lee Woodcock; Carol Deutsch; Edward P O'Brien
Journal:  J Am Chem Soc       Date:  2018-04-06       Impact factor: 15.419

  3 in total

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