Literature DB >> 16248649

Knots in globule and coil phases of a model polyethylene.

Peter Virnau1, Yacov Kantor, Mehran Kardar.   

Abstract

We examine the statistics of knots with numerical simulations of a simplified model of polyethylene. We can simulate polymers of up to 1000 monomers (each representing roughly three CH(2) groups), at a range of temperatures spanning coil (good solvent) and globule (bad solvent) phases. We quantify the abundance of knots in the globule phase and in confined polymers, and their rarity in the swollen phase. Since our polymers are open, we consider (and test) various operational definitions for knots, which are rigorously defined only for closed chains. We also associate a typical size with individual knots, which are found to be small (tight and localized) in the swollen phase but large (loose and spread out) in the dense phases.

Entities:  

Year:  2005        PMID: 16248649     DOI: 10.1021/ja052438a

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  29 in total

1.  The fractal globule as a model of chromatin architecture in the cell.

Authors:  Leonid A Mirny
Journal:  Chromosome Res       Date:  2011-01       Impact factor: 5.239

2.  Knot formation in newly translated proteins is spontaneous and accelerated by chaperonins.

Authors:  Anna L Mallam; Sophie E Jackson
Journal:  Nat Chem Biol       Date:  2011-12-18       Impact factor: 15.040

3.  Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot.

Authors:  Wenfei Li; Tsuyoshi Terakawa; Wei Wang; Shoji Takada
Journal:  Proc Natl Acad Sci U S A       Date:  2012-07-02       Impact factor: 11.205

4.  Slipknotting upon native-like loop formation in a trefoil knot protein.

Authors:  Jeffrey K Noel; Joanna I Sułkowska; José N Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  2010-08-11       Impact factor: 11.205

5.  Experimental detection of knotted conformations in denatured proteins.

Authors:  Anna L Mallam; Joseph M Rogers; Sophie E Jackson
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-14       Impact factor: 11.205

6.  The folding mechanics of a knotted protein.

Authors:  Stefan Wallin; Konstantin B Zeldovich; Eugene I Shakhnovich
Journal:  J Mol Biol       Date:  2007-02-22       Impact factor: 5.469

7.  Tightening the knot in phytochrome by single-molecule atomic force microscopy.

Authors:  Thomas Bornschlögl; David M Anstrom; Elisabeth Mey; Joachim Dzubiella; Matthias Rief; Katrina T Forest
Journal:  Biophys J       Date:  2009-02-18       Impact factor: 4.033

8.  Dodging the crisis of folding proteins with knots.

Authors:  Joanna I Sułkowska; Piotr Sułkowski; José Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  2009-02-11       Impact factor: 11.205

9.  Exploring knotting mechanisms in protein folding.

Authors:  Anna L Mallam; Elizabeth R Morris; Sophie E Jackson
Journal:  Proc Natl Acad Sci U S A       Date:  2008-11-17       Impact factor: 11.205

10.  KnotGenome: a server to analyze entanglements of chromosomes.

Authors:  Joanna I Sulkowska; Szymon Niewieczerzal; Aleksandra I Jarmolinska; Jonathan T Siebert; Peter Virnau; Wanda Niemyska
Journal:  Nucleic Acids Res       Date:  2018-07-02       Impact factor: 16.971

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