Literature DB >> 16453064

The nucleosome: a transparent, slippery, sticky and yet stable DNA-protein complex.

H Schiessel1.   

Abstract

Roughly three quarters of eucaryotic DNA are tightly wrapped onto protein cylinders organized in so-called nucleosomes. Despite this fact, the wrapped DNA cannot be inert since DNA is at the heart of many crucial life processes. We focus here on physical mechanisms that might allow nucleosomes to perform a great deal of such processes, specifically 1) on unwrapping fluctuations that give DNA-binding proteins access to the wrapped DNA portions without disrupting the nucleosome as a whole, 2) on corkscrew sliding along DNA and some implications and on 3) tail-bridging-induced attraction between nucleosomes as a means of controlling higher-order folding.

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Year:  2006        PMID: 16453064     DOI: 10.1140/epje/i2005-10049-y

Source DB:  PubMed          Journal:  Eur Phys J E Soft Matter        ISSN: 1292-8941            Impact factor:   1.890


  54 in total

1.  Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers.

Authors:  M L Bennink; S H Leuba; G H Leno; J Zlatanova; B G de Grooth; J Greve
Journal:  Nat Struct Biol       Date:  2001-07

2.  Nonmonotonic variation with salt concentration of the second virial coefficient in protein solutions.

Authors:  E Allahyarov; H Löwen; J P Hansen; A A Louis
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2003-05-16

Review 3.  Nucleosome sliding: facts and fiction.

Authors:  Peter B Becker
Journal:  EMBO J       Date:  2002-09-16       Impact factor: 11.598

4.  Rapid spontaneous accessibility of nucleosomal DNA.

Authors:  Gu Li; Marcia Levitus; Carlos Bustamante; Jonathan Widom
Journal:  Nat Struct Mol Biol       Date:  2004-12-05       Impact factor: 15.369

5.  Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes.

Authors:  Brent Brower-Toland; David A Wacker; Robert M Fulbright; John T Lis; W Lee Kraus; Michelle D Wang
Journal:  J Mol Biol       Date:  2004-12-22       Impact factor: 5.469

6.  Salt-induced conformation and interaction changes of nucleosome core particles.

Authors:  Stéphanie Mangenot; Amélie Leforestier; Patrice Vachette; Dominique Durand; Françoise Livolant
Journal:  Biophys J       Date:  2002-01       Impact factor: 4.033

Review 7.  The histone tails of the nucleosome.

Authors:  K Luger; T J Richmond
Journal:  Curr Opin Genet Dev       Date:  1998-04       Impact factor: 5.578

8.  Positioning and stability of nucleosomes on MMTV 3'LTR sequences.

Authors:  A Flaus; T J Richmond
Journal:  J Mol Biol       Date:  1998-01-23       Impact factor: 5.469

9.  Crystal structure of the nucleosome core particle at 2.8 A resolution.

Authors:  K Luger; A W Mäder; R K Richmond; D F Sargent; T J Richmond
Journal:  Nature       Date:  1997-09-18       Impact factor: 49.962

10.  Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation.

Authors:  K J Polach; J Widom
Journal:  J Mol Biol       Date:  1995-11-24       Impact factor: 5.469

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  15 in total

Review 1.  Chromatin physics: Replacing multiple, representation-centered descriptions at discrete scales by a continuous, function-dependent self-scaled model.

Authors:  C Lavelle; A Benecke
Journal:  Eur Phys J E Soft Matter       Date:  2006-02-22       Impact factor: 1.890

2.  Multiscale modeling of nucleosome dynamics.

Authors:  Shantanu Sharma; Feng Ding; Nikolay V Dokholyan
Journal:  Biophys J       Date:  2006-12-01       Impact factor: 4.033

Review 3.  Biological consequences of tightly bent DNA: the other life of a macromolecular celebrity.

Authors:  Hernan G Garcia; Paul Grayson; Lin Han; Mandar Inamdar; Jané Kondev; Philip C Nelson; Rob Phillips; Jonathan Widom; Paul A Wiggins
Journal:  Biopolymers       Date:  2007-02-05       Impact factor: 2.505

4.  The homology recognition well as an innate property of DNA structure.

Authors:  Alexei A Kornyshev; Aaron Wynveen
Journal:  Proc Natl Acad Sci U S A       Date:  2009-03-09       Impact factor: 11.205

5.  Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs.

Authors:  A Benecke
Journal:  Eur Phys J E Soft Matter       Date:  2006-03-07       Impact factor: 1.890

6.  Nucleosome dynamics as studied by single-pair fluorescence resonance energy transfer: a reevaluation.

Authors:  Miroslav Tomschik; Ken van Holde; Jordanka Zlatanova
Journal:  J Fluoresc       Date:  2008-05-15       Impact factor: 2.217

7.  The dynamics of individual nucleosomes controls the chromatin condensation pathway: direct atomic force microscopy visualization of variant chromatin.

Authors:  Fabien Montel; Hervé Menoni; Martin Castelnovo; Jan Bednar; Stefan Dimitrov; Dimitar Angelov; Cendrine Faivre-Moskalenko
Journal:  Biophys J       Date:  2009-07-22       Impact factor: 4.033

8.  Rigid-body molecular dynamics of DNA inside a nucleosome.

Authors:  Arman Fathizadeh; Azim Berdy Besya; Mohammad Reza Ejtehadi; Helmut Schiessel
Journal:  Eur Phys J E Soft Matter       Date:  2013-03-13       Impact factor: 1.890

Review 9.  Modulation of toll-like receptor signaling by antimicrobial peptides.

Authors:  Ernest Y Lee; Michelle W Lee; Gerard C L Wong
Journal:  Semin Cell Dev Biol       Date:  2018-02-12       Impact factor: 7.727

10.  Anomalously Rapid Hydration Water Diffusion Dynamics Near DNA Surfaces.

Authors:  John M Franck; Yuan Ding; Katherine Stone; Peter Z Qin; Songi Han
Journal:  J Am Chem Soc       Date:  2015-09-10       Impact factor: 15.419

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