(Q38699004)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22004754%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

title

Dissecting DNA-histone interactions in the nucleosome by molecular dynamics simulations of DNA unwrapping (English)

1 reference

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14 January 2020

4

1 reference

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14 January 2020

Karsten Rippe

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22004754%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

author name string

Ramona Ettig

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22004754%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

Nick Kepper

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22004754%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

Rene Stehr

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22004754%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

language of work or name

English

0 references

publication date

1 October 2011

1 reference

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14 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22004754%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

volume

101

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22004754%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

issue

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22004754%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

page(s)

1999-2008

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22004754%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

14 January 2020

molecular dynamics simulation

1 reference

Histone H2A C-terminus regulates chromatin dynamics, remodeling, and histone H1 binding

inferred from title

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Mechanisms of ATP-dependent nucleosome sliding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Histones: annotating chromatin

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Mechanical signaling on the single protein level studied using steered molecular dynamics.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

spFRET using alternating excitation and FCS reveals progressive DNA unwrapping in nucleosomes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Geometry of the nucleosomal DNA superhelix

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Single-molecule experiments in vitro and in silico

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Effect of force on mononucleosomal dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Physical methods used to study core histone tail structures and interactions in solution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

A computational study of nucleosomal DNA flexibility

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Scalable molecular dynamics with NAMD

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

X-ray structure of a tetranucleosome and its implications for the chromatin fibre

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Fast, long-range, reversible conformational fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Single chromatin fiber stretching reveals physically distinct populations of disassembly events

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Rapid spontaneous accessibility of nucleosomal DNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

HP1 and the dynamics of heterochromatin maintenance

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Use of optical trapping techniques to study single-nucleosome dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Bromodomain: an acetyl-lysine binding domain

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Crystal structure of the nucleosome core particle at 2.8 A resolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Reconstructing potential energy functions from simulated force-induced unbinding processes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

The H3-H4 N-terminal tail domains are the primary mediators of transcription factor IIIA access to 5S DNA within a nucleosome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Mechanically induced titin kinase activation studied by force-probe molecular dynamics simulations

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Force spectroscopy of chromatin fibers: extracting energetics and structural information from Monte Carlo simulations

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

A lattice model for transcription factor access to nucleosomal DNA.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Stability of histone modifications across mammalian genomes: implications for 'epigenetic' marking

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

High-resolution dynamic mapping of histone-DNA interactions in a nucleosome

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Protein-protein interaction investigated by steered molecular dynamics: the TCR-pMHC complex

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Multiscale modeling of nucleosome dynamics

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

On the mechanism of nucleosome assembly by histone chaperone NAP1.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

A 'loop recapture' mechanism for ACF-dependent nucleosome remodeling

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

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

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Simulation of the mechanical unfolding of ubiquitin: probing different unfolding reaction coordinates by changing the pulling geometry

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

A new fluorescence resonance energy transfer approach demonstrates that the histone variant H2AZ stabilizes the histone octamer within the nucleosome

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Identifying unfolding intermediates of FN-III(10) by steered molecular dynamics

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

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

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Coarse-grained force field for the nucleosome from self-consistent multiscaling

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3192959

Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites

3 December 2018

1 reference

12 December 2020

Effects of core histone tail domains on the equilibrium constants for dynamic DNA site accessibility in nucleosomes

1 reference

12 December 2020

DNA spools under tension

1 reference

12 December 2020

Molecular dynamics simulations of a nucleosome and free DNA

1 reference

12 December 2020

H4 histone tail mediated DNA-DNA interaction and effects on DNA structure, flexibility, and counterion binding: a molecular dynamics study

1 reference

12 December 2020

10.1016/J.BPJ.2011.07.057

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22004754%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22004754%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

PubMed publication ID

22004754

1 reference