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

Biopolymers ◽  
2007 ◽  
Vol 86 (5-6) ◽  
pp. 409-423 ◽  
Author(s):  
Nikolay Korolev ◽  
Lars Nordenskiöld
Keyword(s):  
Molecular Dynamics ◽  
Dna Structure ◽  
Dna Interaction ◽  
Histone Tail ◽  
Counterion Binding ◽  
Structure Flexibility

A molecular dynamics simulation study of polyamine? and sodium?DNA. Interplay between polyamine binding and DNA structure

2004 ◽  
Vol 33 (8) ◽  
pp. 671-682 ◽  
Author(s):  
Nikolay Korolev ◽  
Alexander P. Lyubartsev ◽  
Aatto Laaksonen ◽  
Lars Nordenski�ld
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Dna Structure ◽  
Dynamics Simulation

scholarly journals Computational Epigenetics: Molecular Dynamics Simulations of the Structure of HP1 Bound to a Variably Modified Histone Tail

2011 ◽  
Vol 100 (3) ◽  
pp. 228a
Author(s):  
George V. Papamokos ◽  
George Tziatzos ◽  
Anastasia Politou ◽  
Demetrios Papageorgiou ◽  
Spyros Georgatos ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Histone Tail ◽  
Dynamics Simulations

Molecular Dynamics Study of the Structure, Flexibility, and Hydrophilicity of PETIM Dendrimers: A Comparison with PAMAM Dendrimers

2015 ◽  
Vol 119 (41) ◽  
pp. 12990-13001 ◽  
Author(s):  
Subbarao Kanchi ◽  
Gorle Suresh ◽  
U. Deva Priyakumar ◽  
K. G. Ayappa ◽  
Prabal K Maiti
Keyword(s):  
Molecular Dynamics ◽  
Pamam Dendrimers ◽  
Structure Flexibility

scholarly journals Specificity of Counterion Binding to a Conjugated Polyelectrolyte: A Combined Molecular Dynamics and NOESY Investigation

2020 ◽  
Vol 53 (4) ◽  
pp. 1119-1128
Author(s):  
Gregor Hostnik ◽  
Črtomir Podlipnik ◽  
Guillaume Mériguet ◽  
Janez Cerar
Keyword(s):  
Molecular Dynamics ◽  
Counterion Binding ◽  
Conjugated Polyelectrolyte

scholarly journals Histone tails cooperate to control the breathing of genomic nucleosomes

2021 ◽  
Vol 17 (6) ◽  
pp. e1009013
Author(s):  
Jan Huertas ◽  
Hans Robert Schöler ◽  
Vlad Cojocaru
Keyword(s):  
Epigenetic Regulation ◽  
Genomic Dna ◽  
Histone H3 ◽  
Molecular Simulations ◽  
Dna Interaction ◽  
Histone Tail ◽  
Chemical Modifications ◽  
Histone Tails ◽  
Chromatin Dynamics ◽  
Nucleosome Dynamics

Genomic DNA is packaged in chromatin, a dynamic fiber variable in size and compaction. In chromatin, repeating nucleosome units wrap 145–147 DNA basepairs around histone proteins. Genetic and epigenetic regulation of genes relies on structural transitions in chromatin which are driven by intra- and inter-nucleosome dynamics and modulated by chemical modifications of the unstructured terminal tails of histones. Here we demonstrate how the interplay between histone H3 and H2A tails control ample nucleosome breathing motions. We monitored large openings of two genomic nucleosomes, and only moderate breathing of an engineered nucleosome in atomistic molecular simulations amounting to 24 μs. Transitions between open and closed nucleosome conformations were mediated by the displacement and changes in compaction of the two histone tails. These motions involved changes in the DNA interaction profiles of clusters of epigenetic regulatory aminoacids in the tails. Removing the histone tails resulted in a large increase of the amplitude of nucleosome breathing but did not change the sequence dependent pattern of the motions. Histone tail modulated nucleosome breathing is a key mechanism of chromatin dynamics with important implications for epigenetic regulation.

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