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Kanaeda, Naoko; Deguchi, Tetsuo*
Progress of Theoretical Physics Supplement, (191), p.146 - 153, 2011/12
no abstracts in English
Kono, Hidetoshi; Kanaeda, Naoko
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no abstracts in English
Kanaeda, Naoko; Ishida, Hisashi; Kono, Hidetoshi
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The nucleosomes are the basic unit of eucaryotic chromosome structure. It has recently been discovered that chromatine remodeling complexes peel the nucleosomal DNA away from the histone octomer(the remodeling). The change in the translational and rotational positioning permits access to the binding site of the nucleosomal DNA by proteins involved in gene expression, DNA replication and repair. The free energy profile in the process of the remodeling should provide important clues to clarify the mechanism of the protein binding to the nucleosomal DNA. We perform the molecular dynamics simulation starting from the high-resolution structure of a nucleosome core particle including explicit water and ions. After the equilibration of the nucleosome core particle, we pull the ends of nucleosomal DNA to peel it away from the histone core and obtain the free energy profile.
Kanaeda, Naoko; Kono, Hidetoshi
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no abstracts in English
Kanaeda, Naoko; Kono, Hidetoshi
no journal, ,
no abstracts in English
Kanaeda, Naoko; Ishida, Hisashi; Kono, Hidetoshi
no journal, ,
The nucleosome, consisting of a histone octomer with DNA wrapped around it, is the basic repeating unit of the eukaryotic chromosome structure. Because the DNA is wrapped around the histone core, it is difficult for proteins that regulate transcription, DNA replication, repair and recombination to access the nucleosomal DNA. Nucleosomes have been known to dynamically change their positions in accordance with cell states. ATP-hydrolyzing chromatin remodelers are considered to loosen the form of the DNA and relocate the DNA inside the nucleosome in order to expose cis-elements to which regulatory proteins bind. We believe that the free energy profile of nucleosomal DNA sliding can provide some important clues to help understand the mechanism of changes in nucleosome positioning.
Kono, Hidetoshi; Kanaeda, Naoko; Yonetani, Yoshiteru; Ishida, Hisashi
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no abstracts in English
Kanaeda, Naoko; Ishida, Hisashi; Kono, Hidetoshi
no journal, ,
no abstracts in English
Kanaeda, Naoko; Ishida, Hisashi; Kono, Hidetoshi
no journal, ,
no abstracts in English
Kanaeda, Naoko; Ishida, Hisashi; Kono, Hidetoshi
no journal, ,
no abstracts in English
Kanaeda, Naoko; Ishida, Hisashi; Kono, Hidetoshi
no journal, ,
no abstracts in English
Kono, Hidetoshi; Kanaeda, Naoko; Ishida, Hisashi
no journal, ,
Kono, Hidetoshi; Ishida, Hisashi; Kanaeda, Naoko
no journal, ,
no abstracts in English
Kanaeda, Naoko; Ishida, Hisashi; Kono, Hidetoshi
no journal, ,
no abstracts in English
Kanaeda, Naoko; Ishida, Hisashi; Kono, Hidetoshi
no journal, ,
no abstracts in English
Kanaeda, Naoko
no journal, ,
no abstracts in English
