Two arginine residues suppress the flexibility of nucleosomal DNA in the canonical nucleosome core

PloS One
Hidetoshi KonoHitoshi Kurumizaka

Abstract

The dynamics of nucleosomes containing either canonical H3 or its centromere-specific variant CENP-A were investigated using molecular dynamics simulations. The simulations showed that the histone cores were structurally stable during simulation periods of 100 ns and 50 ns, while DNA was highly flexible at the entry and exit regions and partially dissociated from the histone core. In particular, approximately 20-25 bp of DNA at the entry and exit regions of the CENP-A nucleosome exhibited larger fluctuations than DNA at the entry and exit regions of the H3 nucleosome. Our detailed analysis clarified that this difference in dynamics was attributable to a difference in two basic amino acids in the αN helix; two arginine (Arg) residues in H3 were substituted by lysine (Lys) residues at the corresponding sites in CENP-A. The difference in the ability to form hydrogen bonds with DNA of these two residues regulated the flexibility of nucleosomal DNA at the entry and exit regions. Our exonuclease III assay consistently revealed that replacement of these two Arg residues in the H3 nucleosome by Lys enhanced endonuclease susceptibility, suggesting that the DNA ends of the CENP-A nucleosome are more flexible than those of the H3 nucleoso...Continue Reading

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Citations

Sep 16, 2016·Journal of Chemical Theory and Computation·Jaewoon JungYuji Sugita
Aug 17, 2016·Scientific Reports·Zhenhai Li, Hidetoshi Kono
Dec 10, 2016·European Biophysics Journal : EBJ·Muthukumaran RajagopalanAmutha Ramaswamy
Feb 22, 2017·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Olga Moreno-MorenoFernando Azorín
Mar 6, 2018·PLoS Computational Biology·Hidetoshi KonoHisashi Ishida
Nov 22, 2017·Journal of Biochemistry·Masako Koyama, Hitoshi Kurumizaka
Jan 28, 2020·Biophysics and Physicobiology·Hidetoshi KonoHisashi Ishida
Sep 26, 2017·Alzheimer's & Dementia : the Journal of the Alzheimer's Association·Paul A ParconW Sue T Griffin
Dec 19, 2019·Frontiers in Molecular Biosciences·Takeru KamedaYuichi Togashi
Nov 13, 2019·Structure·Yoshimasa TakizawaHitoshi Kurumizaka
Dec 15, 2020·Journal of Molecular Biology·Jan Huertas, Vlad Cojocaru
Feb 10, 2021·Proceedings of the National Academy of Sciences of the United States of America·Hisashi Ishida, Hidetoshi Kono
Oct 17, 2020·Journal of Molecular Biology·Hitoshi KurumizakaYoshimasa Takizawa
Aug 6, 2021·Nucleic Acids Research·Shoko SatoHitoshi Kurumizaka

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Methods Mentioned

BETA
X-ray
salt dialysis
electrophoresis

Software Mentioned

PyMOL Molecular Graphics System
AMBER package
AMBER
SANDER
ptraj
PyMol

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