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

Hidetoshi Kono, Kazuyoshi Shirayama, Yasuhiro Arimura, Hiroaki Tachiwana, Hitoshi Kurumizaka

    Research output: Contribution to journalArticle

    11 Citations (Scopus)

    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 nucleosome. This difference in the dynamics between the two types of nucleosomes may be important for forming higher order structures in different phases.

    Original languageEnglish
    Article numbere0120635
    JournalPLoS One
    Volume10
    Issue number3
    DOIs
    Publication statusPublished - 2015 Mar 18

    Fingerprint

    nucleosomes
    Nucleosomes
    arginine
    Arginine
    DNA
    histones
    Histones
    Lysine
    lysine
    Basic Amino Acids
    Centromere
    molecular dynamics
    Endonucleases
    centromeres
    Molecular Dynamics Simulation
    hydrogen
    Molecular dynamics
    Hydrogen
    Assays
    Hydrogen bonds

    ASJC Scopus subject areas

    • Agricultural and Biological Sciences(all)
    • Biochemistry, Genetics and Molecular Biology(all)
    • Medicine(all)

    Cite this

    Kono, H., Shirayama, K., Arimura, Y., Tachiwana, H., & Kurumizaka, H. (2015). Two arginine residues suppress the flexibility of nucleosomal dna in the canonical nucleosome core. PLoS One, 10(3), [e0120635]. https://doi.org/10.1371/journal.pone.0120635

    Two arginine residues suppress the flexibility of nucleosomal dna in the canonical nucleosome core. / Kono, Hidetoshi; Shirayama, Kazuyoshi; Arimura, Yasuhiro; Tachiwana, Hiroaki; Kurumizaka, Hitoshi.

    In: PLoS One, Vol. 10, No. 3, e0120635, 18.03.2015.

    Research output: Contribution to journalArticle

    Kono, H, Shirayama, K, Arimura, Y, Tachiwana, H & Kurumizaka, H 2015, 'Two arginine residues suppress the flexibility of nucleosomal dna in the canonical nucleosome core', PLoS One, vol. 10, no. 3, e0120635. https://doi.org/10.1371/journal.pone.0120635
    Kono, Hidetoshi ; Shirayama, Kazuyoshi ; Arimura, Yasuhiro ; Tachiwana, Hiroaki ; Kurumizaka, Hitoshi. / Two arginine residues suppress the flexibility of nucleosomal dna in the canonical nucleosome core. In: PLoS One. 2015 ; Vol. 10, No. 3.
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