Two Arginine Residues Suppress the Flexibility of Nucleosomal DNA in the Canonical Nucleosome Core

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.

Histone Tail Dynamics in Partially Disassembled Nucleosomes During Chromatin Remodeling

“…6). The behavior of the H3/H4 tails is similar to previous study (29), and not altered by the loss of H2A/H2B.…”

Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome

“…The free energy profiles were cytokinesis defects [19]. We previously carried out molecular dynamics simulations on the canonical and CENP-A nucleosome core particles, which showed that two Arg residues, R49 and R52, in the helix are responsible for the stability of DNA at both ends of DNA in the canonical nucleosome [7]. In the CENP-A NCP, Lys corresponds to these residues and is likely to lose a hydrogen bond with DNA more easily than Arg.…”

“…The conformational parameters were calculated using X3DNA [21]. The missing histone tails of CENP-A NCP were not modelled because the simulation system was set as similar as possible to our previous simulation of H3 NCP [7]. The effect of the histone tails, likely to be of significance, will be the subject of a future investigation.…”

“…We followed the simulation protocol of our previous H3-NCP unwrapping calculation [7]. Therefore, we briefly describe the method.…”

“…However, this nucleosomal DNA must be unwrapped and become accessible to regulatory proteins for achieving gene function such as transcription, duplication and repairs. To study the dynamics of nucleosomes including DNA unwrapping, all atom molecular dynamics simulations were carried out [2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17], however, they mostly suffered from short of conformational samplings due to the large size of the simulation systems and the inclusion of intrinsically disordered regions in the systems.…”