Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome

Nucleic Acids Res. 2016 Aug 19;44(14):6599-613. doi: 10.1093/nar/gkw514. Epub 2016 Jun 7.


Linker histones are essential for DNA compaction in chromatin. They bind to nucleosomes in a 1:1 ratio forming chromatosomes. Alternative configurations have been proposed in which the globular domain of the linker histone H5 (gH5) is positioned either on- or off-dyad between the nucleosomal and linker DNAs. However, the dynamic pathways of chromatosome assembly remain elusive. Here, we studied the conformational plasticity of gH5 in unbound and off-dyad nucleosome-bound forms with classical and accelerated molecular dynamics simulations. We find that the unbound gH5 converts between open and closed conformations, preferring the closed form. However, the open gH5 contributes to a more rigid chromatosome and restricts the motion of the nearby linker DNA through hydrophobic interactions with thymidines. Moreover, the closed gH5 opens and reorients in accelerated simulations of the chromatosome. Brownian dynamics simulations of chromatosome assembly, accounting for a range of amplitudes of nucleosome opening and different nucleosome DNA sequences, support the existence of both on- and off-dyad binding modes of gH5 and reveal alternative, sequence and conformation-dependent chromatosome configurations. Taken together, these findings suggest that the conformational dynamics of linker histones and nucleosomes facilitate alternative chromatosome configurations through an interplay between induced fit and conformational selection.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / chemistry
  • Histones / chemistry*
  • Histones / metabolism*
  • Hydrophobic and Hydrophilic Interactions
  • Molecular Dynamics Simulation
  • Nucleic Acid Conformation*
  • Nucleosomes / chemistry*
  • Nucleosomes / metabolism*
  • Protein Binding
  • Protein Domains
  • Thymidine / metabolism


  • Histones
  • Nucleosomes
  • DNA
  • Thymidine