Holding the Nucleosome Together: A Quantitative Description of the DNA-Histone Interface in Solution

J Chem Theory Comput. 2018 Feb 13;14(2):1045-1058. doi: 10.1021/acs.jctc.7b00936. Epub 2018 Jan 8.


The nucleosome is the fundamental unit of eukaryotic genome packaging in the chromatin. In this complex, the DNA wraps around eight histone proteins to form a superhelical double helix. The resulting bending, stronger than anything observed in free DNA, raises the question of how such a distortion is stabilized by the proteic and solvent environments. In this work, the DNA-histone interface in solution was exhaustively analyzed from nucleosome structures generated by molecular dynamics. An original Voronoi tessellation technique, measuring the topology of interacting elements without any empirical or subjective adjustment, was used to characterize the interface in terms of contact area and occurrence. Our results revealed an interface more robust than previously known, combining extensive, long-lived nonelectrostatic and electrostatic interactions between DNA and both structured and unstructured histone regions. Cation accumulation makes the proximity of juxtaposed DNA gyres in the superhelix possible by shielding the strong electrostatic repulsion of the charged phosphate groups. Overall, this study provides new insights on the nucleosome cohesion, explaining how DNA distortions can be maintained in a nucleoprotein complex.

MeSH terms

  • DNA / chemistry*
  • Histones / chemistry*
  • Molecular Dynamics Simulation*
  • Nucleosomes / chemistry*
  • Solutions
  • Static Electricity


  • Histones
  • Nucleosomes
  • Solutions
  • DNA