A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions

J Chem Theory Comput. 2022 Jun 14;18(6):3948-3960. doi: 10.1021/acs.jctc.2c00083. Epub 2022 May 17.

Abstract

The nucleosome core particle (NCP) is a large complex of 145-147 base pairs of DNA and eight histone proteins and is the basic building block of chromatin that forms the chromosomes. Here, we develop a coarse-grained (CG) model of the NCP derived through a systematic bottom-up approach based on underlying all-atom MD simulations to compute the necessary CG interactions. The model produces excellent agreement with known structural features of the NCP and gives a realistic description of the nucleosome-nucleosome attraction in the presence of multivalent cations (Mg(H2O)62+ or Co(NH3)63+) for systems comprising 20 NCPs. The results of the simulations reveal structural details of the NCP-NCP interactions unavailable from experimental approaches, and this model opens the prospect for the rigorous modeling of chromatin fibers.

MeSH terms

  • Chromatin
  • DNA / chemistry
  • Histones* / chemistry
  • Ions / metabolism
  • Nucleosomes*

Substances

  • Chromatin
  • Histones
  • Ions
  • Nucleosomes
  • DNA