Active nucleosome displacement: a theoretical approach

Biophys J. 2009 Jun 3;96(11):4387-98. doi: 10.1016/j.bpj.2009.02.071.

Abstract

Three-quarters of eukaryotic DNA are wrapped around protein cylinders forming so-called nucleosomes that block the access to the genetic information. Nucleosomes need therefore to be repositioned, either passively (by thermal fluctuations) or actively (by molecular motors). Here we introduce a theoretical model that allows us to study the interplay between a motor protein that moves along DNA (e.g., an RNA polymerase) and a nucleosome that it encounters on its way. We aim at describing the displacement mechanisms of the nucleosome and the motor protein on a microscopic level to understand better the intricate interplay between the active step of the motor and the nucleosome-repositioning step. Different motor types (Brownian ratchet versus power-stroke mechanism) that perform very similarly under a constant load are shown to have very different nucleosome repositioning capacities.

MeSH terms

  • Algorithms
  • Computer Simulation
  • DNA / chemistry*
  • DNA-Directed RNA Polymerases / chemistry*
  • Models, Chemical*
  • Motion
  • Nucleosomes / chemistry*
  • Stochastic Processes

Substances

  • Nucleosomes
  • DNA
  • DNA-Directed RNA Polymerases