Dynamics of forced nucleosome unraveling and role of nonuniform histone-DNA interactions.

ABSTRACT: A coarse-grained model of the nucleosome is introduced to investigate the dynamics of force-induced unwrapping of DNA from histone octamers. In this model, the DNA is treated as a charged, discrete worm-like chain, and the octamer is treated as a rigid cylinder carrying a positively charged superhelical groove that accommodates 1.7 turns of DNA. The groove charges are parameterized to reproduce the nonuniform histone/DNA interaction free energy profile and the loading rate-dependent unwrapping forces, both obtained from single-molecule experiments. Brownian dynamics simulations of the model under constant loading conditions reveal that nucleosome unraveling occurs in three distinct stages. At small extensions, the flanking DNA exhibits rapid unwrapping-rewrapping (breathing) dynamics and t

SUBMITTER: Dobrovolskaia IV 

PROVIDER: S-EPMC3433614 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature