Free energy profiles for nucleosome position changes

Kono, Hidetoshi; Kanaeda, Naoko; Ishida, Hisashi

Nucleosome, consisting of a histone octamer with DNA wrapping around it, is the basic structural unit of the chromatin structure. It has been known that nucleosome positions are closely associated with the regulations of transcription, DNA replication, repair and recombination. How does the nucleosome dynamically change the position according to the states of the cell ? To understand the mechanism, we carried out molecular dynamics simulation to obtain free energy profiles for the position changes. We forcefully changed the relative position between DNA and a histone core with an adaptively biasing force method and obtained the free energy profile as a function of the relative rotational angle. The energy profiles show that the position change spontaneously occurs at some angles, while it costs about 10 to 15 kcal/mol to pass through the several angle regions where the strong electrostatic interactions exit between DNA phosphate atoms and histone tail atoms. Our result suggests that some factors such as remodelers are essential to pass through these energy barriers.