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Conformational sampling of unmodified and acetylated H3 histone tails on a nucleosome by all-atom model molecular dynamics simulations

Ikebe, Kimiyoshi; Sakuraba, Shun; Kono, Hidetoshi

A nucleosome, 146 or 147 base-pair DNA wrapped around a histone octamer composed of two copies of each H3, H4, H2A, and H2B histone proteins, is a compact unit structure to store eukaryotic DNA into the cell nucleus. Although the X-ray conformations of the core region have been already determined, the conformations of the disordered histone terminal regions (histone tails) remain poorly understood. Recent experimental evidences suggest that chemical modifications on the histone tails regulate DNA functions, such as transcription, duplication, and splicing. To understand the regulation mechanism, it is necessary to elucidate difference between conformational states of unmodified and modified histone tails. Thus, we applied adaptive lambda square dynamics (ALSD) simulation we developed recently to investigate the conformations of H3 histone tails. ALSD dynamically scales the simulation parameters (charge, van der Walls and torsion energies) only for the histone tails during the simulations. This successfully sampled various histone tail conformations. In this poster, we introduce the ALSD simulation results and the differences in conformational ensembles between unmodified and acetylated H3 histone tails.



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