title: H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation.
abstract: Acetylation of lysine residues in histone tails is associated with gene transcription. Because histone tails are structurally flexible and intrinsically disordered, it is difficult to experimentally determine the tail conformations and the impact of acetylation. In this work, we performed simulations to sample H3 tail conformations with and without acetylation. The results show that irrespective of the presence or absence of the acetylation, the H3 tail remains in contact with the DNA and assumes an α-helix structure in some regions. Acetylation slightly weakened the interaction between the tail and DNA and enhanced α-helix formation, resulting in a more compact tail conformation. We inferred that this compaction induces unwrapping and exposure of the linker DNA, enabling DNA-binding proteins (e.g., transcription factors) to bind to their target sequences. In addition, our simulation also showed that acetylated lysine was more often exposed to the solvent, which is consistent with the fact that acetylation functions as a post-translational modification recognition site marker.
authors.affiliation: Molecular Modeling and Simulation Group, Japan Atomic Energy Agency, Kizugawa, Japan.
authors.forename: Jinzen
authors.initials: J
authors.lastname: Ikebe
authors.affiliation: Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Japan.
authors.forename: Shun
authors.initials: S
authors.lastname: Sakuraba
authors.affiliation: Molecular Modeling and Simulation Group, Japan Atomic Energy Agency, Kizugawa, Japan.
authors.forename: Hidetoshi
authors.initials: H
authors.lastname: Kono
mesh_terms: D000107:Acetylation; D000465:Algorithms; D001665:Binding Sites; D006657:Histones / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D009707:Nucleosomes / Q000737:chemistry* / Q000648:ultrastructure*; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: D006657:Histones; D009707:Nucleosomes