title: Nucleosome Histone Tail Conformation and Dynamics: Impacts of Lysine Acetylation and a Nearby Minor Groove Benzo[a]pyrene-Derived Lesion.
abstract: Histone tails in nucleosomes play critical roles in regulation of many biological processes, including chromatin compaction, transcription, and DNA repair. Moreover, post-translational modifications, notably lysine acetylation, are crucial to these functions. While the tails have been intensively studied, how the structures and dynamics of tails are impacted by the presence of a nearby bulky DNA lesion is a frontier research area, and how these properties are impacted by tail lysine acetylation remains unexplored. To obtain molecular insight, we have utilized all atom 3 μs molecular dynamics simulations of nucleosome core particles (NCPs) to determine the impact of a nearby DNA lesion, 10S (+)-trans-anti-B[a]P-N2-dG-the major adduct derived from the procarcinogen benzo[a]pyrene-on H2B tail behavior in unacetylated and acetylated states. We similarly studied lesion-free NCPs to investigate the normal properties of the H2B tail in both states. In the lesion-free NCPs, charge neutralization upon lysine acetylation causes release of the tail from the DNA. When the lesion is present, it stably engulfs part of the nearby tail, impairing the interactions between DNA and tail. With the tail in an acetylated state, the lesion still interacts with part of it, although unstably. The lesion's partial entrapment of the tail should hinder the tail from interacting with other nucleosomes, and other proteins such as acetylases, deacetylases, and acetyl-lysine binding proteins, and thus disrupt critical tail-governed processes. Hence, the lesion would impede tail functions modulated by acetylation or deacetylation, causing aberrant chromatin structures and impaired biological transactions such as transcription and DNA repair.
authors.forename: Iwen
authors.initials: I
authors.lastname: Fu
authors.forename: Yuqin
authors.initials: Y
authors.lastname: Cai
authors.forename: Nicholas E
authors.initials: NE
authors.lastname: Geacintov
authors.affiliation: NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China.
authors.forename: Yingkai
authors.initials: Y
authors.lastname: Zhang
authors.forename: Suse
authors.identifier: 0000-0002-3802-7511
authors.initials: S
authors.lastname: Broyde
mesh_terms: D000107:Acetylation; D000595:Amino Acid Sequence; D001564:Benzo(a)pyrene / Q000737:chemistry*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004249:DNA Damage; D004260:DNA Repair; D006657:Histones / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D008239:Lysine / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D011485:Protein Binding; D000072417:Protein Domains; D055503:Protein Multimerization; D011499:Protein Processing, Post-Translational; D017433:Protein Structure, Secondary
chemical_list: D006657:Histones; D009707:Nucleosomes; D001564:Benzo(a)pyrene; D004247:DNA; D008239:Lysine