title: Probing interactions between lysine residues in histone tails and nucleosomal DNA via product and kinetic analysis.
abstract: The histone proteins in nucleosome core particles are known to catalyze DNA cleavage at abasic and oxidized abasic sites, which are produced by antitumor antibiotics and as a consequence of other modalities of DNA damage. The lysine rich histone tails whose post-translational modifications regulate genetic expression in cells are mainly responsible for this chemistry. Cleavage at a C4'-oxidized abasic site (C4-AP) concomitantly results in modification of lysine residues in histone tails. Using LC-MS/MS, we demonstrate here that that Lys8, -12, -16, and -20 of histone H4 were modified when C4-AP was incorporated at a hot spot (superhelical location 1.5) for DNA damage within a nucleosome core particle. A new DNA-protein cross-linking method that provides a more quantitative analysis of individual amino acid reactivity is also described. DNA-protein cross-links were produced by an irreversible reaction between a nucleic acid electrophile that was produced following oxidatively induced rearrangement of a phenyl selenide derivative of thymidine (3) and nucleophilic residues within proteins. In addition to providing high yields of DNA-protein cross-links, kinetic analysis of the cross-linking reaction yielded rate constants that enabled ranking the contributions by individual or groups of amino acids. Cross-linking from 3 at superhelical location 1.5 revealed the following order of reactivity for the nucleophilic amino acids in the histone H4 tail: His18 > Lys16 > Lys20 ≈ Lys8, Lys12 > Lys5. Cross-linking via 3 will be generally useful for investigating DNA-protein interactions.
authors.affiliation: Department of Chemistry, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States.
authors.forename: Liwei
authors.initials: L
authors.lastname: Weng
authors.forename: Chuanzheng
authors.initials: C
authors.lastname: Zhou
authors.forename: Marc M
authors.initials: MM
authors.lastname: Greenberg
mesh_terms: D004247:DNA / Q000737:chemistry*; D006657:Histones / Q000737:chemistry*; D007700:Kinetics; D008239:Lysine / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000378:metabolism*; D010084:Oxidation-Reduction; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: D006657:Histones; D009707:Nucleosomes; D004247:DNA; D008239:Lysine