title: A possible overestimation of the effect of acetylation on lysine residues in KQ mutant analysis.
abstract: Acetylation of lysine residues, one of the most common protein post-transcriptional modifications, is thought to regulate protein affinity with other proteins or nucleotides. Experimentally, the effects of acetylation have been studied using recombinant mutants in which lysine residues (K) are substituted with glutamine (Q) as a mimic of acetyl lysine (KQ mutant), or with arginine (R) as a mimic of nonacetylated lysine (KR mutant). These substitutions, however, have not been properly validated. The effects lysine acetylation on Ku, a multifunctional protein that has been primarily implicated in DNA repair and cell survival, are characterized herein using a series of computer simulations. The binding free energy was reduced in the KQ mutant, while the KR mutant had no effect, which is consistent with previous experimental results. Unexpectedly, the binding energy between Ku and DNA was maintained at almost the same level as in the wild type protein despite full acetylation of the lysine residues. These results suggest that the effects of acetylation may be overestimated when the KQ mutant is used as a mimic of the acetylated protein.
authors.affiliation: Division of Radiological Protection and Biology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan. fuj@nih.go.jp
authors.forename: Hirofumi
authors.initials: H
authors.lastname: Fujimoto
authors.forename: Mariko
authors.initials: M
authors.lastname: Higuchi
authors.forename: Manabu
authors.initials: M
authors.lastname: Koike
authors.forename: Hirotaka
authors.initials: H
authors.lastname: Ode
authors.forename: Miroslav
authors.initials: M
authors.lastname: Pinak
authors.forename: Juraj Kotulic
authors.initials: JK
authors.lastname: Bunta
authors.forename: Toshiyuki
authors.initials: T
authors.lastname: Nemoto
authors.forename: Takashi
authors.initials: T
authors.lastname: Sakudoh
authors.forename: Naoko
authors.initials: N
authors.lastname: Honda
authors.forename: Hideaki
authors.initials: H
authors.lastname: Maekawa
authors.forename: Kimiaki
authors.initials: K
authors.lastname: Saito
authors.forename: Kozo
authors.initials: K
authors.lastname: Tsuchida
mesh_terms: D000107:Acetylation; D034961:Antigens, Nuclear / Q000737:chemistry; D004247:DNA / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry; D000072200:Ku Autoantigen; D008239:Lysine / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009154:Mutation
chemical_list: D034961:Antigens, Nuclear; D004268:DNA-Binding Proteins; D004247:DNA; D000072200:Ku Autoantigen; D008239:Lysine