title: Comparing native and irradiated E. coli lactose repressor-operator complex by molecular dynamics simulation.
abstract: The function of the E. coli lactose operon requires the binding of the tetrameric repressor protein to the operator DNA. We have previously shown that gamma-irradiation destabilises the repressor-operator complex because the repressor gradually loses its DNA-binding ability (Radiat Res 170:604-612, 2008). It was suggested that the observed oxidation of tyrosine residues and the concomitant structural changes of irradiated headpieces (DNA-binding domains of repressor monomers) could be responsible for the inactivation. To unravel the mechanisms that lead to repressor-operator complex destabilisation when tyrosine oxidation occurs, we have compared by molecular dynamic simulations two complexes: (1) the native complex formed by two headpieces and the operator DNA, and (2) the damaged complex, in which all tyrosines are replaced by their oxidation product 3,4-dihydroxyphenylalanine (DOPA). On a 20 ns time scale, MD results show effects consistent with complex destabilisation: increased flexibility, increased DNA bending, modification of the hydrogen bond network, and decrease of the positive electrostatic potential at the protein surface and of the global energy of DNA-protein interactions.
authors.affiliation: Centre de Biophysique Moléculaire, UPR 4301, CNRS (affiliated to the University of Orléans and to INSERM), Orléans, France.
authors.forename: Samia
authors.initials: S
authors.lastname: Aci-Sèche
authors.forename: Norbert
authors.initials: N
authors.lastname: Garnier
authors.forename: Stéphane
authors.initials: S
authors.lastname: Goffinont
authors.forename: Daniel
authors.initials: D
authors.lastname: Genest
authors.forename: Mélanie
authors.initials: M
authors.lastname: Spotheim-Maurizot
authors.forename: Monique
authors.initials: M
authors.lastname: Genest
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites / Q000502:physiology / Q000528:radiation effects; D004269:DNA, Bacterial / Q000737:chemistry / Q000378:metabolism / Q000528:radiation effects*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism / Q000528:radiation effects*; D004295:Dihydroxyphenylalanine / Q000737:chemistry / Q000378:metabolism / Q000528:radiation effects; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism / Q000528:radiation effects*; D005720:Gamma Rays; D006860:Hydrogen Bonding; D056968:Lac Repressors / Q000737:chemistry / Q000378:metabolism / Q000528:radiation effects*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009875:Operator Regions, Genetic; D010084:Oxidation-Reduction; D055672:Static Electricity
chemical_list: D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D056968:Lac Repressors; D004295:Dihydroxyphenylalanine