Comparing native and irradiated E. coli lactose repressor-operator complex by molecular dynamics simulation.
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.
Aci-Sèche
Samia
S
Centre de Biophysique Moléculaire, UPR 4301, CNRS (affiliated to the University of Orléans and to INSERM), Orléans, France.
Garnier
Norbert
N
Goffinont
Stéphane
S
Genest
Daniel
D
Spotheim-Maurizot
Mélanie
M
Genest
Monique
M
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
D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D056968:Lac Repressors; D004295:Dihydroxyphenylalanine