title: Incorrect nucleotide insertion at the active site of a G:A mismatch catalyzed by DNA polymerase beta.
abstract: Based on a recent ternary complex crystal structure of human DNA polymerase beta with a G:A mismatch in the active site, we carried out a theoretical investigation of the catalytic mechanism of incorrect nucleotide incorporation using molecular dynamics simulation, quantum mechanics, combined quantum mechanics, and molecular mechanics methods. A two-stage mechanism is proposed with a nonreactive active-site structural rearrangement prechemistry step occurring before the nucleotidyl transfer reaction. The free energy required for formation of the prechemistry state is found to be the major factor contributing to the decrease in the rate of incorrect nucleotide incorporation compared with correct insertion and therefore to fidelity enhancement. Hence, the transition state and reaction barrier for phosphodiester bond formation after the prechemistry state are similar to that for correct insertion reaction. Key residues that provide electrostatic stabilization of the transition state are identified.
authors.affiliation: Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA.
authors.forename: Ping
authors.initials: P
authors.lastname: Lin
authors.forename: Vinod K
authors.initials: VK
authors.lastname: Batra
authors.forename: Lars C
authors.initials: LC
authors.lastname: Pedersen
authors.forename: William A
authors.initials: WA
authors.lastname: Beard
authors.forename: Samuel H
authors.initials: SH
authors.lastname: Wilson
authors.forename: Lee G
authors.initials: LG
authors.lastname: Pedersen
mesh_terms: D000225:Adenine; D020137:Base Pair Mismatch / Q000235:genetics*; D001665:Binding Sites; D002384:Catalysis; D003198:Computer Simulation; D019951:DNA Polymerase beta / Q000378:metabolism*; D006147:Guanine; D006801:Humans; D008958:Models, Molecular; D008962:Models, Theoretical; D009038:Motion; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D006147:Guanine; D019951:DNA Polymerase beta; D000225:Adenine