Structural and dynamic characterization of polymerase κ's minor groove lesion processing reveals how adduct topology impacts fidelity

Lee Lior-Hoffmann, Shuang Ding, Nicholas E. Geacintov, Yingkai Zhang, Suse Broyde

Research output: Contribution to journalArticle

Abstract

DNA lesion bypass polymerases process different lesions with varying fidelities, but the structural, dynamic, and mechanistic origins of this phenomenon remain poorly understood. Human DNA polymerase κ (Polκ), a member of the Y family of lesion bypass polymerases, is specialized to bypass bulky DNA minor groove lesions in a predominantly error-free manner, by housing them in its unique gap. We have investigated the role of the unique Polκ gap and N-clasp structural features in the fidelity of minor groove lesion processing with extensive molecular modeling and molecular dynamics simulations to pinpoint their functioning in lesion bypass. Here we consider the N2-dG covalent adduct derived from the carcinogenic aromatic amine, 2-acetylaminofluorene (dG-N2-AAF), that is produced via the combustion of kerosene and diesel fuel. Our simulations reveal how the spacious gap directionally accommodates the lesion aromatic ring system as it transits through the stages of incorporation of the predominant correct partner dCTP opposite the damaged guanine, with preservation of local active site organization for nucleotidyl transfer. Furthermore, flexibility in Polκs N-clasp facilitates the significant misincorporation of dTTP opposite dG-N2-AAF via wobble pairing. Notably, we show that N-clasp flexibility depends on lesion topology, being markedly reduced in the case of the benzo[a]pyrene-derived major adduct to N2-dG, whose bypass by Polκ is nearly error-free. Thus, our studies reveal how Polκs unique structural and dynamic properties can regulate its bypass fidelity of polycyclic aromatic lesions and how the fidelity is impacted by lesion structures.

Original languageEnglish (US)
Pages (from-to)5683-5691
Number of pages9
JournalBiochemistry
Volume53
Issue number35
DOIs
StatePublished - Sep 9 2014

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Topology
Kerosene
2-Acetylaminofluorene
Gasoline
Molecular modeling
Benzo(a)pyrene
DNA
Structural dynamics
Guanine
DNA-Directed DNA Polymerase
Molecular Dynamics Simulation
Diesel fuels
Processing
Amines
Molecular dynamics
Catalytic Domain
Organizations
Computer simulation
3-(deoxyguanosin-N2-yl)-2-acetylaminofluorene
thymidine 5'-triphosphate

ASJC Scopus subject areas

  • Biochemistry
  • Medicine(all)

Cite this

Structural and dynamic characterization of polymerase κ's minor groove lesion processing reveals how adduct topology impacts fidelity. / Lior-Hoffmann, Lee; Ding, Shuang; Geacintov, Nicholas E.; Zhang, Yingkai; Broyde, Suse.

In: Biochemistry, Vol. 53, No. 35, 09.09.2014, p. 5683-5691.

Research output: Contribution to journalArticle

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