TY - JOUR

T1 - The Role of Active-Site Plasticity in Damaged-Nucleotide Recognition by Human Apurinic/Apyrimidinic Endonuclease APE1

AU - Bulygin, Anatoly A.

AU - Kuznetsova, Alexandra A.

AU - Vorobjev, Yuri N.

AU - Fedorova, Olga S.

AU - Kuznetsov, Nikita A.

N1 - Publisher Copyright: © 2020 by the authors. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

PY - 2020/9/1

Y1 - 2020/9/1

N2 - Human apurinic/apyrimidinic (AP) endonuclease APE1 hydrolyzes phosphodiester bonds on the 50 side of an AP-site, and some damaged nucleotides such as 1,N6-ethenoadenosine (εA), α-adenosine (αA), and 5,6-dihydrouridine (DHU). To investigate the mechanism behind the broad substrate specificity of APE1, we analyzed pre-steady-state kinetics of conformational changes in DNA and the enzyme during DNA binding and damage recognition. Molecular dynamics simulations of APE1 complexes with one of damaged DNA duplexes containing εA, αA, DHU, or an F-site (a stable analog of an AP-site) revealed the involvement of residues Asn229, Thr233, and Glu236 in the mechanism of DNA lesion recognition. The results suggested that processing of an AP-site proceeds faster in comparison with nucleotide incision repair substrates because eversion of a small abasic site and its insertion into the active site do not include any unfavorable interactions, whereas the insertion of any target nucleotide containing a damaged base into the APE1 active site is sterically hindered. Destabilization of the α-helix containing Thr233 and Glu236 via a loss of the interaction between these residues increased the plasticity of the damaged-nucleotide binding pocket and the ability to accommodate structurally different damaged nucleotides. Nonetheless, the optimal location of εA or αA in the binding pocket does not correspond to the optimal conformation of catalytic amino acid residues, thereby significantly decreasing the cleavage efficacy for these substrates.

AB - Human apurinic/apyrimidinic (AP) endonuclease APE1 hydrolyzes phosphodiester bonds on the 50 side of an AP-site, and some damaged nucleotides such as 1,N6-ethenoadenosine (εA), α-adenosine (αA), and 5,6-dihydrouridine (DHU). To investigate the mechanism behind the broad substrate specificity of APE1, we analyzed pre-steady-state kinetics of conformational changes in DNA and the enzyme during DNA binding and damage recognition. Molecular dynamics simulations of APE1 complexes with one of damaged DNA duplexes containing εA, αA, DHU, or an F-site (a stable analog of an AP-site) revealed the involvement of residues Asn229, Thr233, and Glu236 in the mechanism of DNA lesion recognition. The results suggested that processing of an AP-site proceeds faster in comparison with nucleotide incision repair substrates because eversion of a small abasic site and its insertion into the active site do not include any unfavorable interactions, whereas the insertion of any target nucleotide containing a damaged base into the APE1 active site is sterically hindered. Destabilization of the α-helix containing Thr233 and Glu236 via a loss of the interaction between these residues increased the plasticity of the damaged-nucleotide binding pocket and the ability to accommodate structurally different damaged nucleotides. Nonetheless, the optimal location of εA or αA in the binding pocket does not correspond to the optimal conformation of catalytic amino acid residues, thereby significantly decreasing the cleavage efficacy for these substrates.

KW - 5,6-dihydrouridine

KW - Active site plasticity

KW - AP endonuclease

KW - Apurinic/apyrimidinic site

KW - Base excision repair

KW - Conformational dynamics

KW - apurinic

KW - PROTEIN

KW - base excision repair

KW - 6-dihydrouridine

KW - INCISION ACTIVITY

KW - GLYCOSYLASES

KW - active site plasticity

KW - apyrimidinic site

KW - conformational dynamics

KW - 5

KW - DIVALENT METAL-IONS

KW - KINETIC MECHANISM

KW - DYNAMICS

KW - CHEMISTRY

KW - BASE-EXCISION

KW - DNA-REPAIR

KW - BINDING

UR - http://www.scopus.com/inward/record.url?scp=85090182163&partnerID=8YFLogxK

U2 - 10.3390/molecules25173940

DO - 10.3390/molecules25173940

M3 - Article

C2 - 32872297

AN - SCOPUS:85090182163

VL - 25

JO - Molecules

JF - Molecules

SN - 1420-3049

IS - 17

M1 - 3940

ER -