An AP endonuclease 1-DNA polymerase β complex: Theoretical prediction of interacting surfaces

Alexej Abyzov, Alper Uzun, Phyllis R. Strauss, Valentin A. Ilyin

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Abasic (AP) sites in DNA arise through both endogenous and exogenous mechanisms. Since AP sites can prevent replication and transcription, the cell contains systems for their identification and repair. AP endonuclease (APEX1) cleaves the phosphodiester backbone 5′ to the AP site. The cleavage, a key step in the base excision repair pathway, is followed by nucleotide insertion and removal of the downstream deoxyribose moiety, performed most often by DNA polymerase beta (pol-β). While yeast two-hybrid studies and electrophoretic mobility shift assays provide evidence for interaction of APEX1 and pol-β, the specifics remain obscure. We describe a theoretical study designed to predict detailed interacting surfaces between APEX1 and pol-β based on published co-crystal structures of each enzyme bound to DNA. Several potentially interacting complexes were identified by sliding the protein molecules along DNA: two with pol-β located downstream of APEX1 (3′ to the damaged site) and three with pol-β located upstream of APEX1 (5′ to the damaged site). Molecular dynamics (MD) simulations, ensuring geometrical complementarity of interfaces, enabled us to predict interacting residues and calculate binding energies, which in two cases were sufficient (∼-210.0 kcal/mol) to form a stable complex and in one case a weakly interacting complex. Analysis of interface behavior during MD simulation and visual inspection of interfaces allowed us to conclude that complexes with pol-β at the 3′-side of APEX1 are those most likely to occur in vivo. Additional multiple sequence analyses of APEX1 and pol-β in related organisms identified a set of correlated mutations of specific residues at the predicted interfaces. Based on these results, we propose that pol-β in the open or closed conformation interacts and makes a stable interface with APEX1 bound to a cleaved abasic site on the 3′ side. The method described here can be used for analysis in any DNA-metabolizing pathway where weak interactions are the principal mode of cross-talk among participants and co-crystal structures of the individual components are available.

Original languageEnglish (US)
Article numbere1000066
JournalPLoS Computational Biology
Volume4
Issue number4
DOIs
StatePublished - Apr 2008
Externally publishedYes

Fingerprint

DNA-(Apurinic or Apyrimidinic Site) Lyase
Transcription Factor AP-1
DNA-directed DNA polymerase
DNA-Directed DNA Polymerase
DNA
prediction
molecular dynamics
Prediction
Molecular Dynamics Simulation
crystal structure
Crystal Structure
repair
Interfaces (computer)
Repair
Molecular dynamics
DNA Polymerase beta
Deoxyribose
Pathway
Crystal structure
Electrophoretic Mobility Shift Assay

ASJC Scopus subject areas

  • Cellular and Molecular Neuroscience
  • Ecology
  • Molecular Biology
  • Genetics
  • Ecology, Evolution, Behavior and Systematics
  • Modeling and Simulation
  • Computational Theory and Mathematics

Cite this

An AP endonuclease 1-DNA polymerase β complex : Theoretical prediction of interacting surfaces. / Abyzov, Alexej; Uzun, Alper; Strauss, Phyllis R.; Ilyin, Valentin A.

In: PLoS Computational Biology, Vol. 4, No. 4, e1000066, 04.2008.

Research output: Contribution to journalArticle

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