Dynamic light scattering study of base excision DNA repair proteins and their complexes

Inna A. Vasil'eva, Rashid O. Anarbaev, Nina A. Moor, Olga I. Lavrik

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)

Abstract

Base excision repair (BER) involves many enzymes acting in a coordinated fashion at the most common types of DNA damage. The coordination is facilitated by interactions between the enzymes and accessory proteins, X-ray repair cross-complementing protein 1 (XRCC1) and poly(ADP-ribose) polymerase 1 (PARP1). Here we use dynamic light scattering (DLS) technique to determine the hydrodynamic sizes of several BER enzymes and proteins, DNA polymerase β (Polβ), apurinic/apyrimidinic endonuclease 1 (APE1), tyrosyl-DNA phosphodiesterase 1 (TDP1), XRCC1 and PARP1, present alone or in the equimolar mixtures with each other. From the DLS data combined with glutaraldehyde cross-linking experiments and previous quantitative binding data the oligomeric states of BER proteins and their complexes are estimated. All the proteins have been proposed to form homodimers upon their self-association. The most probable oligomerization state of the binary complexes formed by PARP1 with various proteins is a heterotetramer. The oligomerization state of the binary complexes formed by XRCC1 varies from heterodimer to heterotetramer, depending on the partner. The DLS technique is applied for the first time to measure the hydrodynamic sizes of PARP1 molecules covalently bound with poly(ADP-ribose) (PAR) synthesized upon the automodification reaction. PARP1 has been detected to form huge conglomerates stabilized by Mg2+ coordinated bonds with PAR polymers.

Original languageEnglish
Pages (from-to)297-305
Number of pages9
JournalBiochimica et Biophysica Acta - Proteins and Proteomics
Volume1867
Issue number3
DOIs
Publication statusPublished - 1 Mar 2019

Keywords

  • DNA base excision repair complexes
  • Dynamic light scattering
  • Oligomeric state
  • Poly(ADP-ribosyl)ation
  • Protein-protein interactions
  • SPECIFICITY
  • XRCC1
  • MECHANISMS
  • IDENTIFICATION
  • DAMAGE
  • IN-VITRO
  • POLY(ADP-RIBOSE) POLYMERASE 1
  • BINDING
  • ASSOCIATION
  • DOMAINS
  • DNA Polymerase beta/chemistry
  • X-ray Repair Cross Complementing Protein 1/chemistry
  • Poly (ADP-Ribose) Polymerase-1/chemistry
  • DNA Repair
  • Phosphoric Diester Hydrolases/chemistry
  • Dynamic Light Scattering
  • DNA-(Apurinic or Apyrimidinic Site) Lyase/chemistry

Fingerprint

Dive into the research topics of 'Dynamic light scattering study of base excision DNA repair proteins and their complexes'. Together they form a unique fingerprint.

Cite this