TY - JOUR

T1 - Dynamic light scattering study of base excision DNA repair proteins and their complexes

AU - Vasil'eva, Inna A.

AU - Anarbaev, Rashid O.

AU - Moor, Nina A.

AU - Lavrik, Olga I.

N1 - Publisher Copyright: © 2018 Elsevier B.V.

PY - 2019/3/1

Y1 - 2019/3/1

N2 - 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.

AB - 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.

KW - DNA base excision repair complexes

KW - Dynamic light scattering

KW - Oligomeric state

KW - Poly(ADP-ribosyl)ation

KW - Protein-protein interactions

KW - SPECIFICITY

KW - XRCC1

KW - MECHANISMS

KW - IDENTIFICATION

KW - DAMAGE

KW - IN-VITRO

KW - POLY(ADP-RIBOSE) POLYMERASE 1

KW - BINDING

KW - ASSOCIATION

KW - DOMAINS

KW - DNA Polymerase beta/chemistry

KW - X-ray Repair Cross Complementing Protein 1/chemistry

KW - Poly (ADP-Ribose) Polymerase-1/chemistry

KW - DNA Repair

KW - Phosphoric Diester Hydrolases/chemistry

KW - Dynamic Light Scattering

KW - DNA-(Apurinic or Apyrimidinic Site) Lyase/chemistry

UR - http://www.scopus.com/inward/record.url?scp=85055124596&partnerID=8YFLogxK

U2 - 10.1016/j.bbapap.2018.10.009

DO - 10.1016/j.bbapap.2018.10.009

M3 - Article

C2 - 30321662

AN - SCOPUS:85055124596

VL - 1867

SP - 297

EP - 305

JO - Biochimica et Biophysica Acta - Proteins and Proteomics

JF - Biochimica et Biophysica Acta - Proteins and Proteomics

SN - 1570-9639

IS - 3

ER -