Molecular and structural characterization of disease-associated APE1 polymorphisms

Area of Science:

• Biochemistry
• Molecular Biology
• Genetics

Background:

• Oxidative stress generates reactive oxygen species (ROS), causing DNA damage like nucleobase oxidation and fragmentation.
• Altered nucleobases can lead to mutations, contributing to diseases such as cancer.
• Base excision repair (BER) is crucial for removing DNA base damage, with Apurinic/apyrimidinic endonuclease 1 (APE1) being a key enzyme in this pathway.

Purpose of the Study:

• To investigate the structural and functional consequences of prevalent disease-associated single nucleotide polymorphisms (SNPs) in the APEX1 gene, which encodes APE1.
• To elucidate how these APE1 variants affect its critical AP-endonuclease and 3' to 5' exonuclease activities in Base Excision Repair (BER).

Main Methods:

• Determined X-ray crystal structures of three disease-associated APE1 SNPs (D148E, L104R, R237C).
• Conducted comprehensive biochemical characterization, including pre-steady-state kinetic and DNA binding analyses.
• Analyzed variant APE1:DNA complex structures with both AP-endonuclease and exonuclease substrates.

Main Results:

• Each APE1 SNP variant exhibited unique localized structural changes, affecting protein dynamics and DNA binding interactions.
• Biochemical analyses revealed how these structural alterations potentially perturb the AP-endonuclease and exonuclease functions of APE1.
• The study provides mechanistic insights into how specific APE1 SNPs may compromise DNA repair efficiency.

Conclusions:

• Disease-associated APE1 SNPs result in distinct structural modifications that impact enzyme function.
• Understanding these SNP-induced alterations is vital for assessing individual disease risk and developing targeted therapies.
• These findings highlight the importance of APE1's structural integrity for maintaining genome stability and preventing disease.