As important as DNA’s role is in the evolution of life, DNA is subject to damage by a vast array of physical and chemical agents. Translesion DNA synthesis (TLS) is an important pathway to tolerate DNA damage. DNA polymerase zeta (Pol ζ) is one of the several error-prone polymerases involved in the TLS. It contains two subunit, REV3 which encodes the catalytic subunit and REV7 which encodes a regulatory subunit. Dictyostelium discoideum was the model system used because of the similarity of its DNA repair proteins compared to humans. The fragment of REV3 protein studied here (2138-2701 aa) contains the catalytic site which offers the binding to its DNA decamer substrate, specifically, a decamer that contains cis-syn thymine cyclobutane, a known damages that REV3 can bypass. This work is based on predicted structures of REV3 sequence from I-TASSER server and PDB crystalline structure of DNA 1T4I. Strand B of 1T4I was isolated because this is the strand that contains the thymine dimer damage. Docking study was performed using DOT 2.0.1 then further molecular dynamics simulation was carried out using NAMD software. DOT docking treats both protein and DNA molecules as rigid structures, therefore MD simulation is necessary to observe the micromotion of these molecules once they bound together. It was found that DOT was able to predict the binding site on REV3 protein that is consistent with BLAST-P search. It also showed a close interaction between the active site and the thymine dimer of 1T4I. MD simulation indicates that this binding is relative strong as MD simulation up to 20 nanosecond did not show significant motion or distortion of either molecule. Further interaction between thymine dimer and REV3 active site is under investigation.

Docking study of thymine-dimer containing DNA decamer on translesion DNA polymerase zeta from Dictyostelium discoideum

2019 Fall National Meeting

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