Molecular Dynamics Studies of DNA repair enzymes


SNIC 2016/1-398


SNAC Medium

Principal Investigator:

Kwangho Nam


Umeå universitet

Start Date:


End Date:


Primary Classification:

10407: Teoretisk kemi

Secondary Classification:

10603: Biofysik

Tertiary Classification:

10601: Strukturbiologi




To ensure the fidelity of genomic DNA, all organisms employ error correcting mechanisms known as the base-excision repair (BER) to reverse adverse effects caused by lesions in DNA. With the long-term goal to elucidate the working mechanisms of DNA repair enzymes, my lab is undertaking two research projects involved in BER. 1. Human 8-oxoguanine DNA glycosylase (hOGG1) hOOG1 is a key enzyme searching and removing DNA mutations caused by oxidative damage to guanine (G), known as 8-oxoguanine (oxoG). In this project, we aim to elucidate detailed mechanisms of (1) how the enzyme locates lesions in vast excess of normal DNA and (2) multistep reaction pathways leading to the catalytic removal of oxoG. In collaboration with Prof. Gregory Verdine (Harvard University, USA), whose lab has determined high-resolution structures of hOGG1 in action, my lab has been performing computer simulation studies based on the structures determined by Verdine lab. During the previous allocation periods, we have performed μs-long MD simulations and characterized the dynamics of the enzyme in complex with normal and lesion bases and the study of conformational change for the base extrusion process. In the coming allocation period, we will continue the study (1) to determine the complete free energy landscape of the conformational change pathways of base extrusion out of DNA helix and (2) to characterize the effects of DNA damage on the determined free energy landscape by alchemical free energy simulations, by applying the methods developed recently by my lab. The proposed study will yield new insight into the lesion recognition mechanism of this important enzyme. 2. DNA polymerase β (polβ) is an error-prone base-excision repair DNA polymerase that preferentially induces transition mutations over transverse mutations (78 % vs. 11 %). In collaboration with Prof. Seongmin Lee (University of Texas at Austin, USA), we aim to understand how polβ recognizes the mis-matched DNA base before and during its insertion into DNA. Based on the structures of polβ in complex with normal and damaged nucleotides solved by Prof. Lee’s lab and their determined kinetic parameters, my lab has been focusing on elucidating the mismatch discrimination mechanism of polβ in its open and close conformational states. During the coming allocation period, we will continue the study of the conformational change to the closed conformation by applying the targeted molecular dynamics and string method simulations to elucidate the conformational transition mechanism of the enzyme. In addition, we will study the catalytic mechanism of the enzyme by applying the quantum mechanical and molecular mechanical (QM/MM) methods, which are actively developed by my lab. The proposed simulations are to be performed in explicit water and require continued support from SNIC. In particular, the proposed sting method and QM/MM simulations are demanding because they require an ensemble of MD simulations running concurrently, and because of the long running time needed to obtain converged thermodynamic averages (up to microseconds for highly flexible systems such as the DNA/protein complexes).