Title:	Molecular Dynamics Studies of DNA repair enzymes
DNr:	SNIC 2015/1-327
Project Type:	SNIC Medium Compute
Principal Investigator:	Kwangho Nam <kwangho.nam@uta.edu>
Affiliation:	Umeå universitet
Duration:	2015-10-01 – 2016-10-01
Classification:	10407 10603 10601
Homepage:	http://www.chemistry.umu.se/english/
Keywords:

Abstract

Our genome is constantly exposed to threats, exogenous and endogenous, causing damages to DNA. 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 will perform computer simulation studies based on the determined structures. During the previous allocation period, we have performed μs-long MD simulations and characterized the dynamics of the enzyme in complex with normal and lesion bases. In the coming allocation period, we will take two approaches: (1) the string method free energy simulations to determine the free energy landscape of the reversible conformational pathway of base extrusion out of DNA helix and (2) the alchemical free energy simulations to determine the effects of DNA damage on the determined free energy landscape. 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 it is inserted into DNA. Recently, Prof. Lee’s lab has solved the structures of polβ in complex with normal and damaged nucleotides in the open and the closed conformational states. We believe that these structures and our recent MD simulations of polβ put us in a good position to elucidate the mismatch discrimination mechanism of polβ in its open and close conformational states. During the coming allocation period, we will carry out a series of the targeted molecular dynamics simulations and the string method simulation to elucidate the conformational transition mechanisms between the two conformations. In addition, we will initiate the study of catalytic mechanism of this enzyme by applying the ab initio quantum mechanical and molecular mechanical (QM/MM) methods, which were 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 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).