Title:	Molecular Dynamics Studies of DNA repair enzymes
DNr:	SNIC 2014/1-268
Project Type:	SNIC Medium Compute
Principal Investigator:	Kwangho Nam <kwangho.nam@uta.edu>
Affiliation:	Umeå universitet
Duration:	2014-10-01 – 2015-10-01
Classification:	10407 10603 10402
Homepage:	http://www.chemistry.umu.se/english/
Keywords:

Abstract

The long term goal of this project is to elucidate the lesion discrimination mechanism of DNA repair enzymes. My lab is currently carrying out two simulation projects involved in the base-excision repair (BER) systems: human 8-oxoguanine DNA glycosylase (hOGG1) and DNA polymerase β (polβ). hOOG1 is a key enzyme searching and removing DNA mutations caused by oxidative damge to guanine (G), known as 8-oxoguanine (oxoG). Our goal is to elucidate details mechanisms of (1) how the enzyme locates lesions in vast excess of normal DNA and (2) multistep reaction pathways that it utilizes to perform the catalytic removal of the damaged DNA. This work will be carried out in collaboration with Prof. Gregory Verdine (Harvard University, USA), whose lab has solved two sets of high-resolution structures of hOGG1 in action, denoted as the intra- and the extra-helical complex structure, respectively. Based on their structures, we will use all-atom MD simulations to evaluate the thermodynamic stability of the G vs. oxoG to understand energetic difference between the two nucleotides in the protein/DNA complex. Specifically, we will use μs-long MD simulations and the string method (under continued development in our laboratory in collaboration with Dr. Victor Ovchinnikov, Harvard University, USA) to construct reversible transition paths between the intra- and extra-helical intermediates and to compute free energy changes along the determined paths. Over the last several months, we have been carrying out the proposed simulation study, and will continue the proposed simulation during the coming allocation period. The enzyme polβ is an error-prone base-excision repair DNA polymerase that preferentially induces transition mutations over transverse mutations (78 % vs. 11 %). Polβ is overexpressed in many cancer cells and overexpression of the enzyme in mammalian cells have been shown to significantly increase spontaneous DNA mutations. In collaboration with Prof. Seongmin Lee (University of Texas at Austin, USA), we aim to understand how polβ recognizes the damaged DNA base before its insertion into DNA. In particular, Prof. Lee’s lab recently solved the structures of polβ in complex with normal and damaged nucleotides in the open and the closed conformational states (private communication). Based on these structures, we are currently carrying out MD simulations to elucidate the role of protein dynamics on the discrimination of matched versus mismatched base pairs. During the coming allocation period, we will continue the MD simulations. In addition, we plan to 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. This information will provide new insight regarding the preferential insertion of certain base mismatches by polβ. The proposed simulations are to be performed in explicit water and thus 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).