Unraveling the role of (6-4) Photolyase in DNA repair through homology modeling, consensus docking, and MD simulations

COMP 202

Chris Harrison, charris5@nd.edu and Olaf Wiest, owiest@nd.edu. Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670
(6-4) photolyase repairs the (6-4) DNA photolesion, 1, via a light-induced electron-transfer (ET) catalyzed cycloreversion. Site-directed mutagenesis studies have previously suggested the crucial hydrogen donor/acceptor role of two active site histidines. In the absence of an x-ray structure of the enzyme-substrate complex, the details of enzymatic contributions to the repair reaction remain unclear. Homology modeling to CPD photolyase was used to construct a (6-4) photolyase enzyme model with the bound cofactors, FADH and HDF. Consensus docking of 1 followed by minimization and NVT equilibrations provided several refined models of the enzyme-substrate complex and identified the active site as the only binding position for 1. Catalytically relevant histidines were found in contact with 1, reinforcing their role as hydrogen donors/acceptors in the mechanistic pathways to yield two thymines. MD simulations of the enzyme-substrate complex were used to investigate the enzymatic contributions to this light-induced ET catalyzed DNA repair reaction.