Computational Simulations of DNA Transaction Enzymes - Application and Development

Computational Simulations of DNA Transaction Enzymes: Application and Development Project Summary Computational simulations based on classical molecular dynamics (MD) and hybrid quantum mechanical (QM)/molecular mechanical (MM) methods have been shown to provide a very important tool to investigate the reaction mechanism of enzymes with atomic level detail. Our long-term goal is to develop accurate QM/MM methods to understand the mechanism, structure and function of enzymes involved in DNA transactions by computational simulations. Both of these approaches have been pivotal to achieve detailed understanding of certain aspects of DNA transaction enzymes. The accurate synthesis, maintenance, repair, and modification of DNA is crucial for organismal survival since errors in DNA can lead to the onset of different diseases. Therefore, enzymes related to DNA transactions need to perform their activities accurately and efficiently. Mutations arising from exogenous or endogenous factors can result in changes that affect the structure and/or function of these enzymes. There are a large number of enzyme families involved in the synthesis, repair and modification of DNA. To this end, the goals of the present proposal are: 1) To improve the accuracy of computational simulations by continuing the development of LICHEM, our QM/MM software, which interfaces QM programs with advanced anisotropic/polarizable force fields (GEM and AMOEBA) to accurately describe the MM environment; and to improve the sampling of QM/MM simulations using machine learning approaches for applications with polarizable force fields. 2) To apply these techniques to understand evolutionary convergence of function on DNA synthesis proteins; how distal mutations affect these functions and other functions on DNA synthesis and other DNA transaction enzymes; and exploit this knowledge to develop inhibitors that can be used as therapeutics for specific DNA polymerases and iron/2-oxoglutarate enzymes related to DNA transactions.