Computational Simulations of DNA Associated Enzymes Using Both Quantum and Molecular Mechanics Methods

This dissertation concerns the development and usage of computational methods to explore a variety of biological systems involved in DNA replication or repair. First, we improve the polarization component of our group’s quantum mechanics/molecular mechanics (QM/MM) software, Layered Interacting Chemical Models (LICHEM), by incorporating the effects of induced dipoles from the MM into the Hamiltonian. We found that one round of induced dipoles does not improve the interaction energy between the QM and MM regions. The polarization catastrophe results in much higher interaction energies. Second, we explore the effects of mutations on the β-clamp of DNA Polymerase III (E. coli). We used molecular dynamics (MD) to simulate 6 different variants and found that there is a large reduction in the dynamic motion of all variants as well as a change in the networks formed between the domains of each monomer. Third, we used MD and QM/MM methods to study the effects of 2 different mutations on the β-clamp. This work simulated both the β-clamp and the Pol III core subunits including α, ϵ and θ. These distal mutations change the DNA conformation found within the system altering the exonuclease reaction within the ϵ subunit. Fourth, we used MD to determine how the drug, remdesivir, and two analogues affect the structure of RNA-dependent RNA Polymerase (RdRp) when saturated throughout the dsRNA. Incorporation of this drug along the RNA chain was found to have lead to an overall destabilization of the polymerase. Additionally, remdesivir and the two analogues studied had higher binding affinities than the natural substrate indicating their effectiveness. Fifth, we explore the mechanism of primer synthesis in the CRISPR-Associated Primase Polymerase from Marinitoga piezophila. Here, we used SAPT0 calculations to determine the important components of the primer initiation complex. Last, we provide a review of all computational studies carried out on 2 families of Iron and α–ketoglutarate–Dependent enzymes. We also discuss new results for 2 enzymes not yet explored in the literature.