Modeling of Methyl Transfer Reactions in S-Adenosyl-L-Methionine Dependent Enzymes

A very important trend for studying biomolecules is computational chemistry. In particular, nowadays it is possible to use theoretical methods to figure out the catalytic mechanism of enzyme reactions. Quantum chemistry has become a powerful tool to achieve a description of biological processes in enzymes active sites and to model reaction mechanisms. The present thesis uses Density Functional Theory (DFT) to investigate catalytic mechanism of methyltransferase enzymes. Two enzymes were studied – Glycine N-MethylTransferase (GNMT) and Guanidinoacetate Methyltransferase (GAMT). Different models of the enzyme active sites, consisting of 20 to 100 atoms, are employed. The computed energetics are compared and are used to judge the feasibility of the reaction mechanisms under investigation. For the GNMT enzyme, the methyl transfer reaction was found to follow an SN2 reaction mechanism. The calculations demonstrate that the mechanism is thermodynamically reasonable. Based on the calculations it was concluded that hydrogen bonds to the amino group of the glycine substrate lower the reaction barrier, while hydrogen bonds to carboxylate group raise the barrier. In the GAMT enzyme the methyl transfer reaction was found to follow a concerted asynchronous mechanism which includes transfer of a methyl group accompanied by a proton transfer taking place simultaneously in the same kinetic step. The calculated barrier agrees well with the experimental rate constant.