In silico simulations for prediction and modeling of protein engineering within catalytic subunit of direct electron transfer type FAD glucose dehydrogenase for increases in substrate specificity and structural stability.

Abstract

The bacterial flavin adenine dinucleotide (FAD) glucose dehydrogenase (FADGDH) is composed of three subunits; 1) a catalytic subunit which belongs to the glucose-methanol-choline (GMC) oxidoreductase family contains an FAD cofactor and 3Fe-4S cluster in its redox center, 2) a hitchhiker protein subunit functioning in the bacterial TAT secretion system, and 3) a membrane-bound subunit with three heme c moieties, responsible for the transfer of electrons between the active-site cofactor and external electron acceptors. The presence of the electron transfer subunit makes this enzyme able to transfer electron directly to the electrode, thereby designates this enzyme as a direct electron transfer (DET) type GDH. The recent X-ray crystal structure elucidation of its catalytic subunit complexed with small subunit, revealed the unique substrate binding cavity of this enzyme. This enzyme was then mutated within its substrate pocket to increase substrate specificity towards glucose as a validation for later energy minimization and molecular dynamics simulations using AMBER MD. Modeling both the FAD and 3Fe-4S cluster elucidated a new methodology for modeling proteins involving covalent bonding of cofactors and namely metal ion cluster harboring proteins. From this modeling, the electron transfer pathway involving both cofactors and metal ion clusters can be further investigated in DET type enzymes. With these new modeling techniques, we can take a new approach in designing future mutational candidates by first evaluating them in silico then applying those results to our wet lab testing for higher throughput and a more targeted approach in designing and creating mutations.