(12f) Mechanistic Study of Glycyl Radical Enzyme

Yang, Z., Massachusetts Institute of Technology
Kulik, H. J., Massachusetts Institute of Technology
Glycyl radical enzymes (GREs), such as pyruvate formate lyase (PFL), choline trimethylamine-lyase (CutC), and hydroxyproline dehydratase (HypD), employ protein-based radical intermediates to catalyze a variety of reactions involving C-C/C-N bond formation or cleavage. These enzymes were recently found to be abundant in the human gut microbiome and have been linked to a series of diseases. Here, we focus specifically on the mechanistic investigation of glycyl radical enzymes. The detail of the chemical transformations, the catalytic function of the active site residues, and the potential role of protein dynamics will be discussed. We combined quantum mechanics, multiscale quantum mechanics/molecular mechanics, and molecular dynamics simulations to unveil the mechanism and catalytic action of the enzymes, focusing on both the radical transfer and substrate activation. We observe that protonation states of the substrate and surrounding active site residues have a strong influence on protein conformation and dynamics, leading to changes in protein structure that enhance substrate reactivity. These insights will potentially inform new strategies to engineer GREs for chemical synthesis and drug design.