Using the Theozyme Model to Study the Dynamical Mechanism of the Post-Transition State Bifurcation Reaction by NgnD Enzyme

Post-transition state bifurcation (PTSB) is a fundamental process in which a single transition state leads to multiple products. This phenomenon is important in both biological and chemical contexts and offers valuable insights into reaction mechanisms and their applications. The theozyme model, which focuses on key residues within enzymes, offers a computationally efficient method for studying these processes while preserving the enzyme's catalytic properties. This approach enhances our understanding of how enzymes stabilize and direct the transition state, thereby influencing product distribution and selectivity. In this study, we investigate the dynamics and regulatory mechanisms of the PTSB reaction catalyzed by the enzyme NgnD. The enzyme NgnD facilitates a cycloaddition reaction that produces both [6 + 4] and [4 + 2] adducts, with a preference for the [6 + 4] adduct. By analyzing the potential energy surface, bond length distribution, and interactions between the theozyme and the ambimodal transition state, we elucidate the role of the enzyme's active site residues in determining product selectivity. We illustrate how these key residues contribute to the formation of different adducts, providing insights from various perspectives. Using theozyme models, we propose how the four most influential active residues collectively might control the direction of adduct formation through their cumulative effects.