FROM STRUCTURE TO QUANTUM MECHANICS SIMULATIONS: COMPUTATIONAL STUDIES OF GLYCOPROCESSING ENZYMES

Carbohydrate-active enzymes, specifically glycoside hydrolases (GHs), employ finely tuned molecular mechanisms for substrate recognition and catalysis of complex carbohydrates, which are major biopolymers in nature. Although substrate distortion has traditionally been considered essential to facilitate glycosidic bond cleavage, recent studies demonstrate that some GHs can catalyze reactions without this conformational change. Our group has characterized novel glycosidases, one of them featuring a tunnel-shaped active site, found in several crystallographic structures solved. Through microsecond timescale molecular dynamics simulations, combined with principal component analysis (PCA) and clustering, we elucidated the concerted movements controlling substrate release. Furthermore, hybrid quantum mechanics/molecular mechanics (QM/MM) free-energy calculations revealed the catalytic itinerary of this enzyme. Collectively, these results provide a comprehensive molecular-level understanding of the enzyme’s mechanism for efficiently hydrolyzing carbohydrate substrates. This work was supported by São Paulo Research Foundation (FAPESP) (24/22565-4; 21/04891-3)