Non-functional β-galactocerebrosidase (GALC), a family 59 glycoside hydrolase (GH), is responsible for Krabbe disease, a neurodegenerative disease that is still incurable. The first crystallographic structure of the Michaelis complex (MC) of GALC that was obtained  shows that the galactoside saccharide at the -1 subsite adopts an unusual chair conformation, whereas other β-GHs often feature distorted substrate conformations that are preactivated for catalysis . However, the GALC structure was determined under non-reactive conditions (non-optimal pH), which could affect the conformation of the substrate. In this work, we address this issue by means of quantum mechanics/molecular mechanics (QM/MM) metadynamics methods [2,3], uncovering the substrate conformation along the reaction coordinate on GALC.
- Hill CH.; Graham SC.; Read RJ.; Deane JE. Structural snapshots illustrate the catalytic cycle of β-galactocerebrosidase, the defective enzyme in Krabbe disease. PNAS 2013, 110(51), 20479-84.
- Ardèvol A.; Rovira C. Reaction mechanisms in carbohydrate-active enzymes: glycoside hydrolases and glycosyltransferases. Insights from ab initio quantum mechanics/molecular mechanics dynamic simulations. JACS. 2015, 137(24), 7528-47.
- Laio A.; Parrinello M. Escaping free-energy minima. PNAS 2002, 99.20, 12562-12566