Molecular Dynamics Simulations of 4 GALC Variants Causing Krabbe Disease

Krabbe disease, also known as globoid cell leukodystrophy, is a rare lysosomal disorder affecting the white matter of the central and peripheral nervous systems. It is characterized by neurodegeneration, with infantile-onset Krabbe disease as the most common form, typically diagnosed within the first year of life and associated with high morbidity and mortality. This autosomal recessive disease is caused by mutations in the GALC gene, which encodes the lysosomal enzyme β-galactocerebrosidase (GALC). This study focuses on examining the structural effects of 4 GALC variants (Gly59Arg, Ser68Phe, Thr278Ile, and Ser303Phe) found as mutations in the GALC gene of patients with Krabbe disease. To investigate the effects of these mutations on protein structure, structural models of human GALC were built. These models served as the basis for a series of all-atom molecular dynamics (MD) simulations to analyze the structural stability of the wild type and the mutated enzyme variants. Since GALC is subcellularly localized in the lysosome (pH 4.5 to 5.5), MD simulations were performed with protonation states corresponding to pH 4.5. Differences in protein flexibility and intramolecular interactions between the wild type and the variants were observed. Similarly, we detected the effects of the mutations on the substrate-binding residues and their vicinity, although the mutation sites themselves do not lie within the active site/binding site of the enzyme. Overall, our MD simulations shed light on how these mutations affect the structure of human GALC in the lysosome and offer possible explanations as to why these mutations have an effect on enzyme function.