In silico modelling of the function of disease-related CAZymes

In silico modelling of proteins comprises a diversity of computational tools aimed to ob-tain structural, electronic, and/or dynamic information about these biomolecules, captur-ing mechanistic details that are challenging to experimental approaches, such as elu-sive enzyme-substrate complexes, short-lived intermediates, and reaction transition states (TS). The present article gives the reader insight on the use of in silico modelling tech-niques to understand complex catalytic reaction mechanisms of carbohydrate-active en-zymes (CAZymes), along with the underlying theory and concepts that are important in this field. We start by introducing the significance of carbohydrates in nature and the en-zymes that process them, CAZymes, highlighting the conformational flexibility of their car-bohydrate substrates. Three commonly used in silico methods (classical molecular dy-namics (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and enhanced sampling techniques) are described for nonexpert readers. Finally, we provide three ex-amples of the application of these methods to unravel the catalytic mechanisms of three disease-related CAZymes: beta-galactocerebrosidase (GALC), responsible for Krabbe disease; alpha-mannoside beta-1,6-N-acetylglucosaminyltransferase V (MGAT5), involved in cancer; and O-fucosyltransferase 1 (POFUT1), involved in several human diseases such as leukemia and the Dowling-Degos disease.