(133d) Absolute Ligand Binding Free Energy of Glycoside Hydrolases As a Metric for Processivity and Polysaccharide Morphology Dependence
Multiple glycoside hydrolase (GHs) families have evolved to deconstruct crystalline polysaccharides, such as cellulose and chitin, to sugars. These GHs generally act via a processive mechanism wherein a single carbohydrate chain is decrystallized from the surface, and the glycosidic linkage is processively cleaved along the chain without dissociation. This processive mechanism has long been the focus of structure-function studies, and recent biochemical studies have shown dissociation of processive cellulases is likely rate limiting in cellulose conversion. Despite being a central theme of GH research, a general molecular-level theory of processivity linked to chemical and structural features of enzyme active sites does not yet exist. Here, we hypothesize that the degree of GH processivity is directly linked to an enzyme’s ability to decrystallize a single chain from a crystal and can be quantified by the absolute ligand binding free energy. To understand the thermodynamics of processivity at the molecular level, we calculate the absolute ligand binding free energy of cellulose chains to processive members of the biologically and industrially important enzymes from GH Family 7 with Free Energy Perturbation/Hamiltonian Replica-Exchange Molecular Dynamics. Alongside available experimental observations, the computational results suggest that ligand binding free energies within a GH family correlate well with processivity. When compared to the thermodynamic work required to decrystallize cellulose chains, the calculated binding free energies suggest polymer morphologies susceptible to decrystallization by a given enzyme. Generally, the ligand binding free energy may offer a molecular-level basis for developing a generalized theory of carbohydrate processivity.