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Substrate binding versus escape dynamics in a pH-affected fungal beta-glucosidase revealed by molecular dynamics simulations

Solhtalab, Mina, Flannelly, David F., Aristilde, Ludmilla
Carbohydrate research 2019 v.472 pp. 127-131
Trichoderma reesei, active sites, beta-glucosidase, catalytic activity, cellobiose, fungi, glucose, molecular dynamics, mutagenesis, pH, simulation models
The cellulolytic ability of fungal species is important to both natural and engineered biocycling of plant matter. One essential step is the conversion of cellobiose into glucose catalyzed by beta-glucosidases. Mutagenesis studies have implicated altering the substrate binding pocket to influence the pH-activity profile of this enzyme. However, structural understanding of the pH-affected substrate binding environment is lacking. Here we conducted molecular dynamics simulations of fully hydrated TrBgl2, a beta-glucosidase of Trichoderma reesei, equilibrated at its optimal pH (pH 6) and two unfavorable pHs (pH 5 and pH 7.5). We identified structural arrangement of specific residues that facilitated substrate escape from the catalytic site at pH 5 but locked the bound substrate in an unfavorable orientation at pH 7.5. For comparative analysis, we also performed simulations of a mutated TrBgl2 with previously demonstrated improved catalysis as a function of pH. We captured the responsible conformational changes in the engineered substrate binding pocket.