Molecular modeling of carbohydrate-modifying enzymes

Abstract

Here, we propose to apply modern techniques of Molecular Dynamics (MD) simulations to study enzymes of interest to cellulosic biomass conversion. The primary focus of the proposed research lies on CBHs and EGs and other enzymes from fungi and bacteria. Our interest more specifically here is to explore protein-cellulose substrate binding at the atomistic level and to understand the mechanisms of catalytic hydrolysis of the polysaccharides by the enzymes. For that, we propose applying quantum mechanics/molecular mechanics (QM/MM) methods to polysaccharides docked into the corresponding enzyme active sites. Systems such as an oligosaccharide chain docked along the catalytic active tunnel of CBH I and/or CBH II and on EGs are the primary targets. In a later stage, we will also apply metagenomic and metatranscriptomic approaches to help us to understand the best candidates (cellulases, hemicellulases and auxiliary activities) to compose a cocktail. (AU)