Molecular dynamics of cellulose enzymatic hydrolysis and other studies by QM/MM of chemical reactions in biomolecular systems

Abstract

In this project we propose to apply modern techniques of classical and hibrid quantum-classical MD simulations to study proteins of interest to cellulosic biomass conversion into simple soluble sugars. 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 will use quantum mechanics/molecular mechanics (QM/MM) methods to polysaccharides docked into the corresponding enzyme active sites. Similar approaches will be used to study phosphorylation (and possibly acetylation) reactions in nuclear receptors, which is an important family of hormone-binding proteins that regulate transcription of specific genes, playing a pivotal role both in cell development and metabolic functions. (AU)