Molecular dynamics of cellulose enzymatic hydrolysis and QM / MM simulations of chemical reactions in biomolecular systems

Abstract

The post-doctoral fellow will extensively apply modern techniques of MD simulations to study proteins of interest to cellulosic biomass conversion into simple soluble sugars. Our interest 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 QM/MM methods to polysaccharides docked into the corresponding enzyme active sites. Similar approaches may be used to study phosphorylation and acetylation reactions in other proteins, especially in nuclear receptors, which is an important class of proteins that our group has been studying for nearly a decade. Generalized correlation maps in protein complexes are also of interest of our Cepid Center, particularly on NRs and other transcription factor regulators. Recently, we obtained outstanding results regarding allosteric mechanism in NRs using generalized correlations and community network analysis of the full PPARg/RXR/DNA complex. Here we propose to address a natural extension of this work by investigating community network analysis in the groundbreaking CRISPR/cas protein complexes. (AU)