Molecular dynamics simulations of cellulase homologs in aqueous 1-ethyl-3-methylimidazolium chloride

Pretreating biomass using ionic liquids (ILs) can decrease cellulose crystallinity and lead to improved hydrolysis. However, cellulase activity is often reduced in even low concentrations of ILs, necessitating complete washing between pretreatment and hydrolysis steps. To better understand how ILs interact with enzymes at the molecular scale, endoglucanase E1 from Acidothermus cellulolyticus was simulated in aqueous 1-ethyl-3-methylimidazolium chloride ([Emim]Cl). Homologs with differing surface charge were also simulated to assess the role of electrostatic interactions between the enzyme and the surrounding solvent. Chloride anions interacted with the enzyme surface via Coulomb or hydrogen bond interactions, while [Emim] cations primarily formed hydrophobic or ring stacking interactions. Cations strongly associated with the binding pocket of E1, potentially inhibiting the binding of substrate molecules. At elevated temperatures, cations also disrupted native hydrophobic contacts and caused some loss of secondary structure. These observations suggested that both cations and anions could influence enzyme behavior and that denaturing and inhibitory interactions might both be important in aqueous IL systems.