Molecular Dynamics Studies of the Structure and Dynamics of An Endoglucanase Cel9A In Ionic Liquid Solutions

Molecular Dynamics Studies of the Structure and Dynamics of an Endoglucanase Cel9A in Ionic Liquid Solutions

Hanbin Liu, Supratim Datta, Blake A Simmons and Ken Sale

Joint BioEnergy Institute, Emeryville, CA 94608 and Sandia National laboratories, Livermore, CA

Ionic liquids (ILs) are currently under intense study as solvents and as additives to macromolecules and have recently show great promise as a pretreatment of lignocellulosic biomass for the production of biofuels. Pretreatment of biomass is followed by saccharification using a cocktail of cellulase enzymes (glycoside hydrolases) that catalyze the breaking of the b1-4 glycosidic bonds of the cellulose, which was liberated from the biomass by the ionic liquid, to glucose. This process means that these cellulases must be tolerant of the ionic liquid, making the study of the structures and dynamics of cellulases in the present of ionic liquids of great current interests in biofuels research, especially in industrially relevant processes in which biomass pretreatment is consolidated with the saccharification step (simultaneous pretreatment and saccharification). In this work, we investigated the origins of the tolerance of a thermophilic family 9 cellulase (Cel9A) to ionic liquids. Cel9A is an endoglucanase that also displays exoglucanase activity and has been experimentally shown to be functional in bioprocessing relevant concentrations of the ionic liquid 1-ethyl-2methyl imidazolium acetate [C2mim][OAc]. Using all atom molecular dynamics simulations of Cel9A over a wide range of [C2mim][OAc] concentrations (weight range from 0% IL to 50% IL), we show that the cel9A structure is stable in [C2mim][OAc] over the entire 80ns simulation at these IL concentrations. We also show that, due to the slow diffusion of [C2mim][OAc] and interactions between [C2mim][OAc] and Cel9A, [C2mim][OAc] stabilizes the dynamics of Cel9A. During our simulations, [C2mim][OAc] diffused into the active site of the enzyme and interacts directly with the two catalytic residues, indicating that [C2mim][OAc] may also promote enzymatic activity by altering either the dynamics of the overall active site, the dynamics of the catalytic residues or the electrostatic environment of the active site; we are currently investigating these possibilities.