(376as) Modeling Inhibition of Biocatalysts By Ionic Liquids Using Metadynamics

Alamdari, S., University of Washington
Pfaendtner, J., University of Washington
Ionic liquid (ILs) are salts that are liquid at room temperature and possess a number of unique and tunable properties among which include; high dissolution of cellulosic biomass, and limited inhibition and degradation of certain enzymes when solvated in low concentrations.[1, 2] These properties are exciting in the field to biocatalysis, as they provide a stark contrast in stability and safety compared to the harsh organics currently implemented in industry. Similarly, the selection of unique cation/anion pairs may result in a number of tunable properties.[3] IL solvents provide a promising framework as we work towards developing a one-step process for the conversion of biomass into fuel (i.e., both the pretreatment of biomass and enzymatic hydrolysis occurring in a single batch process). However, little is known about the mechanisms by which ILs inhibit the function of many biocatalysts. With the goal of using simulations to guide the rational design of biocatalysts suspended in ILs, we have used molecular dynamics to understand their deactivation mechanisms. Of the many modes by which IL solvents may deactivate proteins, we are specifically interested in probing their effects on protein ligand binding.

To this end, we will present our work on a model system: a retaining cellulase (endocellulase 1) in complex with a cellotetraose molecule, solvated at varying concentrations of an aqueous IL (1-butyl-3-methylimidazolium chloride) solution. Preliminary results indicate that preferential solvation of cellulose in ionic liquids, and inhibition of important binding site residues by cations may result in a decreased affinity between cellulose cellulase binding. To overcome the time-scale limitations of classical simulations and further understand the energetic driving forces of these interactions, we have implemented the funnel metadynamics variant to increase sampling of ligand binding and unbinding events.[4] To this end, we hope to gain a better molecular understanding of how protein-solvent, ligand-solvent, and protein-ligand interactions are impacted in the presence of ILs.


[1] V. Jaeger, P. Burney, J. Pfaendtner, “Comparison of Three Ionic Liquid-Tolerant Cellulases by Molecular Dynamics”, Biophys. J., 2015, 108(4) 880–892.

[2] P. Engel, R. Mladenov, H. Wulfhorst, G. Jager, & A. C. Spiess. “Point by point analysis: how ionic liquid affects the enzymatic hydrolysis of native and modified cellulose”, Green Chem., 2013, 12, 1959-1966.

[3] Wilkes, J. S. “Properties of ionic liquid solvents for catalysis”, J. Mol. Catal. A, 2004, 11-17, 1381-1169.

[4]V. Limongelli, M. Bonomi, M. Parrinello, "Funnel Metadynamics as accurate binding free-energy method", PNAS, 2013, 110 (16) 6358-6363