(189b) Probing Enzyme Catalyzed Hydrolysis of Cellulose in Ionic Liquids Using Enhanced Sampling Techniques

Alamdari, S., University of Washington
Pfaendtner, J., University of Washington
Ionic Liquids could transform the biofuel industry from an inefficient multi-step process requiring harsh organics and extreme processing conditions into a one-step, environmentally friendly process. They possess a variety of unique properties (e.g. negligible flammability, and vapor pressure), are hailed as “green-solvents”, demonstrate wide chemical and thermal stability, and can be easily recycled.1 Unfortunately, ILs are known to negatively affect the activity of cellulases. With the goal of rapid conversion of biomass to glucose, molecular level detail can assist in the rational design of enzymes and ILs. The work in this poster will demonstrate our approach to gaining molecular level insight of the Cel5A catalyzed hydrolysis of cellotetraose in an aqueous IL 1-butyl-3- methylimidazolium chloride [BMIM][Cl] solution.

The key challenge in modeling these systems is to find the balance needed between computational cost and accuracy. The hybrid quantum mechanics/molecular mechanics (QM/MM) approach is a method that can be used to probe these enzymatic reactions with the strength of QM accuracy, and the speed of MM forcefields. Still, the timescales needed to observe these phenomena occur on much larger scales than are computationally affordable. Enhanced sampling techniques can be used to circumvent these issues. For example in metadynamics2, a powerful enhanced sampling algorithm, a time dependent bias is applied to a few coarse slow degrees of freedom to enhance phase space exploration by discouraging the system from visiting previous states. These methods have been used on a number of glycoside hydrolase catalyzed reactions in water3,4 however, these methods have never been applied to study reactions in ILs. Our results indicate that the presence of IL in the active site plays an important role on the thermodynamics of the glycosylation reaction. A number of variants of metadynamics have been developed to further improve sampling, and speed up convergence. This poster presents our results and the challenges of applying the enhanced sampling technique well-tempered5 metadynamics with adaptive gaussians6 to resolve molecular level insight of these systems.


[1] J. Serra Moreno, S. Jeremias, A. Moretti, S. Panero, S. Passerini, B. Scrosati, G.B. Appetecchi. “Ionic liquid mixtures with tunable physiochemical properties”, Electrochimica Acta., 2015, 599-608.

[2] A. Laio and M. Parrinello. “Escaping free energy minima”, Proc. Natl. Acad. Sci. USA, 2002, 99:12562–12566.

[3] L. J. Petersen, P. Reilly, A. Ardèvol, C. Rovira. “Mechanism of cellulose hydrolysis by inverting GH8 endoglucanases: A QM/MM metadynamics study” J. Phys. Chem. B., 2009. 113(20), 7331-7339.

[4] A. Ardèvol, J. Iglesias-Fernández, C. Rovira, X. Biarnés, A. Planas. “Catalytic itinerary in 1,3-1,4-β-glucanase unraveled by QM/MM metadynamics. Charge is not yet fully developed at the oxocarbenium ion-like transition state” J. Am. Chem. So., 2011. 133(50), 20301-20309.

[5] A. Barducci, G. Bussi, M. Parinello. “Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method”, Phys. Rev. Lett, 2008, 100(2), 020603.

[6] D. Branduari, G. Bussi, M. Parrinello, “Metadynamics with Adaptive Gaussians”, J. Chem. Theory Comput., 2012. 8,2247-2254