Biomass Depolymerization projects

Molecular Dynamics Studies of Biomass Degradation in Biofuel Production

We are developing a joint computational and experimental approach where we will take advantage of molecular modeling and dynamics tools, together with some of the fastest supercomputers available, to tackle two major problems of the second-generation biofuel industry, namely: the product inhibition and the effects of pretreatment with EBI developed polymers on hydrolysis of cellulose fibers by glycoside hydrolases. In the first, in collaboration with Dr. Doug Clark's group, we plan to address the problem of product inhibition of glycoside hydrolases, by studying mutants identified by the experimental group. In the second, in collaboration with Dr. Matt Francis's group, we will model the effects of a synthetic polymer on the cellulose fiber and also the interaction of this polymer with enzymes of the glycoside hydrolase family.

project Highlights

2014 Highlights

Two critical bottlenecks for the production of second-generation biofuels are pretreatment of the biomass and inhibition of the glycoside hydrolases enzymes by non-suitable substrates or by their own product. Employing molecular dynamics simulations, we observed that Poly(NIPAm), a polymer employed in biomass pretreatment, interacts preferably with the hydrophobic regions of the cellulose fiber. Studying the product inhibition of glycoside hydrolases, our results are indicating that the inhibition of CEL7A by its product might be directly related to the cellobiose that was just cleaved and does not leave the exit pocket because of the already high concentration of cellobiose in solution.


Published in 2014

Molecular Dynamics Study of Enhanced Man5B Enzymatic Activity, R. C. Bernardi, I. Cann, K. Schulten, Biotechnology for Biofuels, V. 7, pp. 83, June 5, 2014. 


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