TCB Publications - Abstract

Rafael C. Bernardi, Isaac Cann, and Klaus Schulten. Molecular dynamics study of enhanced Man5B enzymatic activity. Biotechnology for Biofuels, 7:1-8, 2014. (PMC: PMC4074406)

BERN2014 Background Biofuels are a well-known alternative to the largely used fossil-derived fuels, however the competition with food production is an ethical dilemma. Fortunately a solution is offered by second-generation biofuels, which can be produced from agricultural waste, or more specifically, from plant cell wall polysaccharides. The conversion process involves typically enzymatic hydrolysis of lignocellulosic biomass and then separation of its constituent sugars that are further fermented to produce ethanol. Over the years, several technologies have been developed that allow this conversion process to occur and the objective is now to make this process cost-competitive in today’s markets. Results We observe that reduction of enzymatic efficiency in the presence of gluco- oligosaccharides is associated with a loss of the enzyme’s flexibility, the latter being required to bind new substrate, while the presence of manno-oligosaccharides does not pose this problem. Molecular dynamics simulations identify key contacts between substrates and the enzyme catalytic pocket that might be modified through mutation to prevent loss of enzymatic efficiency. Conclusions Based on previous experimental studies and the new molecular dynamics data, we suggest that cellohexaose in the active site pocket inhibits or slows down enzymatic activity. Such mechanism is reasonable since the gluco-oligosaccharide substrate, when attached to the catalytic pocket, takes longer to leave the pocket and thus prevents other substrates to reach the active site. The insight is of crucial importance since the inhibition of enzymes by the enzymatic product or by an unsuitable substrate is a major technological problem reducing the competitiveness of second-generation biofuel production.

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