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)
BERN2014Background
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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