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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. Using the strategy of microorganisms, several enzymes are employed in the production of this advanced biofuel. However the biofuel industry faces problems such as the loss of efficiency of the enzymes that arises over time due to intermittent high concentration of non-suitable substrates. Simulations can guide biochemical experiments aimed at investigating the mechanism that makes the enzymes vulnerable to such substrates, helping the development of more efficient and, thereby, less costly enzymes. A recent study, based on molecular modeling with NAMD, reported that reduction of efficiency in an important enzyme, know as Man5B, is associated with a loss of the enzyme's flexibility. Molecular dynamis simulations showed that a poor substrate slows down a crucial opening and closing movement of the enzyme's catalytic cleft while a good substrate keeps the movement almost intact. The insight is of crucial importance since it suggests mutations to enzymes presently employed in second-generation biofuel production that need to be replaced less often and, thereby, rendering the production more cost-effective. Read more on our biofuels website.