It’s a real waste to break down biomass to its smallest components. ‘If you could keep part of the structure of the starch and cellulose, that would be valuable raw material for the chemical industry,’ says Marco Fraaije. As a biochemist and microbiologist specializing in enzyme engineering, he is always looking for new enzymes that can be used in industrial applications.
Earlier this month, his quest secured him a EUR 600,000 grant from Dutch research organization NWO. ‘We are going to look for enzymes that oxidize starches and other complex sugars,’ Fraaije explains. Although plenty of hydrolyzing enzymes have been described that break down complex carbohydrates into simple sugars that can be used to produce bio-ethanol, for example, few enzymes are known that can modify complex carbohydrates by oxidation. Such modified carbohydrates are a valuable resource for the chemical industry.
‘Oxidized carbohydrates can be used to make glue or plastic. But there are also applications in paper production, for example as additives that make paper water resistant.’ There are chemical ways to oxidize complex sugars, but, says Fraaije, these are neither very specific nor very environmentally friendly. ‘With chemical methods you can oxidize all carbons in a sugar molecule, but enzymes will oxidize just one specific carbon.’ And they work best in water at room temperature, which is clean and energy efficient.
The grant he has been awarded will enable him to investigate a new class of oxidizing enzymes. ‘We originally found one such enzyme, and based on its genome sequence and 3D protein structure we discovered there are potentially hundreds more, mostly in fungi and bacteria.’ A characteristic of this class of enzymes is that they can oxidize large molecules. ‘Normally, an enzyme has an active site, like a cavity, where the reaction takes place. That limits the size of the molecules that the enzyme can accept.’
The new class has its active site on the surface. ‘More like a groove on the outside. It is still very specific in the reaction it catalyzes, but much less in the size of the molecules it will handle.’ To oxidize its target, the enzyme needs a cofactor, usually a flavin (vitamin B2) molecule. ‘It’s interesting to see that in many oxidizing enzymes, the flavin is bound by one covalent flavin-protein bond. That means it really becomes part of the enzyme. But in this new enzyme class, the flavin is attached by two covalent bonds.’
Fraaije speculates that this double bonding is meant to stop the flavin group from moving. ‘In most enzymes, movement is restricted because the flavin is basically stuck in the narrow active site. But these new enzymes have the flavin in the groove on the outside and therefore need to secure it more firmly.’ It’s an example of the puzzles nature needs to solve in order to create new functions for enzymes. ‘That is what is interesting for me as a scientist. You want to know why this double covalent bonding has evolved.’
There’s another interesting side-issue concerning the flavin cofactor. ‘I’ve discovered in the literature that humans have problems breaking down proteins when they have a covalent bond with vitamin B2. And it turns out that protein fragments with the flavin group attached are strong allergens.’ This is not something that he will tackle in his research project. ‘But it’s fascinating to see how different fields like enzyme engineering and health can be interconnected.’
Fraaije applied for the grant together with Avebe, a large food company specialized in potatoes and potato starch, and Dyadic, a small biotech firm that specializes in the production of enzymes using fungi. A PhD student and a postdoc at Fraaije’s lab will focus on characterizing the new class of enzymes. ‘We want a better understanding of the way they work.’ The industrial partners will develop interesting enzymes into commercial products. The grant is part of the NWO TA-Biomass programme, which stimulates the eco-efficient use of biomass for bulk and fine chemical production. The project will run for four years.
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