A thousand years in nature, one year in a lab: How 3D modelling is speeding enzyme evolution

Enzymes are proteins that have a wide variety of functions in the food industry, including extending shelf life, tenderising meat, shortening the time required for cheese ripening, and creating lactose-free dairy products. They do not end up as ingredients in the finished food product, but catalyse processes and carry out tasks like breaking down sugars or fats.

Novozymes’ system creates 3D computerised models of enzymes sourced from nature to help researchers identify ways in which they could be optimised for different functions.

“What takes thousands of years in nature to evolve a protein, we can speed it up to about a year,”​ Fiona Becker, department manager, R&D in baking, told FoodNavigator. “Bacteria and fungi have been evolving, adapting to various environments, and that’s where we get our enzymes from.”​

For example, Novozymes scientists might look for enzymes present in hot water springs to find those that have evolved to be tolerant to high temperatures. However, these enzymes are still not optimised for use in food.

“We can’t wait a thousand years,”​ Becker said. “We copy nature’s way of doing it and select for things that give the improvements we need in a more directed way.”​

 “Proteins have a three dimensional structure and you can make models of how you would expect them to look in a three dimensional form,” ​she added.

“You can look at how it might look in a high salt or high sugar environment…You can also simulate high temperatures and see whether it would unravel or be more flexible. You can go in and see which parts of the enzyme have the most effect on its characteristics.”​

The company produces enzymes from various microorganisms in its factories, which have been given specific genetic instructions about the types of enzymes they must make.

 “If we have a good amylase or asparaginase, it may be that we want to optimise its activity again…We could then go in and look at it in 3D and work out what amino acids could be unstable at high temperatures or could be too flexible for example,”​ she said.

As the company continues to use its 3D modelling, generating more prototype enzymes, the chances increase of finding the crucial parts of an enzyme to manipulate.

For the food industry, the result might be that a traditional synthetic ingredient could be replaced by renewable, biological materials, helping to clean up labels and, ultimately, produce foods that consumers prefer.