Scientists design algorithm to construct improved enzymes

Scientists have prototyped a new method for “rational engineering” of enzymes to ensure better performance. They devised an algorithm that takes into account the evolutionary history of the enzyme to indicate where mutations with a high probability of providing functional improvements could be introduced.

Their work – published in the journal today The nature of communication—can have a significant and wide-ranging impact on a range of industries, from food production to human health.

Enzymes are essential to life and key to the development of innovative medicines and tools to solve society’s problems. They have evolved over billions of years due to changes in the amino acid sequence that underlies their 3D structure. Like beads on a string, each enzyme consists of a sequence of several hundred amino acids that encode its 3D shape.

With one of 20 amino acid “balls” possible at each position, enormous sequence diversity is possible in nature. After forming their 3D shape, enzymes perform a specific function, such as digesting protein in the diet, converting chemical energy into power in our muscles, and destroying bacteria or viruses that invade cells. If you change the sequence, you can disrupt the 3D shape, which usually changes the functionality of the enzyme and sometimes makes it completely useless.

Finding ways to improve enzyme activity would be extremely beneficial for many industrial applications, and with modern tools in molecular biology, it is simple and cost-effective to design changes in amino acid sequences to facilitate improved performance. However, randomly introducing just three or four changes into a sequence can lead to a dramatic loss of their activity.

Here, researchers report a promising new strategy to rationally engineer an enzyme called “beta-lactamase.” Instead of introducing random mutations in the scattergun approach, researchers at the Broad Institute and Harvard Medical School developed an algorithm that takes into account the enzyme’s evolutionary history.

“At the heart of this new algorithm is a scoring function that uses thousands of beta-lactamase sequences from many different organisms. Instead of a few random changes, up to 84 mutations were generated in sequence 280 to increase functional performance,” said Dr. Amir Khan, Associate Professor in the School of Biochemistry and Immunology at Trinity College Dublin, one of the co-authors of the research.

“And remarkably, the newly designed enzymes had both improved activity and stability at higher temperatures.”

Eve Napier, second year Ph.D. student at Trinity College Dublin determined the 3D experimental structure of a newly designed beta-lactamase using a method called X-ray crystallography.

Her 3D map revealed that despite the 30% amino acid changes, the enzyme had an identical structure to wild-type beta-lactamase. It also revealed how coordinated changes in amino acids, introduced simultaneously, can effectively stabilize the 3D structure—as opposed to individual changes that typically disrupt the enzyme’s structure.

Eve Napier said: “Overall, these studies reveal that proteins can be modified to improve activity by making dramatic ‘jumps’ into new sequence space.

“This work has wide applications in industry, in processes that require enzymes for food production, enzymes for breaking down plastics and those that are important for human health and disease, so we’re quite excited about the future possibilities.”