Scientists have prototyped a new method to “rationally engineer” enzymes to deliver improved performance. They have devised an algorithm, which takes into account the evolutionary history of an enzyme, to pinpoint where mutations could be introduced with a high probability of generating functional improvements.
His work, published today in a leading magazine Nature Communications — could have significant and wide-ranging impacts on a range of industries, from food production to human health.
Enzymes are fundamental to life and key to developing innovative medicines and tools to address societal challenges. They have evolved over billions of years through changes in the amino acid sequence that underpins their three-dimensional structure. Like beads on a string, each enzyme is composed of a sequence of several hundred amino acids that encodes its three-dimensional shape.
With one of 20 possible amino acid ‘beads’ at each position, there is an enormous amount of sequence diversity possible in nature. After forming their three-dimensional shape, enzymes perform a specific function, such as digesting proteins in our diet, converting chemical energy into strength in our muscles, and destroying bacteria or viruses that invade cells. If you change the sequence, you can alter the 3D shape, and that usually changes the functionality of the enzyme, sometimes making it completely ineffective.
Finding ways to improve enzyme activity would be hugely beneficial for many industrial applications and, using modern molecular biology tools, it is simple and cost-effective to engineer changes to amino acid sequences to facilitate improvements in their performance. However, randomly introducing just three or four changes to the sequence can cause a dramatic loss of activity.
Here, scientists report a promising new strategy to rationally engineer an enzyme called “betal-lactamase.” Instead of introducing random mutations with a scattershot approach, researchers at the Broad Institute and Harvard Medical School developed an algorithm that takes into account the evolutionary history of the enzyme.
“At the heart of this new algorithm is a scoring function that exploits thousands of beta-lactamase sequences from many diverse organisms. Instead of a few random changes, up to 84 mutations were generated in a sequence of 280 to improve 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 surprisingly, the newly designed enzymes improved their activity and stability at higher temperatures.”
Eve Napier, a second-year PhD student at Trinity College Dublin, determined the experimental 3D structure of a newly designed beta-lactamase, using a method called X-ray crystallography.
Their 3D map revealed that despite changes in 30% of the amino acids, the enzyme had an identical structure to wild-type beta-lactamase. It also revealed how coordinated changes in amino acids, introduced simultaneously, can efficiently stabilize the 3D structure, in contrast to individual changes that normally impair the enzyme structure.
Eve Napier said: “Overall, these studies reveal that proteins can be engineered to improve their activity by dramatic ‘jumps’ into new sequence space.
“The work has a wide range of applications in industry, in processes that require enzymes for food production, enzymes that degrade plastic and those relevant to human health and disease, so we are very excited about the future possibilities.” “.