In the quest for novel, renewable energy sources and green industrial processes, a new player has emerged: enzymes. A Northeastern University Ph.D. student found that enzyme active sites are actually multilayer assemblies on the nanometer scale. Heather Brodkin’s findings discussed in her thesis served as the basis for a proposal submitted to the National Science Foundation that resulted in a $410,000 grant to study how nature designs enzymes and protein molecules that serve as highly specific catalysts for chemical reactions in living systems.

“Enzymes may be the ideal catalysts for green industrial processes as they are energy efficient, highly selective, clean, and tend not to produce unwanted byproducts,” said Brodkin.

Working with professor Mary Jo Ondrechen at Northeastern, Brodkin first gathered computational and bioinformatics evidence for the larger enzyme active sites. She performed experiments on nitrile hydratase, an enzyme used in the “green” industrial productions of amides, and was able to show that amino acids in the second and third layers contribute to the catalyzed reaction rate.

Under the tutelage of Ondrechen and Penny J. Beuning, assistant professor of chemistry and chemical biology, Northeastern students will use Brodkin’s data and explore the roles played by amino acids that are nanometers away from the site of reaction in order to understand how they contribute to the catalytic rate and the specificity of the enzyme.

“Understanding how nature engineers enzymes is an important problem and will provide guidance to new efforts in protein engineering,” said Ondrechen, professor of chemistry and chemical biology. “Heather’s work is the perfect example of the groundbreaking scientific research taking place at the University.”