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.”