Researchers design allosteric protein from scratch

In a milestone for protein engineering, researchers have designed from scratch a protein that exhibits allosteric regulation. With allostery, binding at one site of a protein affects binding or activity at a distant second site. This finding opens the door to designing controllable biological catalysts.

As a proof of concept, Marco Chino and Angela Lombardi of the University of Naples Federico II, William F. DeGrado of the University of California, San Francisco, and coworkers combined two previously designed proteins with different functions into a single protein that links these functions (Proc. Natl. Acad. Sci. U.S.A. 2020, DOI: 10.1073/pnas.2017062117). Each protein consists of a bundle of four α-helices. One protein binds a zinc-porphyrin, whereas the other catalyzes phenol oxidation.

Guided by computer simulations, the researchers stacked the proteins on top of each other, connecting them via four linkages—a complex arrangement that ensured a tight connection between the two functional parts of the new protein. The use of four linkers is a first for protein design, Chino says. When one domain binds a Zn-porphyrin, its structure shifts, slowing down the oxidation reaction in the other domain, the researchers found.

They hope they can further tune catalysis in future iterations by taking advantage of porphyrin’s light absorption. By bringing the functional sites closer to each other, it should be possible to further change the oxidation reaction rate by shining light on the bound porphyrin, DeGrado says.

Allostery is “hard even to predict in natural proteins and much harder to design,” Aitziber L. Cortajarena, who designs protein building blocks at the Center for Cooperative Research in Biomaterials–CIC biomaGUNE, writes in an email, calling the work “very interesting and significant.” The research will create opportunities for applications using allostery for responsive regulation, according to Cortajarena.