Protein Designers Roll Out A Barrel

The goal of de novo protein design is to understand protein architecture well enough to create new enzymes or other useful proteins from first principles, without modifying natural proteins. There have been many successes in the field, such as the design of globular proteins that fold with hydrophobic interiors and hydrophilic exteriors.

But the field has experienced at least one notable failure. As many as 10% of known enzymes adopt the cylindrically shaped triosephosphate isomerase-barrel (TIM-barrel) fold. For 28 years, protein designers have tried to create a TIM-barrel protein from scratch. But TIM-barrel design sequences have never folded into any tertiary structure—a three-dimensional assembly of α-helices, β-strands, and/or connecting loops—much less a TIM-barrel.

Now, a collaborative team reports that they have created the elusive barrel-shaped fold (Nat. Chem. Biol. 2015, DOI: 10.1038/nchembio.1966).

The researchers, led by Po-Ssu Huang and David Baker of the University of Washington, Seattle, and Birte Höcker of the Max Planck Institute for Developmental Biology, used rational design principles and calculations from the Baker group’s Rosetta protein modeling and design software to create sequences likely to fold into a TIM-barrel’s eight α-helices, eight β-strands, and connecting loops. They combined different features into an initial set of 22 sequences. They studied common elements in five sequences that folded well and zeroed in on a single prospect. The researchers then used X-ray crystallography to confirm that the sequence folded into a TIM-barrel conformation.

The work “represents a landmark achievement,” says macromolecule designer Deepesh Nagarajan of the Indian Institute of Science. “The implications are numerous,” including opening new avenues in enzyme design.

Indeed, the collaborative team now hopes to use designed barrel folds to create a new generation of custom-designed enzymes and as structural components of designed protein complexes, Huang says.