Cassie Bryan’s success at crafting a protein that worked as she intended was a long time coming. When it finally happened, after six long years, she hit the bar and celebrated with beers — and a karaoke rendition of Joan Jett’s ‘Bad Reputation’.
Bryan joined the protein-design laboratory of David Baker in 2012 as a graduate student at the University of Washington, Seattle. Her project was to design a protein that could bind to PD-1 — a protein on the surface of white blood cells that throttles the activity of the immune system.
At first, Bryan did what protein engineers have long done: she tweaked an existing natural protein to make it bind to PD-1. But, two years into her project, she decided that approach was going nowhere. And an explosion of interest in PD-1 as a cancer-immunotherapy target during that time meant her goalposts kept moving. Meanwhile, the lab was growing ever more adept at a different approach. Instead of modifying natural proteins to fit a particular need, the Baker lab began creating proteins from scratch.
Although considerably harder than conventional protein engineering, de novo protein design offers several advantages, says Brian Kuhlman, a protein engineer at the University of North Carolina at Chapel Hill, who as a postdoc with Baker in 2003 led the lab’s first de novo success1, a 93-amino-acid molecule called Top7. Natural proteins are difficult to modify without disrupting their overall structure. But by making proteins from scratch, researchers can design proteins to be more forgiving. They can build enzymes with activities unknown to nature, using co-factors and amino acids that are not part of the standard macromolecular toolkit. And scientists can test their understanding of protein biology, to ensure that they truly grasp the fundamentals.
“We’re making everything up from scratch,” says Baker. “And that’s a very strict rule in the lab: you’re not allowed to start with anything that exists in nature, because we wanted to be able to be sure we understand everything and design everything from first principles.”
