New Principles Optimize Design of Large Functional Proteins

A new set of design principles for creating large proteins was published today in Nature Communications. The team behind the study had previously developed principles to design small versions of what they call "ideal proteins," which are structures without internal energetic frustration.

"The ideal proteins we have created so far are much more stable and more soluble than proteins commonly found in nature. We think these proteins will become useful starting points for designing new biochemical functions of interest," said co-first author Rie Koga from Japan's National Institutes of Natural Sciences.

The team found that while the designed proteins were structurally ideal, they are too small to harbor functional sites so they set out to test the generality of the design principles they developed previously by applying them to the design of larger alpha-beta proteins with five and six beta strands.

The results were puzzling. They found that their experimental structures differed from their computer models, resulting in proteins that folded differently by swapping the internal locations of their beta strands. The team struggled with the strand swapping puzzle, but by iterating between computational design and laboratory experiments, they reached a conclusion. "We emphasize that experimental structure determination is important for iterative improvement of computational protein design," said co-first author Gaohua Liu.

The reason for the strand swapping, they determined, was due to the strain of the whole system on the foundational backbone structure. According to co-first author Nobuyasu Koga, the strain is global, instead of connection to connection. Proteins can adjust the length and register of strands across the system to alleviate this backbone strain.

Next, the researchers plan to continue studying the trade-off between more functional proteins with what could be considered less-than-ideal qualities. "We would like to design proteins with more complex functional sites by incorporating non-ideal features such as longer loops, which are important not only for function but also for relieving global backbone strain," said co-author David Baker.