Novel proteins, created from scratch with no particular design in mind, can sometimes do the work of a natural protein. The discovery may widen the toolkit of synthetic biologists trying to build bespoke organisms.
There are more proteins possible than there are atoms in the universe, and yet evolution has tested only a minuscule fraction of them. No one knows whether the vast, untried space of proteins includes some that could have biological uses.
Until now, most researchers assembling novel proteins have meticulously selected each amino acid building block so that the resulting protein folds precisely into a pre-planned shape that closely fits the molecules it is intended to interact with.
Michael Hecht, a chemist at Princeton University, decided to try a much looser approach. “I was trying to see what the hell’s out there,” he says.
Proteins fold because certain amino acids associate easily with water, while others tend to be tucked away in the interior of the protein.
Hecht chose a common shape for folded proteins, called a four-helix bundle – reminiscent of four fingers pressed tightly together – and worked out which positions in the protein needed to have water-loving amino acids and which parts water-avoiding in order to take that shape.
Then he randomly picked amino acids from those two categories to fill those positions. He repeated the process over and over, eventually designing around a million different semi-random proteins.
Next, Hecht built DNA molecules coding for each of these proteins and inserted this genetic material into bacteria so they would make them.
To test whether any of these proteins had biological functions, Hecht supplied each one to E. coli bacteria that were missing a single gene (and hence, the protein it coded for). The missing genes Hecht tested were ones that coded for enzymes that catalyse biochemical reactions.
Would the novel proteins “rescue” the bacteria and help them survive? Most of the time, they didn’t.
But for four of the 80 gene deletions Hecht worked on, at least one – and in one case, hundreds – of the semi-random novel proteins did restore the missing function. “”We were ecstatic,” says Hecht.
|The main character of the news is the bacteria of E. coli at high magnification
When he looked more closely, he got a surprise. Not a single one of the rescue proteins replaced the missing enzyme by catalysing its reaction. Instead, they somehow upregulated other, related enzymes in the bacteria so that they could take over for the absent one, he told the Astrobiology Science Conference in Mesa, Arizona, last week.
In a follow-up experiment, Hecht has found at least one novel protein that does act as an enzyme, catalysing a chemical reaction needed to make the amino acid serine.
Hecht suggests that this direct catalysis should be even more common in proteins with basic shapes other than the four-helix bundle, which is normally a structural protein rather than an enzyme.
Eventually, synthetic biologists should be able to use Hecht’s approach to find a wide range of novel proteins for their toolkit. For instance, new proteins might be able to provide functions similar to today’s antibody-based drugs but without their unwanted tendency to clump together, says Hecht. Other proteins might bind to or break down toxins.
But fulfilling this promise is probably some way off. So far, Hecht has been unable to predict the function of his novel proteins, notes Nicholas Hud, a chemist at the Georgia Institute of Technology, meaning a huge amount of trial and error is needed to find something useful. “De novo design of enzymes is still a bit beyond our reach,” says Hud.