In a major step forward for computational protein design, University of Washington scientists have built from scratch a handful of enzymes that successfully catalyze a specific chemical reaction. These proteins have no naturally occurring counterparts, and the reaction–which breaks down a man-made chemical–has no natural catalyst.
David Baker and his colleagues at the University of Washington focused on a reaction that would break certain bonds between carbon atoms. The ability to design enzymes that can break and make carbon-carbon bonds could potentially enable scientists to break down environmental toxins, manufacture drugs, and create new fuels.
As they report in the journal Science, Baker and his group first designed what an ideal active site would look like for the reaction. An active site is a pocket within an enzyme where the catalyzed reaction takes place. In order to do its job, an active site must have precise geometry and chemical makeup, tailored to the reaction it catalyzes. Some components hold the reacting molecules in place, while others participate in the reaction’s chemical mechanisms.
Once the researchers computed the active site, they used a newly developed set of algorithms to model proteins that have such a site. Each designed protein was ranked according to its ability to bind the reacting chemicals and hold them in the proper position.
The next step was to actually synthesize the selected proteins. The researchers derived gene sequences for 72 of the designed enzymes, ordered snippets of DNA containing those genes, and used bacteria to turn the genes into proteins. Each protein was then tested for its ability to catalyze the carbon-carbon bond breaking reaction.
Of the 72 proteins selected, 32 successfully helped along the reaction. The most efficient proteins sped up the reaction to 10,000 times the rate without an enzyme.
While that’s an impressive feat compared with earlier enzyme design attempts, the synthesized enzymes pale in comparison to naturally occurring ones. “It’s not very good at all,” says Baker. “Naturally occurring enzymes can increase the rate of reactions by much, much greater amounts”–as much as a quadrillion-fold.
“One of our research problems is to figure out what’s missing from our designs that naturally occurring enzymes have figured out,” says Baker. In follow-up studies, his group has taken two approaches to this problem: refining its computer algorithms, and asking nature to step in where the researchers left off. By using their minimally functional enzymes as evolutionary starting points, the researchers can use directed evolution to create more efficient catalysts.