Enzymes Built from Scratch

Researchers engineer never-before-seen catalysts using a new computational technique.

In a major step forward for computational protein design, 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.

Catalyst creativity: Researchers developed a computational technique to build enzymes from scratch. An enzyme called retro-aldolase, a portion of which is shown above, was designed to break carbon-carbon bonds in a non-natural chemical substrate (yellow and white stick model). The gray mesh is the enzyme's active site, its geometry carefully crafted to hold the substrate in place. The orange and green stick models indicate components of the enzyme that are particularly important in prodding the reaction forward. Credit: Lin Jiang

"It makes it clear that we can compute a structure that will catalyze a reaction where there was none before," says Frances Arnold, professor of chemical engineering and biochemistry at Caltech, who was not involved in the research. Arnold calls new enzymes the "holy grail" of computational protein design. Designing any protein from scratch is a tall order; engineering a protein that can carry out a given function requires far more sophistication.

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.

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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.