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A team led by David Baker designed and experimentally tested a protein from scratch to catalyze ester hydrolysis through its four-step reaction mechanism. Chemistry World reported that the strongest designs showed activity comparable to natural proteases, but supplied no exact rate for that comparison. The result is a laboratory advance in enzyme design—not evidence of a commercial enzyme or industrial process.
What the team designed
The researchers created a synthetic serine hydrolase, an enzyme designed to break an ester bond by using water. Rather than adapting a naturally occurring enzyme, the team began with the chemistry it wanted the protein to perform and designed an active site around that reaction.
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The target reaction proceeds through four mechanistic steps. Its active site uses a catalytic triad—serine, histidine and aspartate—to promote the chemistry. A nearby oxyanion hole helps position the substrate in conformations that support the reaction. Getting the protein to support the whole sequence matters: a design that favors one stage but not the next may leave the reaction stalled at an intermediate.
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How the design pipeline worked
- Specify the active-site geometry. The team defined the spatial arrangement of the amino acids needed for the reaction, rather than beginning with an existing protein scaffold.
- Build a protein around the site. The researchers fed the site’s three-dimensional coordinates to RFdiffusion, which generated candidate protein structures intended to hold the active site in place.
- Generate a compatible sequence. A second AI algorithm proposed amino-acid sequences predicted to fold into the generated structures.
- Assess reaction intermediates. A third program evaluated whether candidate designs could stabilize intermediates formed during the successive reaction stages.
- Test candidates experimentally. The team generated close to 1,000 designs, then prepared and tested candidates predicted to facilitate the complete reaction. Fluorescent markers were used to track ester hydrolysis.
As postdoctoral researcher Sam Pellock described the structure-generation step to Chemistry World: “We take the 3D coordinates of this site and feed it into an AI algorithm called RFdiffusion which generates an entire protein that perfectly holds this active site.”
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What “life-like performance” means here
Chemistry World characterized the best tested enzymes as having activity comparable to natural proteases and described the result as a substantial improvement over earlier designed proteins. That is a qualitative comparison in the report: it does not give an exact kinetic value or a numerical, side-by-side comparison with a named natural enzyme. The claim should therefore be read as a reported laboratory result, not as proof that the designed enzyme matches natural enzymes in every condition or application.
The advance is the attempt to design for the successive stages of a reaction, rather than optimize a protein around only one snapshot of the chemistry. As David Baker put it in the report: “Most enzyme engineering has started with a naturally occurring enzyme and tried to modify it to carry out a different reaction.” He contrasted that approach with “starting from the reaction,” arranging key amino acids in a particular geometry and using generative models to produce proteins containing that active site.
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What has—and has not—been demonstrated
The reported experiments concern a designed serine hydrolase and a selected ester-hydrolysis reaction. They do not establish that the strategy works across enzyme classes or reaction types, or that the enzyme is ready for industrial use. Extending the method to reactions involving metals or cofactors, and finding an industrial application, were described as future steps by protein-modelling researcher Victor Guallar.
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The underlying study is identified by the University of Groningen research portal as A. Lauko et al., Science (2025), DOI 10.1126/science.adu2454. The accessible reporting and portal record do not establish exact experimental conditions or quantitative kinetics, so those details cannot be responsibly inferred from the qualitative performance comparison.
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Why the result matters
Designing an enzyme around a desired reaction could, in principle, widen the range of transformations scientists can pursue without relying only on modifying existing enzymes. Anna Lauko, a postdoctoral researcher in the Baker lab, summarized that ambition as: “We want to harness their chemical power on demand.” Enzymologist Max Fürst praised the stepwise design pipeline for helping dissect the requirements of the mechanism, while noting the broader potential of designing reactions as well as enzymes. Those observations describe the promise of the approach; they are not demonstrations of new industrial processes.
Source: Victoria Atkinson, “Designer protein performs multi-step catalysis with life-like performance,” Chemistry World, 25 February 2025; University of Groningen research portal record citing the study DOI.
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