enzymes

Neural network finds an enzyme that can break down polyurethane

AI, biochemistry, Biology, chemistry, enzymes, neural networks, polymers, polyurethane, protein design, proteins, Science / Tim Belzer / October 31, 2025

You’ll often hear plastic pollution referred to as a problem. But the reality is that it’s multiple problems. Depending on the properties we need, we form plastics out of different polymers, each of which is held together by a distinct type of chemical bond. So the method we use to break down one type of polymer may be incompatible with the chemistry of another.

That problem is why, even though we’ve had success finding enzymes that break down common plastics like polyesters and PET, they’re only partial solutions to plastic waste. However, researchers aren’t sitting back and basking in the triumph of partial solutions, and they’ve now got very sophisticated protein design tools to help them out.

That’s the story behind a completely new enzyme that researchers developed to break down polyurethane, the polymer commonly used to make foam cushioning, among other things. The new enzyme is compatible with an industrial-style recycling process that breaks the polymer down into its basic building blocks, which can be used to form fresh polyurethane.

Breaking down polyurethane

Image of a set of chemical bonds. From left to right there is an X, then a single bond to an oxygen, then a single bond to an oxygen that's double-bonded to carbon, then a single bond to a nitrogen, then a single bond to another X. — The basics of the chemical bonds that link polyurethanes. The rest of the polymer is represented by X’s here.

The new paper that describes the development of this enzyme lays out the scale of the problem: In 2024, we made 22 million metric tons of polyurethane. The urethane bond that defines these involves a nitrogen bonded to a carbon that in turn is bonded to two oxygens, one of which links into the rest of the polymer. The rest of the polymer, linked by these bonds, can be fairly complex and often contains ringed structures related to benzene.

Digesting polyurethanes is challenging. Individual polymer chains are often extensively cross-linked, and the bulky structures can make it difficult for enzymes to get at the bonds they can digest. A chemical called diethylene glycol can partially break these molecules down, but only at elevated temperatures. And it leaves behind a complicated mess of chemicals that can’t be fed back into any useful reactions. Instead, it’s typically incinerated as hazardous waste.

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Genetically engineered bacteria break down industrial contaminants

biochemistry, Biology, enzymes, Genetics, Genomics, pollution, Science / Tim Belzer / May 8, 2025

Once that was done, the researchers started looking through the genomes of species that have been identified as breaking down industrial contaminants. The breakdown of complex molecules typically involves more than one enzyme, and the genes for these enzymes tend to end up clustered together so they can be produced as a single, large RNA that encodes all the proteins needed. This simplifies regulating their production, making it easy to ensure the bacteria only make the proteins if the molecule they break down is actually present. In this case, the clusters ranged from just three genes all the way up to 11.

Once nine of these gene clusters were identified, the DNA that would encode them was ordered and assembled into a single DNA molecule in yeast. The researchers took some time while ordering this DNA to better optimize the genes to be active and produce proteins in Vibrio natriegens, as opposed to whatever species the genes were normally used by.

From yeast, each of these individual gene clusters was inserted into Vibrio natriegens, creating different strains that could digest one of the following: benzene, toluene, phenol, naphthalene, biphenyl, DBF29, and dibenzothiophene (DBT). (Some of the nine clusters target the same contaminant.) Each of these bacterial strains was then put in a solution with the chemical they were engineered to digest. Five of the nine worked, giving researchers strains that could digest biphenyl, phenol, napthalene, DBF, and toluene.

Good, but limited

From there, the researchers developed a system that would enable them to iteratively insert a new gene cluster at the tail end of a previously inserted gene cluster. This allowed them to build up a cluster of clusters, eventually including all five of the ones that had shown activity in the earlier tests. Given two days, this single strain could remove about a quarter of the phenol, a third of the biphenyl, 30 percent of the DBF, all of the naphthalene, and nearly all of the toluene.

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AI used to design a multi-step enzyme that can digest some plastics

AI, biochemistry, Biology, catalysts, chemistry, Computer science, enzymes, Science / Kris Guyer / February 15, 2025

And it worked. Repeating the same process with an added PLACER screening step boosted the number of enzymes with catalytic activity by over three-fold.

Unfortunately, all of these enzymes stalled after a single reaction. It turns out they were much better at cleaving the ester, but they left one part of it chemically bonded to the enzyme. In other words, the enzymes acted like part of the reaction, not a catalyst. So the researchers started using PLACER to screen for structures that could adopt a key intermediate state of the reaction. This produced a much higher rate of reactive enzymes (18 percent of them cleaved the ester bond), and two—named “super” and “win”—could actually cycle through multiple rounds of reactions. The team had finally made an enzyme.

By adding additional rounds alternating between structure suggestions using RFDiffusion and screening using PLACER, the team saw the frequency of functional enzymes increase and eventually designed one that had an activity similar to some produced by actual living things. They also showed they could use the same process to design an esterase capable of digesting the bonds in PET, a common plastic.

If that sounds like a lot of work, it clearly was—designing enzymes, especially ones where we know of similar enzymes in living things, will remain a serious challenge. But at least much of it can be done on computers rather than requiring someone to order up the DNA that encodes the enzyme, getting bacteria to make it, and screening for activity. And despite the process involving references to known enzymes, the designed ones didn’t share a lot of sequences in common with them. That suggests there should be added flexibility if we want to design one that will react with esters that living things have never come across.

I’m curious about what might happen if we design an enzyme that is essential for survival, put it in bacteria, and then allow it to evolve for a while. I suspect life could find ways of improving on even our best designs.

Science, 2024. DOI: 10.1126/science.adu2454 (About DOIs).

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