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Global pocket exploration of FraC binding sites using PELE. aEnergy profile of the global study with the branched ester glyceryl tripropionate and poses highlighted in color from each binding site (positions are highlighted only when the interaction energy is equal to or below -15 kcal mol−1). bEnergy profile of the global study with the small-sized aromatic phenyl acetate and color-highlighted poses from each binding site (positions are highlighted only when the interaction energy is equal to or below -12.5 kcal mol−1). ° СEnergy profile of the global study with the short-chain alkenyl ester vinyl acetate and poses highlighted in color from each binding site (positions are highlighted only when the interaction energy is equal to or below -10 kcal mol−1). e, Cross-section of FraC with two opposing strands to visualize the localization of the various indicated binding sites (Protein Data Bank (PDB) ID: 4TSY). Computational data were collected and analyzed with PELE. Calculations and raw data are shown in Supplementary Data 1. Credit: Natural catalysis (2023). DOI: 10.1038/s41929-023-01048-6
About 400 million tons of plastic are produced worldwide each year, a number that is increasing by about 4% per year. Emissions resulting from their production are one of the elements contributing to climate change, and their ubiquitous presence in ecosystems leads to serious environmental problems.
One of the most used is PET (polyethylene terephthalate), which is found in many packaging and beverage bottles. Over time, this material breaks down into smaller and smaller particles – so-called microplastics – which worsens environmental problems. PET already accounts for more than 10% of global plastic production and recycling is scarce and inefficient.
Now scientists from the Barcelona Supercomputing Center—Centro Nacional de Supercomputación (BSC-CNS), together with research groups from the CSIC Institute of Catalysis and Petrochemistry (ICP-CSIC) and the Complutense University of Madrid (UCM), have developed artificial proteins capable of to break down PET microplastics and nanoplastics and reduce them to their basic components, which would allow them to be degraded or recycled.
They used a defense protein from the strawberry anemone (Actinia fragacea) to which they added the new function after being designed using computational methods. The results are published in the journal Natural catalysis.
“What we’re doing is kind of like adding arms to a person,” explains Victor Gualar, an ICREA professor at BSC and one of the authors of the work. These arms consist of only three amino acids that function as scissors capable of cutting small PET particles. In this case, they were added to a protein from the anemone Actinia fragacea, which in principle does not have this function and which in nature “functions as a cellular drill, opening the pores and acting as a defense mechanism”, explains the researcher.
Machine learning and supercomputers like BSC’s MareNostrum 4 used in this protein engineering make it possible to “predict where the particles will connect and where we need to put the new amino acids so they can do their thing,” Gualar says. The resulting geometry is quite similar to that of the PETase enzyme from the bacterium Idionella sakaiensis, which is capable of degrading this type of plastic and was discovered in 2016 at a packaging recycling plant in Japan.
The results show that the new protein is capable of degrading PET micro- and nanoplastics with “an efficiency between 5 and 10 times higher than that of PETases currently on the market and at room temperature,” explains Guallar. Other approaches require temperatures above 70 °C to make the plastic more moldable, resulting in high CO2 emissions and limits its applicability.
In addition, the pore-like structure of the protein was chosen because it allows water to pass through and because it can be anchored to membranes similar to those used in desalination plants. This would facilitate its use in the form of filters that “can be used in treatment plants to break down those particles that we don’t see but which are very difficult to eliminate and which we swallow,” says Manuel Ferrer, research professor at the ICP -CSIC and also responsible for the study.
A design that allows for purification and/or recycling
Another advantage of the new protein is that two variants have been designed, depending on where the new amino acids are placed. The result is that each produces different products.
“One variant breaks down the PET particles more thoroughly so that it can be used for degradation in treatment plants. The other gives the start to the initial components needed for recycling. This way we can either purify or recycle, depending on the need,” explains Laura Fernández López, who is working on her PhD thesis at CSIC’s Institute of Catalysis and Petrochemistry (ICP-CSIC).
The current design may already have applications, according to the researchers, but “the flexibility of the protein, as that of a multi-functional tool, will allow the addition and testing of new elements and combinations,” explains Dr Sara García Linares, of the Complutense University of Madrid, who also participated in the study.
“What we are looking for is to combine the potential of proteins provided by nature and machine learning with supercomputers to produce new designs that allow us to achieve a healthy, zero-plastic environment,” says Ferrer.
“Computational methods and biotechnologies can allow us to find solutions to many of the environmental problems that affect us,” Gualar concludes.
Ana Robles-Martín et al, Submicro- and nanoscale deconstruction of polyethylene terephthalate with engineered protein nanopores, Natural catalysis (2023). DOI: 10.1038/s41929-023-01048-6