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Enzyme transforms biomass into bioproducts

The international group that identified the structure included the participation of researchers from Unicamp

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An international research group, in which researchers from Unicamp participate, identified a new enzyme and elucidated its mechanism of action, which plays an important role in the process of converting lignocellulosic biomass, coming from renewable sources such as sugar cane and corn, into high-value-added products, including biomaterials, biofuels and bioplastics. Scientific article with the results of the study was published on June 27th by the magazine Nature Communications., from the Nature Group. The contribution of University professionals to the project was in the computational area, through simulations that guided the experiments.

From Unicamp, post-doctoral student in Chemistry Rodrigo Leandro Silveira and his supervisor, Professor Munir Skaf, who also responds to the University's Dean of Research (PRP), participated. Silveira explains that although enzymes from the same family, known as cytochromes P450, occur commonly in nature, including in the human body, accounting for a large part of drug metabolism in the liver, until now no representative involved in lignin conversion processes was known. . The researchers named this enzyme GcoA, its acronym in English. This tiny structure, according to the researcher, has very special attributes. “Unlike other enzymes, it is an extremely versatile entity, with the ability to act on different substrates”, points out Silveira.

Photo: Perri
Postdoctoral student Rodrigo Silveira: Brazilian collaboration was in the computational area, through simulations that guided the experiments

The researcher provides more details about GcoA's mechanism of action. According to him, the enzyme is related to the bacterial metabolism of lignin, a polymer that, together with cellulose and hemicellulose, provides resistance and defense to plants. Simply put, a certain class of bacteria uses the enzyme to degrade lignin and use it as a source of energy, that is, as food. “This is a very sophisticated process because lignin has a very heterogeneous chemical composition. From a molecular point of view, it is composed of many different units, which in turn have equally diverse chemical bonds, which must be carefully undone during the chemical reactions of bacterial lignin metabolism”, says Silveira.

In these cases, the researcher continues, a wide variety of enzymes are normally needed to break all these bonds and thus degrade lignin, which is an aromatic polymer. “It turns out that the enzyme we discovered, which catalyzes a critical step in the process called aromatic O-demethylation, can act on a wide variety of lignin subunits. As it binds all these different subunits, GcoA transforms them into a single intermediate, called catechol, a precursor of muconic acid, which can be catalytically converted into raw material for the production of plastics, for example. We use metabolic engineering to modify the bacteria's genes, in order to channel this metabolic process towards the objective we want, which is to generate products with high added value, such as biofuels and biomaterials”, details Silveira.

Before promoting this genetic modification, however, scientists sought to understand the enzyme's mechanism of action. This was done through advanced computational techniques, known as molecular dynamics simulations, capable of representing the behavior of the structure. “We used as a starting point the structure of the enzyme obtained experimentally using X-ray diffraction techniques. Then, we used hundreds of computers working together to solve the equations that govern the movement of each of the enzyme's atoms over time, to thus understanding its dynamics and operating mechanism”, explains the researcher. This work was carried out at the Center for Research in Computational Engineering and Sciences, which is funded by the São Paulo State Research Support Foundation (Fapesp) and is based at the Institute of Chemistry (IQ) at Unicamp. The person who coordinates this Cepid is Professor Skaf.

Silveira points out that computers are currently so robust and algorithms so sophisticated that simulations come very close to reality. “When using this type of technique, we verify which elements are present in this enzyme, which make it so versatile to act on different substrates. What we saw was that it works like a carnivorous plant. It opens to capture the substrate, then closes and adapts around it. Furthermore, we found that the enzyme can close completely or partially, depending on the interaction with the substrate, and this has direct consequences on its performance. Based on these observations, experimental researchers are now interfering with this mechanism, with the purpose of improving it and directing it towards our points of interest”, explains the post-doctoral student.

Photo: Perri
Professor Munir Skaf: Unicamp's participation in international consortia reveals the capacity of Brazilian science

The next step within the research project, says Professor Munir, will be to produce the lignin-eating enzyme on a larger scale. “Let’s imagine that our future objective is to produce biofuel from biomass. To meet global demand, we will need many tons of enzyme, which is not a trivial challenge to overcome.” In addition to Unicamp, the following institutions participated in the research: University of Porsmouth (United Kingdom); National Renewable Energy Laboratory (NREL, USA), where Silveira completed a postdoctoral internship; Montana State University (USA), University of Georgia (USA) and University of California, Los Angeles (USA).

Professor Munir notes the importance of Unicamp and its researchers participating in research projects like this, which work at the state of the art of science and involve different institutions and areas of knowledge. “These are essential requirements for the development of good science. However, it is important to emphasize that we do not join these international consortia just to learn. We also have something to teach. We have infrastructure and highly qualified human resources, at levels similar to those in developed countries. Rodrigo Silveira's participation in this study proves our capacity”, analyzes the Dean of Research.

In addition to the scientific issue, Professor Skaf also notes the importance of research of this nature for the construction of a more sustainable planet from an environmental point of view. The dean offers as an example of this reflection the paper production system, which is extracted from wood. Lignin, an object of interest for the manufacture of high-value-added products, is an element that “disrupts” paper, because it makes it dark. “It is necessary to use a series of chemical reagents, which are potentially polluting, to remove lignin from paper. Through the method applied in the study we have just published, this same lignin that is removed during paper production can be converted into bioproducts. This generates a virtuous cycle, since the eucalyptus that provides cellulose for paper production can be planted again and, as it grows, it will capture CO2 [carbon dioxide] from nature and transform it, starting with photosynthesis, into cellulose and lignin . And all this without using oil”, ponders the Vice-Rector of Research.

 

 

JU-online cover image
Three-dimensional structure of GcoA, immediately after capturing the lignin subunit called guaiacol (in yellow) to initiate the chemical reaction | Disclosure

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