Researchers are exploring ways to transform wood, a natural and abundant resource, into valuable materials. At the heart of this effort is a molecular machine found in fungi, which breaks down the complex structure of wood into its basic components. A team led by a Kobe University researcher has now developed a test feed for this fungal machine, allowing them to observe its near-natural behavior. This breakthrough opens the door to enhancing the process and applying it to industrial uses.

Biochemical engineers are particularly interested in converting wood into bioplastics, chemicals for medical use, food additives, or fuel. However, wood’s complex structure has posed a significant challenge. 

Kobe University bioengineer Koh Sangho explains, “Wood is composed of different, chemically linked materials such as lignin and hemicellulose that first need to be separated to become available as source materials.” 

Essentially, the process requires the wood to be broken down. Fungi possess enzymes, essentially tiny molecular machines, capable of doing this. However understanding how these enzymes work—crucial for industrial applications—has been difficult because researchers lacked a suitable substrate, or feed, for the enzyme. “As a graduate student at Shinshu University, I failed to produce the typical enzymatic reaction dynamics graph we know from the textbooks using the commonly used test substrate. I even reached out to the researcher who first found the enzyme to ask what I was doing wrong, but he replied that I wasn’t doing anything wrong and that my results were typical of attempts to characterize this enzyme,” Koh recalls.

This challenge led Koh and his team to create a new material that mimics the natural substrate of the enzyme while still being simple enough to modify chemically and simulate computationally. “The key to our ability to create a suitable substrate was that we had previously found another enzyme that allowed us to create very specific hemicellulose fragments that could not be produced in any other way. Only with these fragments we could chemically synthesize a suitable test substrate,” Koh explains, shedding light on why others had not been able to fully characterize the enzyme before.

The team’s findings were recently published in Biochemical and Biophysical Research Communications. Being the first to observe the enzyme in a near-natural environment, they were able to determine its reaction speed and affinity—critical data for anyone working with enzymes. Koh says, “When, as a result of using the substrate I designed, the textbook-like reaction dynamics emerged, I was really happy. With this we can finally characterize the enzyme’s ‘true’ nature, and improve and apply it industrially, too.”

Their computational simulations revealed why their approach worked where others failed. Previous studies focused solely on the specific part of the substrate where the enzyme cleaves, meaning test substrates mainly consisted of this connecting structure. In contrast, Koh’s new substrate includes a short hemicellulose tail attached to the reaction site, and the enzyme binds to this tail when performing its function.

Now that they have a clear understanding of the enzyme’s performance and reaction mechanism, the researchers plan to search for better enzyme alternatives in different fungi and chemically modify the molecule to enhance its performance. They also believe their test substrate will help in studying how this enzyme interacts with others to break down wood into its various components. Koh concludes, “We think this was a significant step towards the process’s industrial application to the generation of useful chemicals from the abundant natural resource.”