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Larger molecules, fewer traffic jams, faster biomass degradation

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Posted March 22, 2019
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Biofuel and biochemical production may soon become ten times faster thanks to research on the breakdown of biomass. Researchers at the University of Tokyo predict that increasing the physical size of the enzyme domain responsible for attaching to cellulose will avoid the molecular traffic jam that makes the natural reaction so slow.

Cellulose is a long carbohydrate that builds leaves, straw, and tree trunks. It is a major component of plant cell walls and a potential energy alternative to fossil fuels.

Overview of the cellulase kinetics. (a) Schematic illustration of cellulase molecules on crystalline cellulose. (b) The molecules first attach to the surface first by non-productive binding, and then start the reaction after completing productive binding. Image credit: Takahiro Ezaki and Kiyohiko Igarashi

Schematic illustration of the crowding-out effect. (a) Because the volume exclusion effect of non-productive binding is smaller than that of productive binding, the surface is covered with non-productive molecules, which strongly suppress productive binding to initiate the reaction. (b) When the non-productive binding requires more space, a sufficiently large open space for the productive binding is emptied frequently and the crowding-out effect does not occur. Image credit: Takahiro Ezaki and Kiyohiko Igarashi

However, cellulose is difficult to decompose. Only specific microbes and fungi can break the long molecule into smaller sugar molecules using an enzyme called cellulase. The cellulase reaction is also notoriously slow, which has prevented industrial use of cellulose as a source material for producing biofuels and biochemicals.

Researchers studied the movement of cellulase as it decomposes cellulose to understand why the reaction naturally happens so slowly.

“Following the spirit of physics, we first tried to explain experimental results using simpler models. However, it turned out that the strong slowdown of the reaction could not be easily explained, giving us a strong feeling that there might be a missing factor that we had overlooked,” said researcher Takahiro Ezaki, first author of the research publication.

Experts in cellulase experiments from the Graduate School of Agricultural and Life Sciences collaborated with experts in theoretical dynamics of moving particles from the Research Center for Advanced Science and Technology.

“After exciting discussions, we determined that the key to understanding the puzzling experimental results lies in the collective behavior of many molecules. The outcome was quite interesting both for experimentalists and theorists,” said Associate Professor Kiyohiko Igarashi, leader of the research team.

Researchers found the answer they were looking for when they studied cellulase reactions at a mesoscopic level – in-between microscopic and macroscopic (visible with the naked eye) levels.

Computer simulations of more than one hundred million (100,000,000) cellulase molecules revealed that the molecules naturally get in each other’s way, preventing one another from actually completing binding to cellulose and decomposing it. In additional computer simulations, increasing the size of a specific domain of the enzyme counterintuitively eased the congestion of cellulase in the reaction, increasing the reaction efficiency.

Researchers named this type of molecular traffic jam the crowding-out effect. Reactions using enzymes are universal in nature, so researchers predict that their discovery might apply to other relevant chemical systems.

This research was partially supported by the Japanese Ministry of Education, Culture, Sports, and Technology (MEXT), the Japan Science and Technology Agency (JST), Business Finland (BF), and the Asahi Glass Foundation.

Source: University of Tokyo

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