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The Power of Proteins

Humans produce more than 300 million tons of plastic waste every year. In excess of 100 million tons of that is single-use and more than eight million tons are dumped in the oceans.

“It has a pretty catastrophic effect on the environment,” said Peik Lund, a sophomore from Sandpoint.

However, in 2016, scientists found a bacterium in a landfill that had evolved so that two of its enzymes worked together to degrade the most common type of plastic produced by humans. This process allows the bacteria to use the plastic as an energy source.

“The bacterium’s degradation process isn’t very fast or efficient though,” said Lund, “so I am modeling the two enzymes and trying to see what mutations could make them more effective.”

In order to conduct this research, he sought out the mentorship of Marty Ytreberg, professor of physics. “I started out as just a bioengineering major working on biofuels,” Lund said, “but one day I was scrolling through the work that different labs were doing, and I saw some of Marty’s research on protein physics and realized the potential for environmental work. I emailed him, got into his lab and added a physics major.”

“Peik developed this project based on his interest in protein engineering to aid the environment,” said Ytreberg, “and since my lab’s focus is on understanding how evolution affects the function of proteins, he came to me with his idea. This project is a great example of how molecular modeling of proteins can improve our quality of life.”

While Lund admits that a double major in bioengineering and physics is daunting, it is essential to learning how to engineer proteins and enzymes to perform certain tasks.

“I’m jumping deeper in the physics now and there is going to be a little bit of a learning curve since I don’t have a physics background,” he said. “I will be spending a lot of time at the computer learning the ins and outs of various physics-specific modeling programs.”

First, Lund must learn how to write scripts in Python, a computer programming language. Once he has mastered this, Lund can use the scripts to run simulations in Rosetta, a modeling software.

The simulations perform analyses of proteins including estimating how amino acid mutations affect binding. Knowing this will allow Lund to use the computer to perform virtual experiments where amino acid mutations are introduced and their effects on enzyme-plastic binding are estimated. Lund will then be able to determine specific mutations that may increase the efficiency of the plastic degradation process. By the time he is finished, Lund hopes to have a list of mutations that will improve the performance of the enzymes.

Lund has a lot of work ahead, but in his opinion, the effort is more than worth it.

“Engineering proteins could change our world,” Lund said. “You could engineer new medicines, you could engineer an algae cell to be more efficient at producing biofuel, you could engineer proteins that could clean up oil spills. With enough research, you could pretty much engineer them to create anything you want.”

Christi Stone, College of Science
May 2020

Peik Lund
Sophomore Peik Lund
Surface representation of MHETase
Surface representation of MHETase, one of the proteins Peik is working with. The orange molecule is the non-hydrolized ligand MHETA.
Stylized representation of MHETase
Stylized representation of MHETase, one of the proteins Peik is working with. The orange molecule is the non-hydrolized ligand MHETA.

EP 319

208-885-6908

ytreberg@uidaho.edu

Research: Biological Physics
View Marty Ytreberg's profile

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