Enzyme Salad Dressing and Metabolite Soup
Steve Abel, an associate professor in the Department of Chemical and Biomolecular Engineering, has spent more than a decade using computational and theoretical tools to understand the physical processes that underlie molecular interactions in cell biology.
He starts by taking the cell out of the equation.
“The idea is to remove some of the complexities of the cell and use less complex, cell-free platforms to build a better understanding of the biology,” he explained.
That made him a perfect fit for the National Science Foundation (NSF) Advancing Cell-Free Systems Toward Increased Range of Use-Inspired Applications (CFIRE) initiative, an intensive workshop dedicated to helping experts from different fields jointly develop research projects that would further cell-free biomanufacturing.
Abel applied to CFIRE in 2024 and was one of only 37 experts invited to attend from across industry and academia. Eight teams were invited to submit research proposals to the NSF. Four of the projects were ultimately funded, including the two Abel helped develop.
“I like to work with people and be collaborative—it’s central to how I do science and research—but it was still surprising how seamlessly people’s expertise came together,” he said.
Abel is a co-principal investigator on a $7.6 million project led by the University of California, Irvine (UCI) that will use liquid phase separation to create locally specialized environments for different enzymes within a single bioreactor.
He is also a participant in CFIRE’s largest grant, a $9.2 million project headed by the Georgia Institute of Technology (Georgia Tech) that will design modular metabolic reaction networks for cell-free production of a variety of molecules.
Abel and his lab members will receive a total of $1.7 million over the next three years for their contributions to both projects.
“I can’t conceive of these projects having happened without the CFIRE workshop because they involve so many different players with different sets of expertise,” Abel said. “Computation is such an important piece of these projects because it brings together multiple experimental aspects in a way that lets us think about the situation collectively.”
A Salad Dressing Bioreactor
Abel’s first project takes advantage of a physics principle that is more familiar than it sounds.
“In liquid-liquid phase coexistence, two or more liquids exist in equilibrium without mixing, separated by an interface. It’s the technical term for how a salad dressing has droplets of oil suspended in vinegar,” Abel explained. “We are using this principle to engineer local environments that can enhance certain reactions that build high-value molecules.”
The team will use this principle to create precursor molecules that go into many valuable agrichemicals and pharmaceuticals but are typically very hard to produce.
University of California, Los Angeles Associate Professor Samanvaya Srivastava will use synthetic polymers to develop two liquid phases that can coexist. Meanwhile, UCI Associate Professor Han Li will engineer enzymes that can perform chemical transformations within each liquid phase, and James Weltz, a cofounder of the Denver-based company Cascade Bio, will scale up the process for industrial systems.
“You really need mathematical models to understand what’s going to happen when you sequester some enzymes in some compartments and other enzymes in others,” Abel said. “The computational and mathematical models we develop will allow us to put all that into one framework, to better understand the system and make informed design decisions that allow us to more efficiently run these biomanufacturing processes.”
Turning Molecular Soup into Insights
Inside a cell, DNA gets translated into messenger RNA (mRNA), which is then transcribed into proteins. For years, it has been possible to insert custom DNA into cells so they create proteins of interest, then fill a bioreactor with those transformed cells to create high-value molecules.
As manufacturing processes go, this is very inefficient. A living cell devotes most of its energy to growth and maintenance, and the desired products have to be isolated from all the other biomolecules.
The second of Abel’s new projects, headed by Georgia Tech Professor Mark Styczynski, will help solve that problem. Researchers will create eight cell-free reaction network ‘modules’—including some capable of transcription and translation—that can be combined in different combinations to efficiently build new biomanufacturing processes.
The components of all the modules will be homogenously mixed in their reactor tank, creating a nearly incomprehensible ‘soup’ of molecules.
“We’re talking about hundreds to thousands of different molecular components,” Abel said, “but my group is used to thinking about complex problems. With mathematical models, we can start to put those pieces together.”
By simulating the intertwined reactions, Abel’s group may be able to identify key enzymes that have disproportionate impacts on reactor efficiency and yield—or components of a module that aren’t necessary. Those are insights that would be prohibitively expensive, or even impossible, to investigate experimentally.
“With both of these projects, we will be able to bring mathematical, computational, and theoretical modeling to piece together different experimental approaches and highlight the things that are going to be most important,” said Abel. “It feels good to be filling that role. I am really excited.”
Contact
Izzie Gall (egall4@utk.edu)