Erica Prates: Bridging science across scales with computational biology

Erica Prates has found a way to help speed the pursuit of healthier ecosystems by linking the function of the smallest molecules to their effects on large-scale processes, leveraging a combination of science, math and computing.

Prates is a computational systems biologist in Oak Ridge National Laboratory’s Biosciences Division. She’s using her interdisciplinary approach to develop hardier plants that can be grown on inhospitable lands to make clean jet fuels, to create healthier plants and improve carbon storage by exploring plant-microbe interactions, and to figure out how viruses affect human health.

“I integrate structural information on molecules into complex systems biology models,” Prates said. “And I am fortunate to get to do so on the world’s fastest supercomputers here at ORNL.”

She works to understand the three-dimensional structure of biomolecules, with a particular interest in proteins and interacting metabolites. “I help predict their structure and interactions using high-throughput methods that run on supercomputers. A molecule’s structure is tightly related to its function and how it creates physical traits in an organism. Those traits then influence ecosystems on a large scale,” Prates said.

If scientists can describe how information passes from genes to a cascade of molecular events that produce a given biological phenomenon, they can predict how genetic variation changes biological behavior, she added.

Versatile science

Prates studies a wide variety of subjects, including plants, microbes, viruses and species interactions. One of her main efforts is building a computational structural systems biology workflow that lets scientists identify protein targets that can be engineered to achieve biological traits of interest.

An example is her work identifying genes encoding proteins that can trigger desirable characteristics in plants for the Center for Bioenergy Innovation, or CBI, at ORNL. A key mission of CBI is developing improved nonfood crops like poplar and switchgrass that have greater biomass yield and resistance to pathogens and pests.

She is also learning the secrets of how microbes such as fungi use molecular signaling to talk to plants to support a healthy ecosystem for both. Those signals, known as lipo-chitooligosaccharides, or LCOs, are believed to govern the beneficial colonization of plant roots by fungus and may be involved in other important biological processes.

Prates played a role in ORNL’s pioneering efforts to characterize all the proteins of the SARS-CoV-2 virus for insights into its evolution and the body’s response to COVID-19. Prates and colleagues recently followed up their research with lab experiments supporting their theories about the virus’s pathogenesis. The team described how the virus inactivates an important protein in the body’s immune system.

“This was very exciting work,” Prates said. “Early in the pandemic there was this idea that the major target of the virus was lung cells. But then it became clearer that COVID-19 was a systemic disease, affecting the whole body.” The team demonstrated at a molecular detail how the virus can dismantle NEMO, a protein in the host cell that is key for an effective immune response.

“One of the things I really enjoy about my work is the ability to migrate between very different systems.” Prates said. “I was working with a lot of plants and microbes, and then at the onset of the pandemic suddenly started working with viruses. Proteins are proteins no matter whether the organism they influence is a virus, a human or a microbe. So it’s easy and useful to migrate to these different subjects using the same tools. That’s one thing I love about this job.”

Encouraging words

Prates cites her mother’s influence for her successful entry into a science career.

“You have to be confident when you practice science,” Prates said. “It was my mother who boosted my confidence every day growing up with messages that ran counter to an often sexist culture.” She also cites the influence of a physician in the family who discussed science and medicine with her routinely from a young age. When her parents built her a doll house, Prates turned it into a play laboratory.

Prates earned her bachelor’s, master’s and doctoral degrees in chemistry from the University of Campinas, or UNICAMP, in Brazil. She first came to the United States with an internship at the University of Washington, and then spent a year at the National Renewable Energy Laboratory, or NREL, as a Sao Paulo Research Foundation Fellow researching biofuels.

In Brazil, Prates was no stranger to bioenergy. The nation is the world’s second largest producer of ethanol. Renewables make up almost half of Brazil’s energy mix, and about 70% of that supply is from plant biomass, according to the International Energy Agency.

It was at NREL, a key partner in CBI, that she became acquainted with ORNL and eventually joined as a postdoctoral researcher in 2018, hiring on as staff three years later.

“I’ve been very lucky in my career to have worked with very generous scientists who opened doors for me and made me feel empowered and capable,” she said. She cited key mentors like Professor Munir Skaf, her doctoral advisor at UNICAMP, Gregg Beckham at NREL and Dan Jacobson at ORNL.

At Oak Ridge, Prates said she feels “lucky to be around very smart co-workers. The team that I work with directly supports my work in systems biology where you need to understand the connections between molecules, and often that requires people with very different expertise working together. It makes you talk a lot, this interdependence of a team where everyone might have a different approach.” By having the same goal, the environment is more cooperative than competitive, she said.

She also enjoys the immense capabilities of working in a national lab environment, including the supercomputers at the Oak Ridge Leadership Computing Facility. “Just working here with Summit and Frontier is a big achievement already,” she said.  

Fearless and flexible

Prates advises young people interested in a career in science to “be fearless. It’s important to be confident and creative. Don’t give up, even on the ideas that at first may feel wrong. Be flexible and resilient. Just like Darwin’s theories in nature, adaptability is key to success.” She also stressed the benefit of learning how to write. “You will write more than you expect to, and it’s critical to be able to effectively communicate your ideas to others.”  

Prates’s enthusiasm extends to her personal life as her family grows. “I’m very excited by the most important project of my life: the baby girl that I’m expecting,” she said. “I plan to be very supportive of her in whatever she wants to do. I want to show her how the universe is complex and beautiful, as my inspirations did for me.”

In her research as well as in parenting, she hopes to continue bridging the gap between the tiniest elements and the largest impact. “When you make this connection between the molecular world and the big picture, then you’re learning which of the tiny gears can influence the entire system.”

UT-Battelle manages ORNL for the Department of Energy’s Office of Science, the single largest supporter of basic research in the physical sciences in the United States. The Office of Science is working to address some of the most pressing challenges of our time. For more information, please visit energy.gov/science. — Stephanie Seay