Every living thing on Earth, from bacteria to humans, uses the same set of 20 amino acids to build all of its proteins, called our “amino acid alphabet.” But why that particular set of 20? If other amino acids are possible, what makes a good alphabet? And how might we recognize life beyond Earth that’s using an alphabet other than our own?

These are all questions that Stephen Freeland, professor of biological sciences, has been asking for over a decade in his theoretical research at UMBC. Now he and colleagues at the Tokyo Institute of Technology, Charles University in the Czech Republic, and Johns Hopkins University will take this work into the laboratory for the first time.

The team seeks to marry Freeland’s theoretical work with his colleagues’ unique laboratory expertise to link together known alternative amino acids to form proteins. The Human Frontier Science Program (HFSP) is supporting the work with a new three-year, $1.8 million grant. The HFSP is a major international funding agency for basic life science research that specializes in supporting collaborations across continents.

The overarching question the project seeks to answer, Freeland says, is “What can we learn about how life could be different at the most fundamental level of biochemistry?” It’s a daunting question, with significant implications from biomedical applications to increasing our chances of detecting life on other planets.

Researchers have already created alternative amino acids in the lab and added individual alternative amino acids to proteins otherwise made of standard ones. However, no one has built entire proteins from scratch using nothing but a set of alternative amino acids. “This work is genuinely novel,” Freeland says. “Nobody knows what will happen. This is a first.”

Finding the essence

Freeland’s prior work has focused on determining what characteristics are necessary for a set of amino acids to function well as a basis for life. He and his students determined what differentiates our set of 20 amino acids from other random sets of 20 taken from a digital library of about 4,000 mathematically-generated amino acid structures. 

That work led to a group of four equations that can be used to describe any set of 20 amino acids. “So it’s almost as if conceptually we boiled it and got the essence of it,” Freeland says, “We identified really unusual, simple characteristics that distinguish life on Earth’s set of 20 amino acids from random.”

With those factors in hand—what Freeland calls “design principles”—his team is now using a powerful computer program they developed to look at other sets of 20 amino acids and find examples that meet the same criteria. And this time around, they are taking the amino acids from a catalog of about 300 that can be obtained commercially—so any “good” set they find can be tested in the lab. 

Going back in time to leap forward

This summer, the work entered a new phase. Sean Brown, a UMBC Ph.D. candidate in biological sciences working with Freeland, traveled to the Czech Republic to work in Klara Hlouchova’s lab, where they are preparing the technology to produce proteins with proposed alternative amino acid alphabets. “Basically, we’re asking, ‘Do our design principles work’?” Freeland says.

In some ways, this work will be like going back in time to the mid-20th century, when researchers were first discovering how life behaves at the molecular level. Since then, techniques for building and analyzing proteins have come to rely on everything we’ve learned about life’s amino acid alphabet. As such, these tools cannot be applied to alternative amino acid alphabets. For this project, the team will return to older approaches and techniques, in which the Czech researchers have retained expertise, to see if their alternative amino acids can actually form proteins.

If the experiments are successful, the team will be able to further hone the design principles for a generic life-producing amino acid alphabet, rather than basing the principles solely on the characteristics of life on Earth. 

“If we can show that unusual, abstract properties of life as we know it are necessary, it helps us to understand why evolution on Earth went the path it did,” Freeland says. “It’s part of our own history, and it answers the question, ‘Why those 20?’”

Knowing what to look for around the universe

Beyond understanding our own history, refining the design principles would better inform our approach to seeking life on other planets, Freeland says. Scientists generally agree that other life forms are most likely to be microbial, but “most of the ways we currently detect microbes absolutely rely on the molecules in use for life on Earth,” Freeland adds. This work could help researchers know how to detect a “molecular signature” of amino acids that are most likely to show up in life forms that originated independent of Earth. 

Like all technologies, these developments come with great promise alongside risk. Freeland isn’t particularly concerned about individual synthetic proteins getting into the wild in the current stage of research, because proteins can’t replicate on their own. But he notes that there are important questions to ask about future, more advanced research. For example, there is potential for scientists working with DNA to build programmable genetic codes. Once this technology merges with fully synthetic proteins, he says, “is where the story takes a really interesting turn.”

Open-source proteins

Possible beneficial applications of synthetic proteins abound, and could include medical treatments or removing toxins from the environment. But without proper oversight, the technology could potentially also lead to harm, Freeland cautions.

Freeland is hoping to avoid the synthetic protein field following in the footsteps of synthetic DNA research. That field is much further ahead, but has mostly been carried out by private companies out of public view, “lending itself to patents and commercial ownership rather than to healthy, transparent debate and legislation,” Freeland says.

To create the best chance for responsible regulation around the use of synthetic proteins, Freeland and his colleagues are trying to quickly get their research into the public domain, he says, to make as robust as possible “what I think will be one of the more important debates of the 21st century when it comes to biotechnology: What are the laws, what are the ethics guiding our use of synthetic proteins and DNA?”

“Life on Earth is an example”

As Freeland and his colleagues lead the way into a new era of synthetic protein research, questions abound. Will proteins form from the amino acid combinations recommended by the algorithm? How can and should we use synthetic proteins, and who will decide? Will the research help us discover life on other planets? As the work develops and more researchers join this burgeoning field, researchers and the public will be constantly reminded of what Freeland describes as “one of the deepest principles of astrobiology.”

“Life on Earth is an example,” he says. “It would seem surprising to think it’s the only example.”

At Summer Undergraduate Research Fest (SURF) on August 9, 132 students presented posters and six gave short oral presentations, called “lightning talks,” about research projects covering topics from “forever” chemicals to prostate cancer to alcohol addiction. The University Center Ballroom buzzed with students, mentors, and guests as students shared their progress, interacted with other student researchers, and received feedback. The annual event, sponsored by the College of Natural and Mathematical Sciences (CNMS) since 2005, gives students who are often in the early stages of their research careers an important opportunity to feel like part of a scholarly community.

“We are proud of all that our students accomplished this summer. Now they are more knowledgeable, experienced, and skilled—they are better scientists,” shares CNMS Dean William R. LaCourse. “Their discoveries, their effort, and their willingness to explore have added to the vault of scientific knowledge, which in the end benefits society through empowerment—an empowerment of understanding, prediction, and invention.”

Undergraduate research boosts confidence, opens doors

Community college students who participated in the BUILD a Bridge to STEM Internship, a component of STEM BUILD at UMBC, presented research they conducted in small groups under the mentorship of Maria Cambraia, assistant director of research and international affairs in CNMS. Each group developed a different research question about the earthworm C. elegans, a common model organism, and then designed and carried out experiments to answer that question. The internship operates as a course-based undergraduate research experience, or CURE, a structure designed to create opportunities for more students to gain authentic research experience.

Emily Paz ’25, biological sciences, studied how high sugar diets affected the worms. It was Paz’s first time conducting quantitative research, and the BUILD internship created opportunities to make mistakes and learn from them, she says. “It expanded my career choices, and made me see I really have an interest in this field,” says Paz, a transfer student from Howard Community College.

In addition to work in the lab, the process of preparing for SURF and completing the Introduction to Research Badge as part of the internship was valuable for BUILD intern Emily Molnar, a Montgomery College student whose project focused on the relationship between stress and alcohol in C. elegans. Interns completed the badge, a sequence of activities designed to help them get ready to find and pursue undergraduate research opportunities, under the guidance of Caitlin Varisco, assistant director of undergraduate initiatives in CNMS.

“The internship gave me experience with abstracts, posters, and skills to get future opportunities, which boosted my confidence,” Molnar says.

Belonging in science

Student research at UMBC is frequently student driven, which was the experience of Samuel Barnett ’25, biochemistry and molecular biology, another Howard Community College transfer. His project looked at how nicotine influenced the appetite of C. elegans. “You have so much freedom in this program, which I love,” he says. “That really made me feel involved in the research process.”

Third- and fourth-year UMBC students, some of them former STEM BUILD Trainees, mentored the interns along with Cambraia. “I found it uplifting,” says mentor Courtney De Leon ’25, biological sciences. “I’m so proud of the students I mentored.” De Leon also presented her own project at SURF on how long-term nicotine consumption affected growth and reproduction in C. elegans.

Cambraia notes that after the eight-week internship, the interns identified much more with being scientists than they had at the outset. “Science identity” is documented to increase the chances that students will complete STEM degrees and then continue in related careers. 

“That’s why mentoring and peer mentoring are so important in this program,” Cambraia says. “We are not just mentoring them in wet lab techniques, experimental design, and data analysis skills. Our main goal is to help them see and feel that they belong in science and that they can be future leaders in this field.”

“A grand scholarly community”

BUILD a Bridge to STEM is just one example of a student research program that participated in SURF. Students in an array of programs supported by the likes of the National Institutes of Health, Howard Hughes Medical Institute, and the Louis Stokes Alliance for Minority Participation participated, as well as those who arranged their research projects individually.  

“These projects all depend on mentors supporting undergraduate research with their time, energy, and resources,” LaCourse notes. UMBC faculty have shown time and again that they are happy to work with students to help them reach their goals, as evidenced by the huge number of students presenting original work at SURF. For many students, SURF is their first time presenting research—but LaCourse hopes it won’t be the last.

“This may be the first of many scientific talks you give,” he told the participants at the end of the day. “By practicing and applying the skills of performing research this summer, you are following in the footsteps of great scientists and researchers—making each of you a part of a grand scholarly community.”