SMU doctoral student’s research shows how protein changes could advance biotechnology

When COVID-19 closed physical laboratories, SMU doctoral student Juliana Rodriguez Antonio made a decision that would reshape her career. Unable to conduct hands-on experiments, she switched to computer modeling, a move that has led to research on how protein modifications could improve our understanding of enzyme design.

Antonio's most recent findings, published in a celebratory issue for the International Year of Quantum Science and Technology in the scientific journal , demonstrate how scientists can fine-tune proteins to develop new treatments more efficiently.

"Since my first year as a graduate student on campus, SMU has really opened a lot of doors for me and my research," said Antonio, who holds a Mustang Fellowship from SMU's Moody School of Graduate and Advanced Studies. "When you have fellowship support, it provides opportunities for collaboration and research that you know is necessary for your career.”

In addition to the Mustang Fellowship, Antonio has received support from the National Science Foundation's Graduate Research Fellowship Program. She credits both with ensuring she can complete her doctoral degree, especially while supporting a young family. 

From Teaching to Computational Chemistry

Antonio's path to SMU began in high school, where a chemistry teacher who also taught computer science first sparked her interest in combining coding with chemistry. At the University of Texas Rio Grande Valley, she initially pursued teaching, even working with fourth graders before realizing the classroom wasn't her calling. She then considered pharmacy but was deterred by potential debt.

The pandemic became an unexpected turning point. When her undergraduate advisor switched to computational chemistry because "no one could be in the lab," Antonio discovered a new research passion. A chance meeting between that advisor and SMU chemistry professor Elfi Kraka at a seminar led to Antonio's recruitment to SMU's Computational and Theoretical Chemistry Group ().

This past summer, Antonio was selected to attend the prestigious Lindau Nobel Laureate Meeting in Germany, where she met with Nobel laureates in chemistry.

“As a mentor and supervisor, the most important thing is to see how students grow throughout the program,” said Kraka. “We could offer Juliana the opportunity to go straight from undergraduate to working on her Ph.D. and provide an environment that’s personalized to contribute to her success. It’s an exciting time to be in this field as we celebrate 100 years of quantum chemistry.”

SMU doctoral student Juliana Antonio with Rachel Ball-Phillips, Assistant Dean of Fellowships and Awards at the Moody School. Antonio received a Mustang Fellowship, which is awarded to Ph.D. students who show exceptional academic promise.

Creating 42 Protein Variations with Quantum Tools

Working with Kraka, Antonio examined myoglobin, an oxygen-carrying protein found in muscle tissue. They created 42 different versions to understand how various modifications affect its behavior — work that could help scientists design artificial proteins for specific medical functions.

The duo made strategic changes to three components:

• Metal centers: They tested chromium, manganese and iron, each offering different chemical properties useful for medical applications
• Scaffold molecules: They used two types of structures called Schiff bases — one with two ring-shaped parts (salophen) and another with one ring (salen), making it more flexible
• Amino acid forms: They modified histidine, a key amino acid near the metal center, into three different configurations that affect how the metal functions

Using SMU's high-performance computing resources, Antonio employed a technique called QM/MM (quantum mechanics/molecular mechanics) that measures chemical bond strengths throughout proteins, like measuring a guitar string's tension by its vibration.

The research revealed that chromium-water bonds proved strongest while iron-water bonds were weakest, and that small modifications in one area affected the entire protein structure. These findings demonstrate that scientists can fine-tune protein behavior by selecting specific metals and modifying the surrounding chemical environment.

"It's not going to replace people, but I do think it should complement and expedite the process," Antonio said about computational chemistry's role. "Most of my dissertation work has been on understanding these interactions using our local vibrational mode theory."

Re-engineering Nature’s Building Blocks for Real-World Applications

Antonio sees her research as fundamental work that lays the groundwork for future advances in biotechnology. By understanding mutations and interactions at the molecular level, scientists can efficiently design and optimize proteins or bio-inspired systems for specific functions, reducing the trial-and-error process often involved in experimental development. 

As she prepares to graduate next spring, Antonio hopes to continue her research at a national laboratory, building on work that bridges fundamental science with practical applications in biotechnology and materials science.

This material is based upon work supported by the National Science Foundation under Award No. CHE2102461 and the National Science Foundation Graduate Research Fellowship Program No. DGE-2034834. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.