Metamorphic proteins have the unique ability to reversibly transition between multiple structures, each of which has a distinct function. Metamorphic proteins are an intriguing puzzle for biophysicists who study the relationship between protein folding and function, including Dr. César A. Ramírez-Sarmiento, an assistant professor at Pontificia Universidad Catolica de Chile and the Biophysical Journal 2020 Paper of the Year recipient.
Dr. Ramírez-Sarmiento first became interested in metamorphic proteins as a PhD student studying the role of protein folding in enzyme function. In June 2016, he launched his own research lab, where he uses molecular dynamics simulations and experimental biophysics to study various metamorphic proteins.
In a serendipitous interaction at a Biochemical Society conference a few years ago, Dr. Ramírez-Sarmiento met microbiologist Dr. Irina Artsimovitch of Ohio State University. Dr. Artsimovitch was the first scientist to describe metamorphic behavior in the protein RfaH. Found in gram-negative bacteria, RfaH regulates the transcription of polysaccharides and foreign genes. RfaH expression is upregulated in infected bacteria, making it a key factor in bacterial virulence and a potential target for antibacterial therapeutics.
Since RfaH is a metamorphic protein, it has several different structures [image 1]. The N-terminal domain is always folded into a α/β sandwich, but the C-terminal domain can refold. In the active state, the C-terminal domain of RfaH folds into a β-barrel and the entire protein binds to the transcription elongation complex, initiating gene transcription. Alternatively, in the autoinhibited state, the C-terminal domain folds into an α-hairpin, which binds to the N-terminal domain α/β sandwich, preventing gene transcription.
Drs. Ramírez-Sarmiento and Artsimovitch began working together to explore how RfaH transitions between its active and autoinhibited states. They reported results from their collaboration in the January 7, 2020 issue of Biophysical Journal. Using molecular dynamics simulations, mass spectrometry, and NMR, the team examined the binding interface between the C-terminal and N-terminal domains of RfaH, which is found in the autoinhibited but not active state of the protein. Specifically, they sought to identify and calculate the thermodynamic contribution of the residues that regulate the interaction between the domains and the transition between RfaH’s two states.
The results demonstrate that this interface can be divided into two regions: one thermodynamically stabilizes the autoinhibited state and the other thermodynamically favors the active state. “We were really surprised to see that the residues stabilizing each state were localized in specific regions. This means that RfaH inhibitors can be designed to specifically target small regions, which is easier than focusing on the entire protein,” he explained.
Biophysical Journal recognized Dr. Ramírez-Sarmiento and his paper with the 2020 Paper of the Year Award. Recipient articles are selected by Biophysical Journal editors, and the honor recognizes the contributions of young investigators. He reflected on the award in a recent interview: “I didn’t believe it at first, it’s amazing. I am very happy for my students, who worked hard to develop the simulations, analyze the experimental results, and understand how RfaH works. Thank you to the Biophysical Society for the award, Biophysical Journal for publishing our article, and the people who selected the paper for recognition.”
Dr. Ramírez-Sarmiento is a proponent of collaborative research [image 2], and his article highlights the value of his approach (additional authors include Dr. Elizabeth A. Komives, a mass spectrometry expert at the University of California, San Diego, and Dr. Stefan H. Knauer, an NMR expert at Universität Bayreuth). “In Chile, we work with limited financial resources. We have to be smart about the experiments we do, and we don’t have access to all the high-end instrumentation necessary to characterize biomolecules experimentally,” he explained. “Instead, we collaborate with experts on experiments that allow us to validate the observations from our simulations.”
“We love to collaborate; the more the merrier,” he continued. “I think that’s how science should be. We should work together instead of trying to do everything ourselves. Instead of competing for funding, why don’t we collaborate?”
Dr. Ramírez-Sarmiento’s current research builds on the findings of his Biophysical Journal article. In one project, he is examining the structures and transitions of RfaH bound to the transcription elongation complex using molecular dynamics simulations and mass spectrometry. In a second project, he is studying other metamorphic proteins, and again seeking to identify the residues that regulate transitions between structures. Future research will implement his discoveries about metamorphic proteins to design biosensors, examine protein evolution, and design inhibitors for RfaH.
Dr. Ramírez-Sarmiento will discuss the 2020 Paper of the Year and his current research during the Best of Biophysical Journal Symposium at the 2021 Biophysical Society Annual Meeting. “I look forward to the virtual conference and the opportunity to meet people from the Biophysical Society who I can collaborate with, so that we can really push this research forward,” said Dr. Ramírez-Sarmiento.
- Nuala Del Piccolo