Host: Professor Wayne Yang

Abstract:
Dr. Edona Karakaci comes to us with a technique capable of watching protein shapes and conformations in real time. Her research direction brings together concepts from physics, engineering, nanofabrication, and biology for a truly interdisciplinary story. We will make efforts to ensure the talk is accessible for students of all backgrounds!

Proteins provide key information for all biological processes and diseases. A complete understanding of the function of many proteins can only be obtained if different conformations and transitions between them can be monitored in aqueous solution, with adequate temporal resolution. Despite the importance, studying conformational dynamics of single proteins, to date, remains challenging. Existing single-molecule techniques for interrogating conformational dynamics often require labeling or modifications, which can disrupt the protein's native state and function. In contrast, plasmonic optical tweezers (POT) have emerged as a compelling tool for monitoring the conformation of single unmodified proteins trapped within a plasmonic hotspot, with an impressive temporal resolution of 40 µs.

To demonstrate how plasmonic optical tweezers (POT) can reveal previously unobserved conformational dynamics of native proteins at the single-molecule level, we investigated a portfolio of functionally important proteins. Using programmable fluidics, we monitored citrate synthase’s substrate-induced conformational changes for hours, uncovering a previously unknown intermediate conformation crucial for enzyme activity. Additionally, with a double nanohole POT, we recorded the first temperature-controlled thermal unfolding and refolding trajectory of single calmodulin proteins. By precisely regulating the temperature in the plasmonic hotspot and observing optical transmission changes, we tracked domain-specific unfolding and refolding without photobleaching limitations. Finally, we used the same approach to capture a single, unmodified hemoglobin molecule, revealing its reversible transition from the deoxygenated, rigid T state to the oxygenated, flexible R state. Together, these studies highlight the power of POT to probe the real-time conformational changes of native proteins with high temporal resolution and minimal perturbation.

Bio:
I am a physicist and biophysicist specializing in single-molecule instrumentation and label-free protein analysis. I am currently a senior researcher at the Adolphe Merkle Institute, University of Fribourg, Switzerland, where I develop plasmonic optical biosensing platforms integrated with microfluidics to study protein conformational dynamics at the single-molecule level.

My work focuses on combining nanofabrication, optical sensing, and real-time signal analysis to investigate biological systems without labeling, enabling high temporal resolution measurements of native protein behavior.

I completed my PhD in Physics/Biophysics at the University of Fribourg, following graduate studies in France and Albania. I have presented my research at international conferences and enjoy working at the interface of physics, biology, and engineering in interdisciplinary environments.