Probing Into Proteins

Life isn’t static. It's a dynamic phenomenon of almost constant movement and change even at the smallest level, where complex protein molecules fold into different three-dimensional shapes and bind with each other in myriad ways. Imaging techniques such as X-ray crystallography can provide static snapshots of protein structure, but the ability to watch proteins move in real time provides crucial insights into how they operate. Jacob Goldberg and Colin Fadzen, both recently named Dean’s Scholars in Chemistry, are developing new ways of watching proteins in action.

Working in Assistant Professor of Chemistry James Petersson’s lab, both Goldberg and Fadzen use chemical synthesis techniques to create “unnatural” amino acid molecules that can be inserted into a protein. This changes the protein’s optical properties so its movements can be more easily observed and traced at certain light wavelengths using spectroscopy. As Goldberg explains, “We're sort of labeling the proteins with small motion-capture probes that we can interrogate with light and see how they respond, and from how their interactions with light change, infer something about their movement.”

Right now everything we’ve been doing is something we can do in a test tube. Our ultimate goal is to develop a general method that investigators in any lab can apply to any protein system.

One great advantage of this technique is that, unlike other imaging techniques, it doesn’t require fancy and expensive equipment that may not be accessible to every researcher. “Right now everything we’ve been doing is something we can do in a test tube,” says Goldberg. “Our ultimate goal is to develop a general method that investigators in any lab can apply to any protein system.” Toward that end, much of the work so far has concentrated on proteins that are already well understood. “By using a very well-characterized model system, we can say, look, this technique works in a model where we know exactly what we expect to observe,” notes Fadzen.

That validates the accuracy of the technique for investigating less well-understood proteins, among them alpha-synuclein, which has been strongly implicated in Parkinson’s disease and is a major focus of Petersson’s lab. “It's a very small protein but one that has conformational dynamics that are incredibly complex,” Goldberg says. “There are a lot of unanswered questions about exactly how alpha-synuclein exists in cells.” Fadzen adds, “Not much is known about its nature. There's a lot of controversy about its structure.”

Goldberg and Fadzen use a phenomenon called fluorescence quenching to study proteins. They label proteins with two markers, one that fluoresces in ultraviolet or visible light and one that quenches that fluorescence in a distance-dependent way. Although this technique is fairly common, the advantage of their approach is the small size of the probes they use. “They require the substitution of only a very few atoms or molecules, so they don’t perturb the native behavior of the protein very much when you incorporate them,” Fadzen says. “We’re interested in tracking dynamic processes, such as protein binding to a peptide or alpha-synuclein aggregation. By doing this in solution and being able to track changes in fluorescence, you can ideally learn more about a dynamic process.”
   
Now a fifth-year graduate student, Goldberg obtained his undergraduate chemistry degree at Dartmouth before coming to Penn. He's already published several papers in leading journals and has been hailed as “an exceptional young chemist, on a trajectory to become a leader in the field.” Lab colleague Fadzen points out, “Jake was foundational in the lab for getting the idea up and running for what we do.” Fadzen, an undergraduate, is a senior in the Roy and Diana Vagelos Scholars Program in the Molecular Life Sciences. His work in the Petersson lab has also earned him the Roy and Diana Vagelos Science Challenge Award, which grants full tuition to outstanding juniors and seniors in chemistry or physics. He's also submatriculating for a master’s degree in chemistry.

Both Goldberg and Fadzen are looking forward to continuing and expanding upon their award-winning careers, with Goldberg moving on to a post-doctoral position and Fadzen aspiring to enter an M.D./Ph.D. program. “I’d like to continue the same theme of using synthetic chemistry to probe biological systems,” Goldberg says. “There are still a lot of unanswered questions, and I think there’s definitely an opportunity for finding new ways of looking at these very fundamental problems.”

Fadzen notes, "I'm happy in the field of chemical biology. It's very interdisciplinary.  Through my work here I've learned basics in molecular biology, biophysics, and chemistry. So it's a very cool integration of lots of different aspects of science."