Alison Holliday: Collaboration on Protein Folding
by Alison Holliday
In 2012, I began collaborating with Professor David Clemmer at Indiana University (IU) in Bloomington, Indiana. Clemmer is a world-renowned expert in ion mobility spectrometry, and his lab has built many of the most advanced ion mobility instruments in existence. In 2012, I was working with a commercial instrument with limited function, and after Clemmer gave a research presentation, we started talking about how I might be able to answer more interesting problems with more sophisticated equipment. He invited me to his lab a couple of months later, and I have been visiting for a week or two every year since then. So far, we have published eight journal articles together.
Ion mobility spectrometry is a very, very fast method to separate molecules based on their size (bulkiness) and charge. Since the way a molecule is connected or folds can affect its bulkiness, ion mobility can separate ions that are identical except for their shape. We use ion mobility to investigate complex biological mixtures, figuring out how the shapes of molecules change with surrounding conditions, but ion mobility is also used by the military and at airports to detect explosives and chemical warfare agents.
My most recent research with the Clemmer lab has focused on following the folding and reactions of proteins. Since a protein’s shape can affect its interactions with other molecules – for example, allowing it to fit perfectly into a pocket to start a reaction – misfolded proteins can play a role in disease. If we can determine the conditions that influence folding in a particular way, we could gain a new perspective into the causes and treatment of these diseases.
Specifically, we have been able to follow the changes in the shape of the small protein polyproline as it folds from one structure to another (Figure 1). Starting off as a tightly packed right-handed corkscrew (helix), polyproline goes through a variety of bent structures before arriving at a more loosely-packed left-handed corkscrew shape.
Figure 1. Folding of polyproline
(a small protein)
More recently, experiments done by students at Moravian have helped to show that our ion mobility experiments – which are done using gas phase ions – can be explicitly linked to the folding processes that are happening in solution. This is very important, as all the protein folding happening in our bodies is happening in solution. To show this connection, we use a solution-phase separation technique called capillary electrophoresis.
The collaboration keeps me constantly engaged in research. One moment I might be testing a new experiment for the instrumental analysis lab or planning an activity for the environmental chemistry class, and the next moment I might be talking to someone about the thermodynamics of protein folding. However, the benefits to Moravian students extend beyond my ability to bring discussion of recent research into the classroom.
When I started at Moravian, Moravian students became a key part of the collaboration. John Barr ’16 and Amanda Miller ’17 have both spent a week doing research at IU. Amanda worked with Clemmer PhD students Chris Conant and Daniel Fuller to follow the fragmentation of a protein using ion mobility. She also carried out a part of her own independent study project with the help of Xiaomei Zhou, a PhD student in Stephen Jacobson’s lab; Jacobson’s group at IU works with capillary electrophoresis. In this research, she used capillary electrophoresis and mass spectrometry to probe for the binding of two proteins after changing conditions to start folding. If we can see the influence of protein shape on interactions in real-time, we will be one step closer to understanding how proteins interact in the body.
Alison Holliday, Chris Conant, Daniel Fuller, and Amanda Miller’17 Xiaomei Zhou, Alison Holliday, and Amanda Miller’17
Moravian students gain more than just the ability to use different or novel instrumentation. As Amanda writes: “Visiting Indiana University allowed me to provide assistance to the graduate students as well as conduct some of my own personal research. I was able to experience what it would be like to attend graduate school, something I hope to do in the future. It gave me the opportunity to work with students who could provide me with advice not only regarding research but also my future.”