One of the newest members of Rensselaer Polytechnic Institute’s Bioinformatics department is Dr. Catherine Royer. Joining the community last September, Dr. Royer was eager to do research at RPI. With a keen interest in proteins, she has spent the last 10 years doing different things with proteins and trying to understand how they have evolved, their structure, their stability and dynamics, and how they react and respond to each other. In her previous work, Dr. Royer states that she has not gotten bored or tired of working with them.
Dr. Royer’s interest in proteins first started with her thesis on protein interactions and protein foldings. Now, she is looking at protein interactions, and how those interactions with each other and other organelles control the cell. So far, she has several graduate students assisting her with her research. Together, they are biochemically doing tests to figure out protein interactions and using fluorescent proteins to create a “quantitative map.”
Only in the past five to 10 years has it been possible to do quantitative research inside the cell. Dr. Royer does several in vitro tests, tests done outside of the body in test tubes, which involves purifying proteins and measuring their interactions. According to her, “It is very difficult to purify proteins because some of them can be very big and not stable.” Part of the process to create the quantitative map is to take pictures of the different clusters of proteins. To do this, Dr. Royer and her team uses a fluctuation microscope to see the fluorescent proteins. From looking at the florescent flux, they take an average count of the number of proteins going in and out of the cell. They use this data to build an image one pixel at a time. This process of examining each cell to take measurements does not take long; however, analyzing the data can take over one month for just one cell.
So far, there is not much in the way of automatic data analysis, so many of the calculations are done by hand and Dr. Royer and her team are very limited at being able to detect what is going on. Many of the calculations done have to do with measuring the variance and brightness intensity between protein clusters. According to Dr. Royer, “It’s a very labor-intensive process, but it’s important to characterize these protein interactions because a lot of drugs target protein interactions specifically. We need to be able to see how these proteins change due to drugs, disease, or mutations. Once we can see how things change and interact, we can make advances in the field of biology; right now, cells are a better biochemist than we are.”