A "Hands-On" Experience

When Kenneth Baumann entered BU as a freshman, he had no idea what he wanted to study.

“At first I played around with the idea of becoming an engineer. I really wanted to work with my hands,” he says. But Baumann grew less enchanted with the engineering program when he found himself spending more time working formulas than actually building. Rather doubtfully, he changed his major to Biology.

Switching to Biology turned out to be a very wise decision, as Baumann discovered during an internship experience in the summer of 2009. Through serendipity and a little networking, he managed to set up a position as research assistant to Drs. Kumaran and Swaminathan at Brookhaven National Laboratories (BNL), a facility renowned for the excellent research it produces and its state-of-the-art equipment.

Baumann’s work at BNL was part of a larger project called the Protein Structure Initiative, or PSI, which aims to collect information on the 3-D structure of all kinds of proteins. His project was to determine the structure of a protein that was sent to him by PSI.

In order to do this, he first had to turn the protein into its crystal form. But crystallizing a protein is much harder than it sounds; since every type of protein has its own unique structure, there is no standardized method of crystallization. Baumann’s strategy was to expose the protein to a slew of different chemicals in varying concentrations to see which combination produced a crystal.

For weeks, Baumann would gaze through his microscope in hopes of finding at least one crystal in the dozens of cultures he had set up the day before.

“Without a crystal, usually you're looking at empty space or just a bunch a brown junk, which means the protein denatured,” he describes. “Other times, you'd get an immature crystal, which basically looks like a spiky sea urchin. But when you get a real crystal, the light from the microscope gives it a multicolored aura and you can see some kind of 3D formed shape, more like box.”

Five 40-hour weeks and hundreds of cultures later, Baumann was ecstatic to find his first legitimate crystal. Finding the crystal meant he could finally begin Step 2.

Once crystallized, the structure of the protein can be determined using BNL’s National Synchrotron Light Source, a rare device that shines a very bright, very focused light through the crystal. Based on the way the crystal diffracts the light, this machine can tell what the protein is made up of in terms of α helices, β pleated sheets, and other structural components, which provide the researchers with vital clues about the identity of the protein.

Once Baumann and his mentors knew that their protein was aminobenzoyl glutamate utilization protein, which Baumann lovingly calls “AGUP,” the next step was to feed the structural 

information into another software program. This generated a three-dimensional structure of the protein.

Information about and a 3-D image of Baumann’s protein can be found on the Protein Data Bank website (see below for link), where anyone can view it and use it for research.

The discovery of the structure of “AGUP” is important because it contributes to a larger framework of questions that seek to understand whether similarities in protein form can indicate similarity of function, and whether or not these generalizations are true across species. Understanding the precise relationship between protein structure and function will allow for new disease treatments and new ways of approaching other types of problems related to the human body.

Once unsure of his career goals, Baumann is now a published scientist with an evident passion for research. He is currently working on securing a position at Brookhaven for next summer as well, and hopes to someday run his own lab at BNL. “My internship was a great experience all around, and I loved every minute of it,” Baumann says. “I’d gladly do it over again.”

Not only has Baumann finally found a career that lets him use his hands, he has also found a thrill in the fact that, when you’re doing research, “you’re responsible for this project which actually could change the world.”

by Sarah E. Fecht

To view Ken’s protein in 3-D, please ciick here. Click on the box labeled “View in JMol.” In a few minutes, a box with the 3D structure will pop up. You can grab the image and turn it around or right click and give instructions to spin it.

Last Updated: 7/1/15