I worked in the lab of Tanja Kortemme at University of California, San Francisco (UCSF). Her lab uses both computational and experimental approaches to engineer novel proteins. My project focused on redesigning the ligand binding site of a transcription factor LacI. Multiple ligands control LacI allosterically, which means they induce a conformational change distant from the binding site.

My design goal was to alter the effects of different ligands on the allosteric response. To improve a current Rosetta design protocol, I added explicit water molecules into the binding site. Water molecules often take on structurally or functionally significant roles in proteins, so mapping water-mediated hydrogen bonds in the LacI binding site gave me useful information to computationally redesign the LacI binding site. I then experimentally created and tested some of my designs with different ligands.

The REU group included 11 interns, a perfect size for creating a tight-knit group. We came from various backgrounds (computer science with no biology experience, to biology with no coding experience) from around the country. We learned a lot from each other!

The first week of the internship was a PyRosetta bootcamp in Chapel Hill, North Carolina where we learned the python interface to Rosetta. Five days were spent in 10 hours of lectures and coding labs (with additional lunch and dinner breaks). This intense environment immediately brought us close, since we collaborated on the challenging assignments. We all grew a lot in this week, and I think we were all excited to run some of our first Rosetta protocols. One of my favorites was a protein folding lab and actually visualizing the protein folding in PyMOL (a molecular visualization software). The long lunch and dinner breaks at restaurants provided ample time for getting to know each other, the instructor, and teaching assistants as well.

During the eight-week internship, we had weekly video chat meetings, where two interns presented a paper to discuss in Journal Club. Two Rosetta lab primary investigators (on a rotating schedule) then moderated a discussion topic.

We then reunited in Seattle, Washington and explored the city a little bit before heading to RosettaCON, a conference for the labs in the Rosetta community. Even though we were only together two weeks bookending the internship, I think we got really close and had a lot of fun together; it was hard to say goodbye to everyone!

This internship solidified my decision to apply to graduate school. This experience helped shaped the type of research programs I am interested in, and I know I definitely want to combine computation and experimentation in my future research. I want to stay in protein science and I am now becoming interested in protein interaction networks and systems biology approaches.