Week 2: June 6 - June 10

This week I continued to work with proteins. Although I first started with small proteins that have been worked with a lot and always give a nice result, I moved on to the proteins MHC and TCR, which is what Dr. Tapia's research is about. MHC is also known as major histocompatibility complex, and it plays an important role in the immune system. TCR, also know as T cell receptors, are responsible for recognizing antigens. TCR interacts with MHC, and the big, three-year project is about demonstrating how protein motion affects the binding of proteins together, starting with how protein motion affects the binding and interacting of TCR to MHC. So this week I began the process of making roadmaps of both TCR and MHC. This week was focused on the node placement part of the roadmap process. The placement on the nodes depended on the parts of the protein that are flexible and the parts that are rigid, and so for each roadmap, I adjusted the percentage of the protein that was flexible (Andrea dealt with the rigid portions). This was to determine which set of conditions for flexibility and rigidity produced not only the most nodes, but also the highest quality nodes. On Thursday we had a meeting about graduate student life, where three computer science graduate students came to talk to all of the computer science summer interns. It was great to hear about grad school from students currently in grad school, but it also made me realize that soon I will be in grad school, which is both a thrilling and terrifying prospect! On Friday, Dr. Tapia, John, Andrea, and myself went to hear a talk at the medical school. The talk was on the modeling of cell signaling, and although some of the biology was beyond me, I enjoyed the talk. Part of the talk was on the modeling of ligands, which might be incorporated into my summer-long project. Finally, this week I journeyed to a used bookstore my cousin had told me about. The bookstore was nice, and I walked away with a couple of used books that I can't wait to read!