100,000 frames of the Ankyrin Repeat Protein simulation
My second week in the lab went by quickly. I began working on a presentation that explains the method that I will be using to analyze ASB9. The analysis method is called protein-protein docking. Protein-protein docking is the computational simulation of a candidate ligand binding to a receptor. This relates to my research project because I am trying to understand how the structure of ASB9 effects binding to creatine kinase.
On Tuesday I was able to download trajectory files for Ankyrin from a server in Ohio that is used by one of my mentors named Jamie. These files contain thousands of coordinates for the molecular structure of Ankyrin. After they were downloaded I was able to open them in VMD in order to analyze the simulation. The simulation consists of 100,000 frames that are combined to make a movie. The protein “wiggles and jiggles,” a term used to describe the unique movement of the protein.
Analyzing the simulation of ASB9 was extremely interesting, but I had a presentation to finish and practice. My goal for this presentation was to condense extremely complex information, so I wouldn’t lose my audience’s focus.
La Jolla Shores
The mentors decided to take us to Home Plate for lunch on Wednesday, which is a burger place on campus. This was a lot of fun as I learned about many of the mentors’ research projects, as well as their journey of being graduate students.
On Wednesdays my generous host family buys us pizza, so we went to La Jolla Shores and enjoyed the sunset as we ate it.
My presentation went well, and I feel that the audience was able to take away the general idea of what protein-protein docking was, as well as what purpose it serves in analyzing proteins. I was also able to summarize the function of ASB9, which is a key component of the ubiquitination process. Ubiquitination affects proteins in many ways, it can mark them for degradation via the proteasome, affect their activity, and promote or prevent protein interactions.
Falling Star
After my presentation, Jamie gathered all of the interns and took us to see a very interesting piece of art. We went to Fallen Star, which is a small house that is attached to the corner of Jacobs Hall. It is placed at a 5° angle to the roof, and a 10° angle in the other direction. After being inside the house for a few minutes, I started to feel nauseous. Overall, this is an amazing piece of art.
I am starting to notice how fast this adventure is passing by, so I am trying many new things and have many goals for next week. This journey would not be possible without the Pinhead Institute or my host family. Again, as always, thank you!
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