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ROSETTA COMMONS: SUMMER REU 2023
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Mohini's Internship Blog
Hello! My name is Mohini and I am a rising senior at Juniata College with a major in Bioinformatics. This summer, I received the opportunity to be a part of the Rosetta Commons REU Program. As a Rosetta intern, my work involves using the Rosetta software/related machine learning models to computationally design proteins.
Although this internship is coordinated by Johns Hopkins University, I will be spending most of my summer working in the Kuhlman Lab, at my host institution, UNC Chapel Hill. Given my prior experience in using deep learning methods to analyze genetic data, I am excited to explore other avenues that bridge my interest in biology and machine learning!
Week 1 (June 5th - June 10th): Bootcamp at Johns Hopkins
For the first week of my internship, I flew to Baltimore to attend the Rosetta Code School, held at Johns Hopkins University. My cohort consisted of students from varying academic backgrounds, so the code school aimed to make sure we were all on the same page and familiarize us with topics such as protein-protein interactions, the RosettaPython code, and related machine-learning models used for protein structure prediction/design.
I reached my hotel at 8 p.m. so I missed the welcome dinner :( However, when I met my fellow interns the next morning, I was pleasantly surprised by how diverse my cohort was (most of us were women of color/international students). It was also great to know that people were just as clueless about the BootCamp as I was.
Our boot camp would start at 9 am and finish at 10 pm so we would be too tired to do anything by the end of the day. However, it was really helpful in terms of making me feel more confident in my computational competencies since I had more of a wet lab experience.
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Some pictures I took at the Baltimore Museum of Art
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Week 2 (June 11th - June 18th) : Settling in North Carolina
This week, I flew to North Carolina to spend the next 8 weeks working on my project at UNC Chapel Hill. Unfortunately, I could not start working this week since I had issues with my work authorization (I still had not received my work authorization approval that is required for international students on an F-1 VISA in the U.S.). Therefore, I spent most of the week doing preliminary research for my project by reading papers.
P.S., North Carolina was WAY more humid than I expected.
Week 3 (June 19th - June 25th)
I got to meet my research mentor, my P.I., and the rest of my lab members this week. Since most of my work is computational, I had the opportunity to work remotely on some days (so that's what I did for most of this week). I zoomed in with my research mentor who introduced me to the project.
My project involved testing the utility of a computational pipeline named EvoPro (that is designed by my mentor) by designing protein binders that detect conformational changes in the integrin protein. Integrin is a cell surface protein that plays an important role in platelet aggregation and cell signaling. It adopts distinct conformations (structures) based on its activity (active vs. inactive) which further affects its affinity to ligands (small molecules that bind with integrin).
Our objective was to investigate the conformations of the α2β3 integrin (a specific kind of integrin protein) in mice by targeting amino acid residues that are exposed in the open confirmation but not in the closed state. Although my project did not have any direct therapeutic implications, it could be applied to other areas of research such as engineering personalized protein therapeutics/medicine.
Different conformations of integrin
Week 4 (June 26th - July 2nd)
This week I started using PyMOL, a protein visualization app, to analyze the structure of human integrin and align it to the mice integrin to be able to start designing the binders. This is because there are no PDB (3D structures of proteins) structures available for mice integrin.
Week 8 (July 24th - July 30th)
This week I was busy preparing to present my progress to my lab members in the weekly meeting. I also presented a paper from my lab to the members of my cohort via the virtual journal club meetings that are held every week.
Week 9 (July 31st -Aug 5th)
I spent my last week at UNC finishing up compiling the results and preparing a poster for the Rosetta Conference I was planning to attend next week.
I also talked with some of my lab members about graduate school applications and got some valuable advice!
Week 10 (Aug 5th-Aug 10th): Rosetta Con 2023
For the final week of my internship, I flew to Seattle to attend the RosettaCon. The RosettaCon is a conference where interns present their summer research and connect with Rosetta developers from around the world.
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