This week, I was assigned my own chunk of the project – looking into modelling Class II MHCs. In structure, these complexes are different from the Class I MHCs because the binding side is formed from two amino acid chains, rather than just one. In function, Class II MHCs present exogenous (foreign) peptides to immune cells, so they’re typically associated with pathogens like viruses and bacteria, whereas Class I MHCs present endogenous/cytoplasmic peptides, which can be indicators for cancer and cell health monitoring.

I enjoyed learning a bit more about Class II MHCs, and it was interesting to see what tools include MHC-II structures (there aren’t many). When I started trying to code the peptide-MHC reconstruction, I started running into a lot more issues than anticipated. Firstly, it was hard to find PDB files that were somewhat logical – many included weird fields I couldn’t understand. When I finally found a couple of good templates, I started preprocessing, but ran into some issues with permissions and with the PDB tools I was using, but eventally I got some nicely formatted data I can begin to use.

Starting Friday and going into next week, I hope to have some preliminary results to see if the current tool is capable of hadeling these Class II MHCs

Beyond work, I’ve been exploring the area around Rice. Hermann Park is nearby, and they placed fake goose statues near the wayer than attracted a ton of other birds – it was kind of surreal to run past.