This week, I finally got some preliminary results for modelling Class II MHCs – and they’re very promising. The orignal concern was that the workflow that’s currently being used for Class I MHCs wouldn’t be transferable to Class II MHCs because the two classes hold their peptides differently. Class I MHCs deal with shorter peptides, have a deeper binding cleft, and the peptide forms an arch; Class II MHCs have longer peptides that often have free-floating ends, the binding site is between two protein chains (rather than one) and the peptide is held much straighter. Random Coordinate Descent (RCD) is the approach used to come up with different peptide configurations, and since it works really well on the Class I arch-shaped peptide, there was some concern that it wouldn’t work as well on the straighter Class II peptide. However, I gather some examples, ran RCD, and determined that the current workflow should work!

Outside of the lab, my friends and I also visited the NASA Space Center – it was super cool to wander around the exhibits, see the Apollo Mission Control Center, and grab some famous Texas fried chicken on the way back.