Allison Weis: Finding Vaccine Candidates for Malaria: A Bioinformatics approach

One project I worked on this summer was finding human transmembrane proteins that interact with the immune protein defensin based on the charges of their extracellular regions. Lysine and arginine add a positive charge while glutamic acid and aspartic acid add a negative charge. I determined which regions in which to count by aligning the proteins with the two transmembrane proteins of known structure. The extracellular portions for the known structures could be determined visually using Rasmol.

The other project I worked on this summer was beginning the search for a set of possible vaccine candidates for malaria and determining the necessary future work. I was looking for proteins which what we believe to be an unusual domain combination, export from the parasite and regulation. I looked for proteins which had either a transmembrane region or a secretion signal and then also a regulatory domain. I identified a set of possible protein candidates, but determined that in many cases the existing annotation is too poor to make significant claims about the proteins’ relevance. Future work would need to include redoing many of these predictions using newer software and also searching for other signs of extracellular regions, such as disulfide bonds.