CD79 fusions
We decided that it would be better to fuse the Gal4VP16 to CD79A and CD79B because they are in close proximity to the binding site of Lyn and Syk and thus make a more promising target for TEV protease cleavage. The heavy chain was barely within the membrane and very distant from the binding site of Syk and Lyn. It was decided to minimize the distance of the CD79X-Gal4VP16 linkers since that would increase the distance between the Syk and Lyn binding sites and the TEV cleavage site (TCS). Thus they were given only the TCS as a linker.
Syk-TEV & Lyn-TEV Fusions
Syk-TEV and Lyn-TEV Fusion proteins were designed with a 15 AA Serine Glycine Linker to allow the TEV protease enough room to reach from the Syk and Lyn binding sites down to the TCS. This long linker was chosen because the distance between the Syk and Lyn binding sites was 15+ amino acids away from the TCS.