Y2H intrigue

[Scie]

Hi All,

I've been intrigued by what I found on my Y2H screen and now I'm starting to loose sleep over it!

I've done a Y2H screen on rat brain cDNA library using the last 49 amino acids of the C-term tail of a transmembrane protein. I've had beautiful results. HOWEVER, similar experiments done by 2 independent labs (and published) have detected completely different interactions (!!!) but in agreement with own another but not my experiment. Somebody else in my lab repeated my experiment and had the exact results as me, which were still different from the published material. The main difference, is that the published material used the last 53 amino acids instead of 49.
I've been thinking about this over and over and cannot come up with an explanation (perhaps difference in stringency?). Would anyone be able to help me with some ideas of what could possibly be happening?

Many thanks in advance

Distressed scientist!

[Sandra_T]

Not sure what the answer is though the first thought is does that affect protein folding? From here, that seems like quite a short section to use as bait? What was the reason?