I assume you mean all the interactions occur outside the cell?
One of the advantages of standard yeast two hybrid systems is that they
level the playing field with respect to protein localization. This can lead
to false positives (extra-cellular/ intra-cellular etc.) but should not be a
problem for you. The problem of course is if the interaction you are
looking for is dependent on a post-translational modification not applied to
intracellular proteins (glycosylation etc...).
If your matrix protein contains a transmembrane domain I would suggest
removing it as well.
There are other membrane based two hybrid systems out there which mount the
bait protein onto the intracellular leaf of the cell membrane. These
systems work by triggering a signal transduction cascade when the bait/ prey
interact. Of course they are also internal so are bound by the same
limitations as the standard transcription factor methods.
> Helo, I hope some people here in this forum familar with yeast
> two-hybrid system. I am working on an extracellular protein and would
> like to identify its interaction partners. I prefer yeast two-hybrid
> approach but it is said that matrix molecule may not suit for the
> screening since all the interactions happen inside the yeast cell.
> However, several papers do describe the isiolation of the binding
> proteins for matrix protein. Can anyone tell me what is chance to get
> succeed? Or is there a modified two-hybrid system for matrix proteins?
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