Tuck, if I understand this, we are talking of a very fundamental limitation, one that people have known about for many years and unlikely to be "fixed" one of these days. The original article on FRET by a man named Forster was published in 1948; BRET, of course, is a slight twist on the basic FRET concept. The fundamental limitation is in the physics of (F/B)RET whereby donor/acceptor partners need to be within some critical distance for the measurement to be possible. For particular proteins one could, I guess, tweak the system to make it work. This would not be possible in general protein-protein mapping proteomics projects, but may be doable for small molecule screening and a *given* pair of interacting proteins. If you really, really want to use the BRET system and your pair does not appear to interact by BRET even though you know it does, then tweaking at the molecular biology level may allow you to "fix" the problem for the particular case. An interesting survey may be found in ncbi.nlm.nih.gov (admittedly full-text would be a lot more informative here, but I think you get a flavor from the abstract on the main issues at hand: this is where I would start with the "tweaking")
Turns out a very tricklish, formerly very active, SI contributor, Richard Haugland of Molecular Probes, would know this area hands down. If anyone is willing to "resurrect" him ...
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