In article <firstname.lastname@example.org >, "Yulia Shifrin" <email@example.com> wrote:
Yulya, welcome to real life
The thing is, no two proteins are the same. And different proteins behave
differently. They have different steady state level of expression (a
balance of transcription/translation and proteolysis/degradation).
What you are describing is *not* proper estimate of transfection
efficiency. You'd be better off co-transfecting two plasmids - one
encoding plain RFP, another your protein. Then the readout of
fluorescence will have more to do with transfection per se (and even then,
it's perfectly possible that your protein influences RFP expression).
If it's of any consolation, I had a case recently expressing two versions
of a ~ 95K protein functional chunk. They differed in 2 kDa, yet shorter
version expressed ~ 10X worse.