You are talking about tagging by expressing with like a GFP. That can and does affect protein function very very much in many cases! Steric hindrance alone of the presence of the massive fluorescent protein tag can block protein protein binding sites, make conformational changes difficult and slow substrate binding and turnover rates.
Every change we make to a protein can have far reaching effects, some of which are actually somewhat small, and when looking at a cell, may not be seen until weeks have passed, when all of the sudden the cells get 'sick' due to an imballance in a pathway.
:)
Unfortunately this doesn't get around that caveat! Detailed stufy of a proteins function is necessary to prove you havent perturbed it too much with your label.
Yeah, I know, but it's still surprising that as best we can tell this or that animal/cell is able to live with no problems and the protein carry out its function even though it's dragging behind a big, fat fluorescent tag!
In many cases yeah it is interesting. :)