idobox wrote:So how do you call a protein with the right sequence of amino acids, but not the right folding?
The fancy name for it is misfolded or unfolded protein. I don't think I've ever heard it referred to as anything else.
idobox wrote:or a precursor protein that could not be used because an enzyme is lacking?
An inactive precursor. There are lots of these around, they are held on to in large quantities, ready to be used upon exposure to protease.
Most prions, last time I checked (and this may have changed, it's an active field that I'm not direectly involved in) work more like precursors than misfolding events.
Take the hypothetical normal host protein Hrmlss, with the sequence GHPPSTWECDAAMQR
. Now say that there's another protein, Crzbov, with the sequence STWECDAAMQR (note the similarity, highlighted in bold). Crzbov is capable of cleaving the amino terminal GHPP- from Hrmlss. If Crzbov comes in contact with any Hrmlss, the Hrmlss is instantly converted into Crzbov, and you now have two copies of Crzbov and a little peptide sequence (GHPP) left over. If this is in a host tissue, full of Hrmlss, this will accelerate exponentially until the Hrmlss is used up.
Transgenes do usually affect and are affected by the areas they lie down in. I used to work on a mouse line that had a trophoblast-specific transgene lie down in an unknown location that caused ectopic expression in the gut, with very welcome grant-generating results. We never did find out what the regulatory event was, but something near the insertion site caused the transgene to get expressed where it shouldn't. A guy I went to grad school with thought he was about to cure cancer (really). But in the end, it was just because his promoter was leaking onto some neighboring cell cycle arresting genes. Whenever he activated his gene, he also turned on some other already well-known genes.
This is why you never make just one transgenic; you make 5-6 at a time. Not only does this hedge your bets in the failure rate of making tg lines, but it protects you from misrepresented results. If you get a phenotype that's just in one line, you know it's probably not from just your gene.