GFP Folding, pcs (not PCs), and GFP Maturation

Today I Learned:

1) Apparently the time required for a genetic biocircuit to run to completion with a circuit using GFP or a similar protein as the output is mostly dominated by the time it takes for GFP to fold. A new paper from Vincent Noireaux includes, among many other things, a series of experiments expressing one- or two-layer gene circuits (with GFP as the output) in a cell-free transcription/translation (TX-TL) extract. The one-layer circuit was just GFP, expressed under a strong promoter. The two-layer circuits were variations of "GFP under an activatable promoter and the activator under a strong promoter".

The striking thing about their results, to me, is that moving from one layer to two layers results in no more than a 50% increase in time required to run, looking at it by eye. Check out figures 8a-8i in http://ift.tt/1RyeKlC to see for yourself.

2) The standard abbreviation for a parsec is "pc". I was also a little fuzzy on *exactly* what a parsec was, so I checked in on that again -- a parsec is the distance that the end of a pole 1 AU* would make if you pivoted it through 1 arcsecond**. EDIT: Nope, this is wrong -- it's the *length of a pole* required so that when you swing it one arc second, it traces out a distance of 1 AU. Also known as a few lightyears.

* ...and an AU is an Astronomical Unit, or the distance from the Earth to the Sun, or about 8 light-minutes, or 150 gigameters, or 150 million kilometers.

** ...and an arcsecond is 1/60th of a degree, or 4 microradians, or the angle spanning about 2 kilometers on the Earth's surface as measured from the Earth's center, or about 4 seconds' worth of time on a clock face.

3) Above I stated that GFP (green fluorescent protein, the standard fluorescent protein) takes a long time to fold after being translated. Turns out that's not really true -- GFP folds relatively quickly. It *does*, however, take a long time to *mature*, which is not the same thing. See, GFP does something really interesting to become fluorescent. The fluorophore in GFP is actually just a single modified amino acid, a tyrosine, in the core of the protein. To become a fluorophore, though, that tyrosine has to do some really weird (for a protein) chemistry -- it actually self-reacts to form a little pentamer with its own backbone. The amino acids immediately flanking the tyrosine are critical to allowing the reaction to happen, and the rest of the protein stabilizes the reaction even further, to the point that it happens on a reasonable timescale. For a more visual explanation, see http://ift.tt/210HtlD.

Thanks, as so often the case these days, to Anders Knight. And yes, I suspect I will be riding this knowledge gradient until Anders finishes his rotation with us.