User:ElNando888/Blog/Aptamers

From Eterna Wiki

< User:ElNando888‎ | Blog

Revision as of 21:38, 23 April 2014 by ElNando888 (talk | contribs) (still mostly a draft)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)

(work in progress)

 

FMN EteRNA.png

We are all so very familiar with this picture. The rotating molecule, bound to its immutable aptamer, and the resulting "bonus", which also seems perfectly constant...

 

I mentioned a few times in this blog that EteRNA simplifies many things. With good reasons, of course. But we will soon need to get past some of these (over)simplifications, so I'd like to give you guys a heads-up.

So, we shall begin with this information acquired from scientific sources (which I need to find back to cite properly here, where the hell did I read that...):

The binding energy for FMN to the RNA aptamer is: -6.8 kcal/mol.

Wait, what? Not -4.9?

Nope, -6.8

Err...

Let me clarify the previous statement: it means that IF the FMN molecule would stay in place bound to the aptamer permanently, then it would provide -6.8 kcal/mol worth of stabilization to the RNA polymer. And of course, everything is in that "if". Because you guessed it now, that's not (actually, never) the case.

I'd like to invite you to watch this animation I made some time ago:

You can observe that the FMN molecule is "inserted" inside the helix, but contrary to the nucleobases that are covalently attached to the backbone, the FMN molecule is free to dock and undock.

If the EteRNA graphical interface could be made more realistic, it would represent the situation as a RNA surrounded by floating molecules (instead of bubbles)

FMN ready.png

It would stay like for say half a second, and then, one molecule would dock:

FMN bound.png

And the molecule would stay attached for about 1.5 seonds, at which point it would undock. And then, the cycle would simply repeat.

 

Now, if you consider the fact that under specific conditions, the RNA is bound to the FMN in average 72% of the time, then you have no problem figuring out that the average stabilization bonus experienced by the RNA sequence is -6.8 times 72% = (drumroll) about -4.9.

 

Multiple factors come into play for the amount of time that is spent bound rather than unbound. The static ones are related to the nature of the ligand. The association (Ka) and dissociation (Kd) constants have been determined experimentally.

Also, it is quite obvious that if more molecules are in the vincinity of the binding site, the higher the chance for a successful binding. Which is simply a question of concentration.

In EteRNA, it was decided long ago to use 10mM (millimolar), as a way to help players figure out switches. That concentration corresponds to the familiar -4.9 value we all know (don't forget that it's an average). But this is also a clearly exaggerated dosis, and for practical purposes, it would be good if we could manage to work with less. 200uM (micromolar) is the concentration we should shoot for in our future efforts about switches, and that corresponds to an average bonus of -2.51 kcal/mol.