Monday, March 18, 2013

How Many Proteins Are Actually In There

Sooo, people simulate proteins using Molecular Dynamics. Basically, you are sticking a single virtual protein molecule in a virtual box of H2O molecules and calculating newtons laws of motion to watch what happens.

When you work with proteins experimentally you can rarely see them unless the concentration is really really high or the protein aggregates. Doing certain Biophyiscal measurements, I know the concentration of the protein because I can calculate it based on light absorbance at specific wavelengths but I never had an intuition for what this meant. Normally experimental concentrations range from 1 micromolar to ~5 millimolar and only 5 millimolar if you have a super stable non-aggregating protein.

So how do I compare a single protein in simulation in a 100nm^3 water box to the proteins I work with in a cuvette or NMR tube?

Ok so let's say that the protein is 4kDa so it's weight in grams would be
 (4000/6.022E23) = ~6.6E-21g
 We just divide it's Mass by Avagadro's number since kiloDalton's are an Atomic Mass Unit.

How big is 100nm^3.

1nm^3 is equal to 1E-24 L. WOW!
An MD simulation is ~100nm^3 so we have 1E-22 L.

How many molecules would 1mM be in 100nm^3?

((4000 g * 1 mM) * 1E-22 L) / 6.6E-21 g per one protein = 0.06 molecules

That is not even one molecule!

16.5mM is ~1 molecule.
100mM is ~6 molecules and 165mM is ~10 molecules

So the effective concentration of a small protein in an MD simulation is much much higher then one could ever measure or use in real life. 

I know this is super lame but I liked it.