Wednesday, April 11, 2012

More thoughts on Water

Well I have been still messing around with the water box simulation and found that 200mM NaCl is not sufficient enough to have large disturbing effects on the water. It is fairly obvious that the effects are largest when two ions of the same charge i.e. negative-negative or positive-positive are near each other you have the biggest effect because waters are trying to align the same way to interact with both i.e. hydrogens near the negative or oxygen near the positive. The concentration of positively charged ions in the cell is ~150mM but this is not including all the other mess of proteins and stuff. Here is an interesting thing I found "Calcium concentration microdomains". I mean if there are in fact microdomains of different ions I think around 300-400mM would be sufficient concentration to start to really mess up the local water structure. I mean empirically we know that ions can help neutralize charges on proteins that can prevent aggregation or other bullshit. But do the ions actually have a significant enough effect to significantly change the thermodynamic equilibrium of a protein and is this change due to water? Things to contemplate.