Is it necessary to genion ions to protein system

User discussions
1

GROMACS version: 2019.6
GROMACS modification: No
Here post your question

I downloaded PDB of protein from PDB bank. But the protein contain -17 charge. Then I dissovled it in formic aicd and calcium chloride and then balanced the charge. Then I removed the calcium chloride and add water (spc216) to study structure change by simulating the interface change between water and formic acid. But during aboved process, I didn’t to balanced the charge. Because, I want to know if it can back to original structure down load from PDB bank. Is it the result right?

2

HI,

Neutralize your protein once in water solution and better neutralize by using ion concentration at which the experiment (“original” structure) was performed (if known)

Alessandra

3

Thanks. If the result, neutralized protein once in water, were not change that can identify ions were not affect the protein system isn’t it?

4

HI,
Just to avoid misunderstanding. What exactly do you want to see? the effect of the formic acid on the protein structure?
Thank you
Alessandra

5

Hi,
Yeah, It not exactly to see the effect of the formic acid on the protein structure. I didn’t got your advice of neutralizing protein once in water solution what that mean? First, put protein in water solution contain ions, and then put it in pure formic acid?

Actually, I made a interface between water and formic acid. In fomic acid solution contain protein. I want to see what will be happen? But, I didn’t neutralize charge in mixed soltution. Beacuse, I wish the protein can back to original structure which was downed load from PDB bank.

image
image345×664 256 KB

JieChen

6

Hi,
my point was that experiments are performed in a buffer, thus to be representative the water phase has to have the same ionic strength of original experiment.
That may be difficult to get in your specific case, since ions can move from one phase to the other, but one could at least to take care that the system ( in your case protein + water phase + formic acid phase+ other ) is neutral. One can achieve this using gmx genion.
I hope it helps
Best regards
Alessandra

1 Like