Extracellular space - no counterions?

User discussions
1

GROMACS version: conda
GROMACS modification: Yes/No

Hi,

I have a protein that binds dsDNA, but this happens in extracellular space. Would it thus make sense not to add counterions in GROMACS simulation?

2

There are ions in the extracellular space as well. But the concentrations are not the same as inside cells.

3

Thanks for the quick reply.

My bacteria are pathogens, having a transmembrane protein that binds dsDNA in extracellular space. This may be in the throat of humans, mucus of fish, etc., so I am not sure what ion concentration (or no ions, if that is appropriate) to use in my simulations.

For the record, I just used the tutorial.ipynb (under Introduction to Membrane-Protein Simulation — GROMACS tutorials https://tutorials.gromacs.org documentation) for my docked protein-DNA complex.

Best regards

4

Firstly, you almost certainly want counter ions to neutralise the system, at least.

Human airway mucus also contains ions, see e.g. Physicochemical properties of mucus and their impact on transmucosal drug delivery - PMC. I presume that the mucus salt concentrations are different between human and fish.

So, I would either use as realistic salt concentrations as possible, or clearly state (in the publication/presentation/poster) that you have not used physiological salt concentrations and why you have assumed it not to be important. In many cases it may not make a large difference if you use physiological salt concentrations or not.