Protein structure preparation

GROMACS
1

Hello forum,

I would like to know if there is an established procedure for dealing with structures having a high net-charge. I am not a chem, but I understand that this will mess with the simulation. I am aware that counter-ions should be added to stabilize the system. Therefore, I have the following questions. Any relevant resources or keywords to search would be really helpful for me.

  1. What is an acceptable non-zero net-charge? How could we estimate this? Does it have to do with the hydrophobic to hydrophilic residues ratio?

  2. Do we have to look for the protonation states in the protein’s isoelectric point? Will that pH be realistic in vivo?

  3. There is a worse scenario of having a non-integer net-charge. Any pointers on this? Is there any guide available how to tackle this?

Thank you in advance.

2

I asked elsewhere and did some more research, so for anyone interested:

1 & 2. This is standard chemistry but some concepts are not so clear at first for people coming from different backgrounds:

“At a pH below their pI (isoelectric point), proteins carry a net positive charge; above their pI they carry a net negative charge.”

Human body’s pH is between 7.35-7.45. My protein’s pI is around 9.3 pH (I used https://www.phosphosite.org/ & http://isoelectricpointdb.org/ to find it), so in α 7.4 pH environment it will have a positive net-charge. I think this is also helpful as a sanity check if there is a pI value available.
Therefore, we should look for the protonation states of the amino acids in a pH near the body’s pH.

  1. A non-integer net-charge is linked to the topology where it was calculated from. Topology is derived from the force field used so this issue lies between these two. It hold the charge values for its atom in your system. In my case, the force field has non-integer values by itself so it was something controlled and expected but I failed to notice it.

You can find it here : https://github.com/paulrobustelli/Force-Fields (DES-Amber)

If I misinterpret something, corrections would have been more than welcome. There are not so detailed answers online so I thought this could help someone. Thank you.