GROMACS for Protein binding help

User discussions
1

GROMACS version: 2024.1
GROMACS modification: Yes/No

Hi all,
I’m very new to GROMACS so I would appreciate some guidance. I am trying to simulate the binding of two proteins using GROMACS but no matter what I do or what I change the two never bind, they simply float around each other. My set up for the simulation included placing both proteins in a PDB file where the binding sites were within 100 Angstroms of one another. I then mostly followed the steps in the Lysozyme in Water tutorial. I have attempted to use both CHARMM36 as well as AMBER 99SB*-ILDN as my force field. If anybody has some suggestions on what would be the fix to the issue I would appreciate some help!

2

can you share the snapshot, you kept two proteins far and expect them to bind together??

3

No, I apologize for the misunderstanding. The two proteins’ binding sites are 6.2 angstroms apart. Here is the PDB file before the GROMACS steps.
image

4

I still dont understand this. How did you find the distance? how long is your simulation? there is no assurance that these two binds together for your simulation time. It would be better to docking and MD (if you have binding site informations)

5

I see, thank you for the input. I will work on that right away. The distance was found using PyMOL’s measuring tools and they were placed in this orientation because we found in a paper that illustrated where the two protein would bind. I ran the simulation for both 1 ns and 2 ns but the same conclusion was reached.

6

1 ns and 2 ns are very low time for even equilibration. If your aim is to study how the protein binding interactions-first choice is docking.

You may find interaction (binding) by keeping both at a certain distance, but that depends on simulation time scale and proteins.

7

Thank you so much! I’ll begin modifying my approach.

8

I realize that perhaps there may have been some miscommunication on my end. I’m not specifically studying the binding of the two proteins (protein binding interaction) because I know for a fact they bind in that area. I am instead studying the conformation change after the proteins are bound but am having problems making them bind in the simulation.

9

If you know how they bind, I suggest starting your simulation from an initial configuration closer to the bound state. Is there a PDB available? Can you generate a structure prediction using Alphafold? Starting from there you may be able to see whether conformational changes take place. Also, you may find that the force field you are using results in dissociation. But there will be less guessing than in your current setup.