EOM for a pentamer with disordered regions

[franke-biosaxs]

On 2023-12-21 01:11:15, user lykos wrote:

I am trying to run EOM on a mixture of a protein and a disordered peptide. I have a .pdb file from the PDB database of the protein that is a pentamer with intrinsically disordered regions and folded domains. How do I use the online GUI to indicate the folded regions? Do I just need to input the residue numbers corresponding to each region, in which case the appropriate region of the .pdb file will be used for the folded domains minus the disordered regions? Or do I need somehow to remove (if possible) the residues corresponding to the disordered regions from the .pdb file? And how do I treat the pentameric aspect?

EDIT: When I enter the PDB for the protein as in the attached screenshot, I get the following errors. I suppose it's related to the above issues. In the fast file, there are two sequences, A and B, corresponding to the protein and the peptide. The .pdb file, as mentioned, corresponds to the entire pentameric protein. Any idea how to correct this?

Errors and/or warnings registered during execution:
error: alignment mismatch of structured domain with chain ID 'A'. Best match found in residue range from 45 to 119
error: structured domain with chain ID 'B' has not been assigned
error: structured domain with chain ID 'C' has not been assigned
error: structured domain with chain ID 'D' has not been assigned
error: structured domain with chain ID 'E' has not been assigned

Attachments:

• 30223_9991958af34f228e54ebefe383e56dc1.png

[franke-biosaxs]

On 2023-12-21 17:09:17, user AL wrote:

lykos wrote

I am trying to run EOM on a mixture of a protein and a disordered peptide.

I don't think you can run EOM online for a mixture of two non-interacting proteins. But you can create two pools of models (one for the pentamer, the other for the peptide) and run FFMAKER on your PC. In EOM online use Advanced settings > Keep generated models.

lykos wrote

I have a .pdb file from the PDB database of the protein that is a pentamer with intrinsically disordered regions and folded domains. How do I use the online GUI to indicate the folded regions? Do I just need to input the residue numbers corresponding to each region, in which case the appropriate region of the .pdb file will be used for the folded domains minus the disordered regions? Or do I need somehow to remove (if possible) the residues corresponding to the disordered regions from the .pdb file? And how do I treat the pentameric aspect?

I think you should remove the disordered regions from the pdb file; make sure that you have five chains in your sequence file; save one file as a pentamer (with five chains) and, if you have other folded domains connected by flexible linkers, save them as separate single-chain pdb files.
Here's an explanation for a dimer case.

[franke-biosaxs]

On 2023-12-21 22:27:36, user lykos wrote:

Thank you, AL. There are two structured regions in each arm of the pentamer. Are you suggesting to keep both structured regions in the same .pdb file? In other words, just remove the disordered regions in each pentamer? I just to want to make sure I'm understanding you correctly. Thank you.

[franke-biosaxs]

On 2024-01-09 16:35:59, user AL wrote:

I'm not sure if keeping both structured regions in the same .pdb file will work but you can try.
I'd save them to two separate files and mark them as 'fixed' (instead of 'free').