HADDOCK, protein protein docking with one protein with a modified Arginine residue

HADDOCK
1

Hi everyone,

I need to investigate the consequences, in particular in terms of docking scores, of a chemical modification of the arginine side chain of a key arginine residue (which is the active residue of one of the two proteins) on its interactions. Unless a mistake (I am a new user of HADDOCK), no chemical modification of ARG appears to be supported by HADDOCK (not included in the list or modifications provided). Is there another way to treat this system with HADDOCK?

Many thanks for your time,

Best

JY

2

Indeed - no modified ARG supported at this time.

Are you looking into ARG methylation?

3

Thanks for the fast answer. It is not a ARG methylation, it corresponds to the addition of a CH(CH3)-COOH fragment that finally leads to a five membered ring, so a rather complicated chemical modifification …

4

Non-trivial indeed…

As a first step you could test if you can get it parametrized in the ATB server - https://atb.uq.edu.au/

5

Ok, thanks, I am going to have a look. But, unless I have not understood, even if I could get it parametrized, I would need to use another protein-protein docking server / program to run the corresponding calculations ?
Thanks for your help

6

There might be tricks we can try…

Would you have a PDB file of that modified ARG?

7

Ok, thanks ! However, as I am a new user, I cannot attached any file apparently. May be I could send it to your by mail ?

8

email is fine

9

Please find attached the modified arginine (I have tried to use the
naming of atoms recommended for the ones introduced). I have also
attached the pdb file of the corresponding proteic structure (32
residues taking into account the capping residues at the N and C ends.

Many thanks for your time

JY

(attachments)

Modifed_ARG.pdb (3.33 KB)
modelpeptide_30AA_R2907_MGHmod_prepared_Hminimized_3.pdb (40.5 KB)

10

As suggested in our previous discussion, I have now obtained parameters for the modified arginine I am interested in through through the ABT server. The questions now is if I can use these parameters (how ?) through the HADDOCK server. I am afraid by looking at previous similar discussions on the server that it is not possible, and that only a local version of the program would do the job. Do you confirm this ? Is there another alternative ?

Thanks again for your time and help