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
Indeed - no modified ARG supported at this time.
Are you looking into ARG methylation?
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 …
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/
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
There might be tricks we can try…
Would you have a PDB file of that modified ARG?
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 ?
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)
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
Dear Jean-Yves
Did you manage to get it running?
Could you share the ATB parameters/topology and PDB files?
Dear Alexandre,
Many thanks for asking. No, unfortunately, I have only been able to
study the natural peptides and one of their mutants.
One of these peptides would be of particular interest (my idea was to
try to study a simplified model of the system with the chemical
modification by DFT calculations…). I am still in the analysis of the
various Haddock results.
Pfease find below the natural peptide
(Model_peptide30AA_R3212_prep_optH.pdb) and a model of the targeted
receptor(1f5y_model2_prepared_Hminimized_v9.pdb) pdb files together with
the ATB parameters and topology files of the modified arginine
To be continued
Best regards
JY
(attachments)
All_Atoms_parameter_file.txt (12.4 KB)
All_Atoms_parameter_file.txt (12.4 KB)
CNS_All_Atoms_topology_file.txt (10.6 KB)
CNS_United_Atoms_parameter_file.txt (9.64 KB)
CNS_United_Atoms_topology_file.txt (8.34 KB)
QM_geom_UnitedAtom.pdb (4.47 KB)
CNS_United_Atoms_topology_file.txt (8.34 KB)
QM_geom_UnitedAtom.pdb (4.47 KB)
Unoptimized_QM_geom_UnitedAtom.pdb (2.97 KB)
Models_peptide30AA_R3212_prep_optH.pdb (40.8 KB)
1f5y_model2_prepared_Hminimized_v9.pdb (94.3 KB)