How to achieve peptide binding at the metal center in the internal pocket of a metalloprotein?

Dear all,

I am studying the enzyme EryP (PDB: 7v9n), which has a zinc metal center inside it. The zinc metal can catalyze peptide hydrolysis. Since there is no crystal structure of a zinc metalloprotein in complex with a peptide, I want to achieve docking of the zinc metalloprotein with the peptide.

I have turned off “Remove buried active/passive residues from selection”, set the “Minimum percentage of relative solvent accessibility (RSA) to consider a residue as accessible” to 0, and added constraints between the zinc ion and the active site in the peptide:
assign (resid 861 and segid A)
(resid 11 and segid B and name O) 0.0 0.0 6.0

However, the peptide still binds to the surface of the protein instead of binding to the zinc ion in the internal pocket.

Could you please tell me if it is possible to use HADDOCK to achieve peptide binding at the metal center in the internal pocket of a metalloprotein?

Sincerely
Tian-Yu

Hi Tian-Yu,

Thanks for your interest in using HADDOCK for your research.

What you are trying to achieve is not trivial, and requires some pre-processing of the PDB structure as well as turning on some parameters to be successful:

  • Ensure you removed water molecules from the input PDB structure ( I see that a lot of them are in the binding site )
  • As the binding site is not on the surface of the protein, it was a very good idea to turn off the Remove buried active/passive residues from selection parameter and set the Minimum percentage of relative solvent accessibility (RSA) to consider a residue as accessible to 0 !
  • But, because you need to drag the peptide inside the pocket, you would also have to reduce the VdW components during rigid body docking (it0). For this, please modify the parameter Energy and interaction parameters -> Scaling of intermolecular interactions for rigid body EM to 0.001.
  • Also set to 0 the weight of the VdW componenet in the scoring function at it0; Scoring parameters -> Evdw 1 = 0.
  • Modify the distances in the assign statement to: 2.0 2.0 0.0 (instead of 0.0 0.0 6.0)
  • Finally, because you know where are the water molecules, you could use some of them as bead-shapes and generate restraints to guide your peptide towards those. Have a look at our ligand-shape-docking tutorial

With the hope this can help you!

Cheers

It the pocket large enough to accommodate the peptide?

If yes, then you need to change a few settings to allow the peptide to go “through” the protein to reach the binding site.

For this you will need expert/guru access to the server (request it in your registration page).

The settings to change for a buried site are the same as for step10 in the small ligand shape docking protocol:

https://www.bonvinlab.org/education/HADDOCK24/shape-small-molecule/#4-setting-up-the-docking

  • Step 10: Change the interaction parameters. For this unfold the Energy and interaction parameter menu if not already unfolded

We scale down the interaction during rigid body docking (it0) to allow for better penetration of the ligand in possiblity buried binding sites.

Energy and interaction parameters → Scaling of intermolecular interactions for rigid body EM → 0.001

  • Step 10: Change the scoring function. For this unfold the Scoring parameter menu if not already unfolded

Because of the changes in Step 9 which can result in clashes, we should set the weight of the van der Waals energy term to 0 for it0

Scoring parameters → Evdw 1 → 0

Dear Victor,

Thank you very much for your quick, patient, and helpful response.
I will follow your suggestions and give it a try.
Thanks again for your kind assistance.

Wish everything goes well with you
Tian-Yu

Dear Professor Bonvin,

I am so excited to get your response. The pocket is large enough to accomodate the peptide.
Thank you very much for bringing me this good message. I will give it a try.

Wish you all the best in your work and life
Tian-Yu