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?
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
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.
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
Sorry to bother you again. I would like to ask for your advice. When I fixed Zn2+860 at the center of the pocket with H305, H309, and E328, as shown below:
assign (resid 860 and segid A and name “ZN+2”)
(resid 305 and segid A and name NE2) 2.5 2.5 0.0
assign (resid 860 and segid A and name “ZN+2”)
(resid 309 and segid A and name NE2) 2.5 2.5 0.0
assign (resid 860 and segid A and name “ZN+2”)
(resid 328 and segid A and name OE1) 2.5 2.5 0.0
assign (resid 860 and segid A and name “ZN+2”)
(resid 328 and segid A and name OE2) 2.5 2.5 0.0
assign (resid 860 and segid A and name “ZN+2”)
(resid 11 and segid B and name O) 2.5 2.5 0.0
The results from haddock show that Zn2+ is very far from the pocket center of H305, H309, and E328. Could you please tell me how to deal with this issue?
Yes, Professor Bonvin. The Zinc is in the binding site at the start.
Could you please tell me if there is something wrong?
Attached please find the PDBs of Zinc protein (7v9q-open.pdb) and the docking peptide (LP.pdb) and the restrain file (TBL-new.txt) and the docking parameters (job_params-2).
My haddock ID is 3868299572, and the lastest task named “20240716-norestrain-Zn-DA”
Your help will make a lot of sense to me. Thanks in advance.
Very strange - the problem occurs when generating the topology and building the missing atoms.
HADDOCK does report high energies of your input protein. How did you get it?
There seem to be something fishy about the structure… Very high van der Waals energies among others.
Could you try to minimise first your structure?
PS: I tested with another system containing two zinc atoms and no issues.