How to perform Membrane Z-positioning restraints on the HADDOCK Web Server?

HADDOCK
1

Hello,

I am working on a protein–protein docking project using the HADDOCK Web Server.
In my system:

Protein A (residues 1–437) is a membrane protein

Protein B (residues 47–558) is a soluble protein

I don’t have any experimental information to define active residues, so I first tried ab-initio docking. However, the results often show Protein B docking at the transmembrane surface of Protein A, which is not desirable.

While reviewing the documentation, I found the Membrane Z-positioning restraints, which seem useful to guide the docking interface away from the membrane core. I would like to apply these restraints to keep Protein B outside the membrane region.

However, I couldn’t find any option related to Z-positioning restraints in the Web Server interface.
Is there currently a way to apply Membrane Z-positioning restraints on the HADDOCK Web Server?
Or, alternatively, is there another way to restrict Protein B to only dock at the solvent-exposed surface of Protein A?

Here are the parameters I would like to use:

zres_on=true
kzres=10.0
zresmax=14.9
zresmin=-14.9
numzres=1
zres_sta_1=“47”
zres_end_1=“558”
zres_seg_1=“B”
zres_type_1=“outside”

Any help or suggestions would be greatly appreciated.
Thank you very much!

2

This is a bit trickier.
It is an experimental “feature” not properly tested and not available on the server.

I would suggest in this case an alternative approach if you want to use the server

  1. Select all the solvent accessible residues of your membrane protein
  2. Pick one residue at the center of your soluble protein
  3. Generate one ambiguous restraint from that residue to all solvent accessible residues, increasing the distance cutoff from the default 2A to e.g. the radius of hydration of your protein (or a bit below that).

For this you will need to create the restraint file (e.g. using the gentbl service on our server), and upload it to the HADDOCK server at unambiguous restraint.

This might fully prevent binding in the transmembrane regions though.

3

I have followed the advice, but something seems to be wrong with the results. The docking results show that Protein A and Protein B are far apart.

I used the gentbl tool to generate the .tbl file and entered the following details:

  • Interactor 1: Chain A, Passive: Residues 34, 35, …, 402, 404, Partner: 2
  • Interactor 2: Chain B, Active: Residue 500, Partner: 1

The resulting .tbl file looks like this:

! HADDOCK AIR restraints
! HADDOCK AIR restraints for 1st selection
!
! HADDOCK AIR restraints for 2nd selection
!
assign ( resid 500 and segid B)
       (
        ( resid 34  and segid A)
     or
        ( resid 35  and segid A)
     or
        ...
     or
        ( resid 402  and segid A)
     or
        ( resid 404  and segid A)
       )  2.0 2.0 0.0

After generating the file, I modified the values from 2.0 2.0 0.0 to 50.0 50.0 0.0. I then submitted the job on the web server by uploading the PDB files under the Input Data tab and left everything in the Input Parameters tab unchanged. Finally, I uploaded this .tbl file under the Distance Restraints section in the Docking Parameters tab.

Additionally, I am still unclear about the difference between ambiguous restraints and unambiguous restraints in this context. I tried both options (Job ID 506173 for upload tbl file under unabigous restraints, Job ID 505672 for uploading tbl file under ambigous restraint), but in either case, the results show that Protein A and Protein B are still positioned very far apart in the docking results.

Is there any mistake I made? Thank you for your reply.

4

50 as uppper limit for the distance restraints is way too much. Because of the way the effective distance is calculated the restraint should be much shorter. Try first with 5 or 10