Protein and peptide-dna complex docking

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Dear Alexandre and HADDOCK users,

I want to do protein -dna docking by haddock2.2. The situation in my case is :

  1. The interaction between my protein A and DNA is weak. The DNA binding sites on protein A can be mapped through NMR titration and the structure of protein A has been solved. But the protein A binding sites on DNA can not be verified.

  2. To solve the problem of 1), we found that peptide B can tightly bind with DNA in the minor groove. The structure of peptide B with DNA is known. Then we linked protein A with peptide B and got the protein A- peptide B by expression.
    But we failed to detect inter-NOES between protein and DNA.

My question is how I can do the docking between protein A and the complex of peptide B-DNA by HADDOCK2.2.

I know that there is a multi-body docking mode in HADDOCK2.2. But as described above, the protein A and peptide B has been integrated into a whole protein and the peptide B is flexible in solution and no interaction with protein A. The orientation of the protein A should be limited by the existence of peptide B, not like separately docking.

In that case, how can I do the docking with the peptide B-DNA complex using protein A?

Thanks in advance.


My question is how I can do the docking between protein A and the complex of
peptide B-DNA by HADDOCK2.2.

Give the complex of the peptide and DNA to HADDOCK. BUT their residue numbering should not overlap (several threads about this in this forum) and they should have a unique chainID. In the web portal, define it then as protein-DNA for the molecule type

And do you have restraints between your protein and the peptide?

Dear Alexandre,

Thanks for your reply.

There are no any restraints between protein and the peptide.


So how were you planning to dock the protein onto the peptide-DNA complex?

Dear Alexandre,

There is no interaction between peptide and protein. And peptide and protein are linked by 4 residues, GSGS, as a whole molecule.

Can I integrate the protein into peptide-DNA complex and allow the protein to do the docking based on CSP data?


So you do have info for docking the protein! (The CSP data).

Follow then the protocol in my first answer:

  • One molecule: the protein
  • The other molecule: the peptide/DNA complex

Define your restraints based on CSP data (are these for the protein side only?) What about the DNA info?
Add a loose distance restraint between your protein and the peptide to mimic the GSGS linkage

Dear Alexandre,

Yes, only the CSP data for protein is available and I can not get the CSP data for DNA.
Both the peptide and protein recognize the GAAATTC fragment of the 12bp B-form DNA. Based on the structure of the peptide/DNA complex and the biochemical data, the peptide and protein bind the minor and major groove of the GAAATTC fragment respectively, how do I define the restraints for dna?



I would then define as passive in HADDOCK the GAATTC fragment

Dear Alexandre,

If define the GAATTC fragment as passive in HADDOCK, how do I define the active sites of the DNA?
As the protein binds with the GAATTC fragment, leave the active sites of the DNA blank or the whole dna as active?


No active on the DNA, only on the protein based on your CSP data