Bidentate ligand docking

HADDOCK
1

Good afternoon,

TLDR; How do I dock a bidentate ligand in which one site is known with atomic resolution and the other is only characterized by AIRs and UIRs.

Full;

I am trying to dock a bidentate protein ligand to another protein. One binding interaction is fully characterized via NMR and X-Ray crystallography. The second binding site is unknown. I have UIRs and AIRs characterizing the second binding site.

When docking the bidentate ligand, 90% of structures incorrectly reproduce the known binding site.

In an attempt to rectify, the system was converted such that one protein contains the known NMR/XRAY structure (protein and first portion of the bidentate ligand) and the docked protein is the second portion of the bidentate ligand. This was accomplished by cutting the bidentate ligand at a disordered region between the binding domains and using employed numerous geometric constraints to preserve a pseudo-peptide bond (C-N distances, N-O distances, dihedrals, etc) and then docking the second portion of the bidentate ligand. In addition, the disordered region is marked as fully flexible.

Despite this, all docked structures are physically impossible. The broken peptide bond COOH and NH2 are ~ 10-20 Angstroms apart despite having ~ 10 restraints with narrow tolerance. This only results in inflated violation energies.

How can I dock this bidentate ligand while preserving the known binding site AND the spatial/geometric limitations imposed by peptide sequence/orientations.

THANKS!

2

You could define unambiguous distance restraints between, e.g. CA atoms of the first domain to the ones in the known binding site and provide those as unambiguous restraints.

But if you you have a flexible linker between your two domains, as the first stage is rigid body docking, you might not satisfy the restraints for the two binding sites…
Best would be to simply remove the flexible linker. You then only need to dock the part to the unknown site, possible adding one distance restraint between the termini for the maximum possible distance that the linker region could bridge.