Extend crystal structure and perform docking using CX-MS data

HADDOCK
1

Hi,

Thanks for giving me access to the HADDOCK server. I am trying to extend a known crystal structure for another 50 residues and to dock this area to another protein (structure unknown but homology modelled) using crosslinking-MS data. Which extra-add ons will be neccessary for that and how reliable will be the outcome?

Thanks,
Simon

2

You can simply define your MS crosslinks as distance restraints in HADDOCK.

But considering you have to model 50 residues… the limiting factor might well be the modelling and not the docking.
You have to model on both side (the missing 50 residues and the other protein).

Also it might be a good idea, once you have models, to check the constancy of your crosslinks using our DISVIS server:

http://haddock.science.uu.nl/enmr/services/DISVIS

3

Thank you very much for your help. Is it, however also possible to enter other parameters? …Like certain residue data from homologous models?!

My problem is that if I enter the two pdb files and the residues that directly interact, HADDOCK turns the two structures so much that somehow then the fit, even though i doubt that I can rely on that data because the bind to each other in a totally different angle than homologous complexes then. Therefore I would also like to enter important aspects of other homologous complexes!!!

Thank you very much,
Simon

4

What do you mean by other parameters exactly?
You can define as active residues what ever you like in principle.
And you could even define CA-CA distances based on your homologous model to drive the docking.

See our paper on this:

L.C. Xue, J.P.G.L.M. Rodrigues, D. Dobbs, V. Honavarand A.M.J.J. Bonvin. Template-Based Protein-Protein Docking Exploiting Pairwise Interfacial Residue Restraints. Briefings in Bioinformatics, 18, 458-466 (2016).

5

Ok…thank you very much. I will try to define all those parameters.

Thanks a lot!!!

Simon