Problem with a docking between glycoprotein and its receptor

HADDOCK
1

Hi all!
I have tried to perform the docking (refinement) of a glycoprotein with its receptor. The glycoprotein was built using DoGlycan, and it appears to have been recognized by Haddock 2.4. However, the result shows the different sugars in proximity but not connected. I have several questions that maybe someone can answer:

  1. How does Haddock recognize the type of connectivity between sugars?
  2. How does Haddock recognize which asparagine the glycan chain attaches to?
  3. My sugar is this:
    image
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The nomenclature of the sugars in my hydrocarbon chain is similar to that obtained from the glycam.org server, which I believe Haddock recommends using to generate the sugars.

  1. After docking:
    image
    image941×763 285 KB

Thank you very much in advance
Sergio

2

Dear Sergio

The server will recognise glycans provided they follow standard PDB nomenclature. The glycam server does not follow that unfortunately.

The list of supported glycans can be found at:

https://bianca.science.uu.nl/haddock2.4/library

You will have to rename your glycans accordingly.

Note that as there are many possible linkages we might not have all of them yet implemented.

3

Thank you, Alexandre, for your response, but I still have doubts regarding how to rename the monomers of my glycan:

According to the names defined in the Haddock library,

image
image722×493 56 KB

a) I should replace my first sugar called UYB with NAG, and the second one called 4YB with NAG since both are NAG. However, will this be sufficient to determine the type of linkage that this sugar has with the next one? I apologize if I am not understanding something more fundamental.
b) In the case of changing, for example, the name of my UYB residue to NAG, should I also rearrange each of the atoms from UYG to their corresponding positions in the NAG topology, correct?
Thank you for your help!

4

a) I should replace my first sugar called UYB with NAG, and the second one called 4YB with NAG since both are NAG. However, will this be sufficient to determine the type of linkage that this sugar has with the next one? I apologize if I am not understanding something more fundamental.

Yes - the linkage is defined automatically by checking distances.

b) In the case of changing, for example, the name of my UYB residue to NAG, should I also rearrange each of the atoms from UYG to their corresponding positions in the NAG topology, correct?

Yes indeed

5

Thank you very much Alexandre!.