Disulfide bonds: How to add them in HADDOCK 3?

HADDOCK
1

Hello,

I want to dock a peptide to a protein with disulfide bonds, using HADDOCK 3. I would like to ask how to tell the program which Cysteine residues will form disulfide bonds before docking?

Best regards,

Hoa

2

Do you mean that disulphide bonds are formed between the protein and the peptide?

If this is the case you should define a few distance restraints between the CYS sulphur atoms.

If you rather refer to the disulphide bonds within your protein, those are automatically detected.

3

Thank you for your information. I mean the disulphide bonds within my protein.

It’s good that they are automatically detected. But can there be cases where two independent, non-bonded sulfur atoms happen to be close to each other, but HADDOCK 3 still forms a disulphide bond between them? If these cases are possible, is there a way to tell HADDOCK 3 not to add the bond between them?

4

HADDOCK uses a distance criterion to detect S-S bonds. You can not really turn this off (or you would have to hack some scripts).

But if these are internal and not close to the binding site it won’t matter I would say.

5

Thank you, Mr. Bonvin. Your insight is helping me making decision for my docking project.

I wish you and your team success in developing the rest of the features for HADDOCK 3!