Docking With Two Substrates

Question

[Elmo]

Hi,

I have some doubts on Docking. I have modeled out a structure from homology modeling and perform some refinement. Now, there are two substrates to be introduced to the protein structure. The protein that I am studying is an enzyme and it catalyzes the reaction of two substrates. I have read about docking with one substrate / ligand, but not with two. How can I possibly do that? Any article references or advice please?

Thanking you in advance.

Best regards, Elmo

[ancient_learner]

If you are using softwares like schrodinger (maestro) you can dock as many ligands as you want at a time

[Elmo]

Hi @anurupadevi, thanks for replying. My enzyme protein has a catalytic triad that when one substrate binds to it, only then the other substrate can bind to it. I was wondering if I should dock one substrate first, and then run some simulation and then only introduce the other substrate, or should I introduce both and then only do simulation? Please advice. Thank you.

[ancient_learner]

If the binding of one substrate brings conformational change to the protein that accommodates the other substrate, Yes i think you have to go with simulation after the docking of first substrate.