I have a protein which is active in its trimeric form. I want to observe the changes on ligand binding (small peptide). I docked the peptide with monomer as well as trimer, but the results are different from each other. In trimer, peptide goes and binds at the center, where a large cavity is being formed due to trimerization, which is kind of expected.. There are reports of residues involved in this interaction similar to those I found in monomer-ligand docking.. how should I go about this correctly? Is it correct to use the monomer-docked structure and then form a trimer of the protein-ligand complex?
If the known active site for ligand binding is formed by the trimer, then the trimer should be used for docking. If the active site is unknown and you are using blind docking to see where the ligand binds, you could try both the monomer and the trimer.
If you are interested in changes in protein conformation and flexibility induced by ligand binding, you should do molecular dynamics simulations rather than docking.
How its trimer is associated will generally influence peptide binding. If you know and the structure of the trimeric complex exists in PDB format you can do the docking with the trimer. If the trimeric structure is not yet available in PDB format, you can dock the monomers to identify the best trimeric conformation (through ClusPro, for example) and thus make a second docking of your peptide with the best output structure. In the latter case, if there is no trimer structure identified, but you know how the trimer is formed (through experimental or predictive data), you can initially do a directed docking (through Haddock, for example) and then do another docking between its peptide and the best output structure of the directed docking. I hope I have helped.
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