Active and inactive states of the predicted model

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MaliheHSD
Posts: 1
Joined: Thu Jun 02, 2022 5:01 pm

Active and inactive states of the predicted model

Post by MaliheHSD »

Hi,
I have a question and I would be really thankful if you could please answer me.
I'm working on a protein that has two active and inactive states, but there is a crystallographic structure of only active state of it in complex with the peptide agonist. I need the 3D model of the inactive structure as well to do some comparison to explain why some inhibitors are more potent than the others and also to investigate selectivity between two isoforms of the protein.
I used I-TASSER server to have a complete 3D model of the protein. When I superimposed the obtained model using I-TASSER and the original PDB structure, I see some differences specially in entrance of the active site! My question is , Since in doing homology modeling there is no ligand in the active site of the protein, so model would be a protein without any ligand in the active site, accordingly, can I propose this model as inactive state of the protein?
Thank you!
zcx@umich.edu
Posts: 24
Joined: Wed Nov 03, 2021 5:59 pm

Re: Active and inactive states of the predicted model

Post by zcx@umich.edu »

I-TASSER does not explicitly consider ligand, just like almost any protein structure prediction program. Therefore, the predicted structure are usually the apo (i.e., ligand-free) conformation of the protein.
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