Build a 3d protein model to compare two TF alleles and test in-silico the protein-DNA binding efficiency

Question

[lessismore]

Dear all,

I'd like to in silico test the protein-DNA binding of a transcription factor for which I've identified some crucial mutations in the binding domain. So first I've followed basic guidelines to obtain the pdb model of my protein (a monomer, I know it acts as a dimer). As suggested here (https://www.youtube.com/watch?v=kfMpOnnBjP8) I should search for at least one template on swiss-model portal with enough GMQE score (>0.3) to then build the model and export the pdb file that will later use to check the docking. I'm a bit stuck as my protein falls below 0.3. Do you have any specific recommendation to perform this task ? After will follow the docking test for which I've identified HDOCK as a reference program to use. Any suggestion is very welcome.

Thanks

Answer 1

[Mensur Dlakic]

You need a good-quality model before doing anything else. I don't know if GMQE is necessarily the best criterion of a good model, but most likely GMQE < 0.3 still means that you don't have a good one. As to why the model is poor, it could be a wrong template, an incorrect alignment, or both. Or it could be that for your protein there is no good template.

Whatever the exact reason for the poor initial model, you may want to try modeling your protein in AlphaFold, It requires only your protein sequence, and it can model homodimers.

• https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb
• https://phenix-online.org/version_docs/1.20rc1-4398/reference/alphafold_in_colab.html

Your protein of interest may have been modeled already:

https://alphafold.ebi.ac.uk/

Once you hopefully get a good model, presumably you would continue with the tutorial.

[lessismore]

Wow! Thanks a lot. Indeed I've found my protein model in pdb on https://alphafold.ebi.ac.uk/ by using its protein ID.