Creating Membrane Protein Heteromers

Question

[Tofayel Ahmed]

I have modeled a membrane protein which has 3 subunits- alpha, beta, gamma. Now, as the native structure of the protein is pentamer, I would like to create the pentamer having 2 alpha, 2 beta and 1 gamma subunit (all modeled pdb files) oriented alternatively. Can anybody suggest some tools for creating the multimeric protein (monomer association)? How do I know if the subunit interfaces are correctly predicted in the generated heteromer?

Thanks in advanced.

Answer 1

[Neilfws]

Can anybody suggest some tools

MODELLER. See for example these notes in the manual; they're rather terse and you'll need more help (e.g. in the MODELLER discussion forums).

How do I know if the subunit interfaces are correctly predicted

To be honest, you don't, unless you have a very good oligomeric template on which to base the modelling. Models allow you to experiment with reality, but they rarely mirror it.

[Tofayel Ahmed]

thanks a lot for your answer.