You are here

Predicting the part of protein strcutrue

2 posts / 0 new
Last post
Predicting the part of protein strcutrue


I have a protein whose sequence is fully known and whose structure is partial known. Most sequences of the protein are folded in the luminal ER domain and this part is resolved by experiments. However, transmembrane and cytosolic parts of the same protein are not resolved. As only the luminal part of the protein is resolved, I would like to predict the structure for transmembrane and cytosolic domains. Is there a way to predict only these parts while I keep the experimentally-resolved luminal domain?

Thanks, Siyoung

Post Situation: 
Tue, 2018-10-16 11:47

You would fold them as separate domains - as this is how they typically would fold.  The Transmembrane domain would need to be folded using RosettaMembrane.  Search the docs and you should find quite a bit on it. You could then fold the cytosolic part independantly.  I'm not sure if folding the cytosolic component with the transmembrane domain and an implicit membrane is feasible at this point.  You could surely try - as if the cytosolic domain has parts that are proximal to the membrane, it could help.  I would probably attempt that using RosettaScripts, but you would need to figure out what all to use and add the membrane info using the AddMembraneMover to your transmembrane domain.  The tricky part is adding a sequence on to an already partially folded protein.  For that, you could use RosettaCM to get the base pdb structure, and model the cytosolic domain.  I'm not sue if the AddMembraneMover and RosettaCM work well together, but they should.  

Fri, 2018-11-09 14:28