Monday, 16 October 2017

Hacking PDBs for fusion protein and missing loops

This is a How-to guide to make structures of fusion protein —the shoddy way.
For the proper way see the how to do it in Rosetta or Pyrosetta.
NB. This assumes medium–advanced PyMol competency.


Representing the structures of fusion protein is a rather annoying task. There are many ways of doing this.
Contrary to expectations, submitting the sequence of a fusion protein to the Phyre server (threading/ab initio predictor) or similar will return spaghetti, just as happens with circular permutations (for which you get a cracked half open domain with spaghetti attached). But give it a go nevertheless —it may save you a lot of time!
Rosetta can be used, but the domains will not be photogenic and it is truly overkill.
So the best way is to simply hack the PDB files and some PyMol ninjutsu.

As an example I will make phusion, i.e. Pyrococcus furiosus DNA polymerase fused to Sulfolobus solfataricus 7D domain (Sso7), because its name basically says it is a fusion.