I used the Rosetta Design server (http://rosettadesign.med.unc.edu) to search for mutations that stzabilize a protein-protein interface.
I have a two questions about this:
1) Is there any controll on the process, e.g., by means of a .res residue file, as is for the structure stabilization procedure? I seems like the settings in the .res file to not influence the PPIface stabilization procedure at all.
2) Is it possible to extract/reproduce the structure of the mutated protein complex, e.g., by using the protein stabilization protocol on this server with specific settings in the .res file ... and how could such settings look like in order to reproduce the structure for an interface stabilizing single-point mutation.
Thanks a lot,
The PPI affinity increase procedure is just an overlay on the protein stabilization procedure. It guesses certain mutation types (http://rosettadesign.med.unc.edu/affinity_increase_help.html) that it thinks may improve binding, runs them through the normal packing run, then outputs whatever ddGs it sees. So, one PPI run is like a large series of regular runs on point mutants.
If you want to use a resfile to search for _stability_ increases for mutations at an interface, just use the regular protocol with a resfile and it will work; the fact that it's at an interface is irrelevant. This won't calculate a ddG for you (you can use the docking server for that, probably?)
If you want to use a resfile to search for _affinity_ increases at an interface, you can't. The packing algorithm ONLY looks for stability increases, not ddG's of binding. The affinity increase mode sidesteps this by preselecting point mutants and testing them individually; you can do the same thing if you wish.
If you got an interesting hit with the PPI mode and want an output structure of that mutation, then yes, you can just make a resfile for that mutation and run the regular design mode to get that structure out. If Rosetta said "mutate chain A position 40 to alanine", then a resfile
40 A PIKAA A
will get you there. See also http://rosettadesign.med.unc.edu/resfile_format.html.