Symmetric abrelax modeling

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    • February 18, 2011 at 6:14 pm #794
      Anonymous

        Is it possible to use the symmetry code to fold something like an Ankyrin repeat?

      • February 18, 2011 at 6:41 pm #5053
        Anonymous

          I think you’re asking, can Rosetta apply symmetry between repeats in a multidomain repeat protein.

          The answer is probably not; as far as I can tell, the symmetry code enforces strict symmetry between units. The rotamer and conformation at position 10A will exactly match those at position 10B. I sent a query to the symmetry guy, but if you don’t get a further response, assume it’s a no…

        • February 18, 2011 at 7:05 pm #5054
          Anonymous

            Thanks Steve, that’s exactly what I was asking.

            I also thought of trying this in an alternative manner: I removed the first 2 and last 2 residues in each “subunit” and am trying to use symmetry docking to assemble my “oligomer” (I removed the first and last couple residues to prevent clashing). What I’d like to do now is apply helical symmetry, but I haven’t found too much about this in the documentation. As far as I can tell, helical symmetry involves a rotation and a translation – would it be best to just generate virtual coordinates and jumps for each subunit in the symmetry file, or there a short-hand notation I can use?

            Thanks for the quick response!

          • February 20, 2011 at 3:16 pm #5063
            Anonymous

              Symmetry assumes perfect structural/chemical identity between all subunits. So for this to work the individual repeats must be assumed to be identical. They must also be repeated in a perfectly symmetrical manner. Given these approximations the repeat system could potentially be modeled as a helix. Because this is a repeat protein there is supposed to be a covalent link between the repeat units. This cannot be modeled symmetrically as of now. But as you mention this can be avoided by trimming of residues at the end. Or adding a hard constraint between the covalently attached termini in repeats.

              The symmetry definition file can be generated from a preexisting helical structure using the make_symmdef_file.pl with the -m HELIX flag. If you want to predict a denovo structure then you have to make sure to edit the symmetry definition file to make sure to completely randomize the starting position of the subunits as to remove the memory of the preexisting helix. The alternative is to make a symmetry definition file denovo. The syntax for this is found at http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/app_symmetry.html. You would need two types of statements: rot Rz_angle VALUE and trans 0,0,VALUE. I haven’t done any denovo stuff with helix symmetry in Rosetta 3 but I did get that to work in Rosetta 2. So unfortunately I don’t have a helical symmetry denovo symmetry definition file lying around. It should not be that difficult to make if you get the hang of it.

              As far as protocol goes, for abinitio use the fold-and-dock app. For docking the SymDock app. In both cases a symmetry definition file needs to be generated.

              If you have problems with generating the symmetry definition file then post it here and I can give you feedback.

            • February 18, 2011 at 7:45 pm #5055
              Anonymous

                I don’t know – hopefully the symmetry developer can weigh in.

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