Dimer of dimers

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    • April 15, 2011 at 5:41 pm #873
      Anonymous

        HI,

        I want to use Fold and Dock on a small domain of a protein that forms a dimer-of-dimers. It is a 50 residue domain that is known to form helixes.

        I am not able to get a reasonable quaternary structure for this protein using the below symm files. Any help would be deeply appreciated. Thanks!

        D2.symm file:
        …
        set_dof BASEJUMP angle_x(0:360) angle_y(0:360) angle_z(0:360)
        set_dof JUMP2 angle_z(0:90)

      • April 17, 2011 at 9:15 pm #5437
        Anonymous

          Your symmetry definition file does not appear to allow for translational moves. Typically, the set_dof statements would look like this:

          set_dof BASEJUMP x(50) angle_x(0:360) angle_y(0:360) angle_z(0:360)
          set_dof JUMP2 z(50) angle_z(0:90.0)

          The x(50) and z(50) items allow for translational optimization and specify that the coordinates of subunits are placed 50 A from the origin at the beginning of each simulation.

          Then nstruct 9999 is probably on the low side given the number of degrees of freedom in the system.

        • April 18, 2011 at 3:39 pm #5448
          Anonymous

            If I add the x(50) and z(50), the monomers don’t come together. In fact, x(1) and z(1) also does not bring the monomers together. But I will run more nstruct to see if it changes my results.

          • April 25, 2011 at 5:01 pm #5490
            Anonymous

              No changes in the results. The lowest energy structure forms dimers but not dimer-of-dimers. Any other suggestions that I can try?

            • April 29, 2011 at 2:12 pm #5501
              Anonymous

                Its hard to say without looking at the result in detail. Is there any sampling of closed conformations at all? Does it converge into a particular dimer structure? This behavior would be expected if the interactions between dimers is not sufficiently large to converge to a particular dimer-dimer orientation.

                The x(1) z(1) does not make much sense because the subunits would end up on top of each other at the beginning of the simulation. You could play around with alternative ways of sliding subunits together. In the make_symmdef_denovo.py script you can control the slide behavior ( -slide_type (RANDOM|SEQUENTIAL|ORDERED_SEQUENTIAL).

                If there is a good convergence for a dimer you can try symmetric docking of these dimers followed by a symmetric relax.

                You could play around wit

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