I am trying to gauge whether I am posing a problem appropriately for HADDOCK usage. If the approach I am proposing makes any sense, I would appreciate a couple of pointers on where to start…
First of all, Sec13 is a WD40 beta propeller domain (show in rainbow coloring, blue-to-red, below) that interacts with other proteins via a domain invasion motif (DIM) that emulates a blade and wedges itself very tightly into the empty blade slot presented by Sec13 (shown in magenta). So, Sec13 adopts a 7-blade topology but provides only 6-blades; in doing so it generates a binding pocket for the DIM.
What I would like to do is to force a structural model that has had the DIM in the binding site deleted (such as show below) to “close” into a 6-blade topology from the 7-blade topology that it currently adopts.
I was wondering if it makes sense to use HADDOCK to (1) define distance restraints (e.g. using a structural superposition of a blade with the DIM as a best guess) between the 1st and 6th blade and then (2) use HADDOCK as a means to refine against no experimental data and force the whole structure to rearrange into a 6-bladed beta propeller. If this makes sense:
a. what kind of restraints should I use?
b. what kind of refinement should I use?
c. would it make more sense to “dock” the structure as a single chain / single input molecule into HADDOCK or would it be better to break the structure up into chains that correspond to individual blades and then perform a 6-tuple docking?
Thanks in advance for any consideration!