Dear Amber users and developers,
I've got a problem I hope you can, yet again, give me some advice for. I am trying to do an emap restrained simulation of an oligomeric protein.
We do have a crystal structure of the monomer, and an electron map from CryoEM of the native dodecamer. If I take the monomer and fit it with the 12 fold symmetry into the map, it actually looks quite nice, but, as a result, the flexible N-terminal domains actually overlap, producing a knot. I believe that the N-terminal domain structure is not a crystallization artifact, but probably the N- to C-terminal domain orientation is.
I've been trying to unfold the N-terminal domains in the dodecamere, and use moving emap restraints based on the folded crystallographic domain to get them in the right position, but the results are discouraging. The N-terminal domains are inside the central cavity of the oligomer, and when I unfold them, the outer, C-terminal domains actually compress. This reduces the internal cavity, and there is no more room for the N-terminal domains.
Thus, my question is, is there a way in which I can use Amber, or any other program you might know about, to disentangle those N-terminal domains?
Thanks for the help in advance!
Manuel
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Received on Tue Feb 10 2015 - 01:30:02 PST
