On Wed, 18 Apr 2012, Wayne Boucher wrote:
> (I guess in theory you could try to study both conformations in
> one structure calculation but Tim says that nobody does that.)
Well not nobody! However, you need a very good reason to do it.
If they're in very slow exchange it can be done with customised CNS
scripts that maintain two copies of the protein and use NCS restraints to
keep them looking alike where they should be and to work around the
under-restrainedness of of the system. If there is a significant
difference in the population of your two forms as judged by relative peak
intensities you can just disregard peaks arising from the minor confomer -
if they're more equal, then you may need to work a bit harder!
If your conformations display significant interconversion on the NOE
timescale, then you need to watch out for exchange peaks that could be
mistaken for NOEs. If the conformational differences appear to be quite
local, you may additionally consider some kind of ensemble averaging
system to accommodate the different conformations. If I rememebr right
Alexandre Bonvin has a paper quite a while ago where they dealt with a
surface aromatic residue that appeared to sample multiple conformations.
Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
College of Medical, Veterinary & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089 Fax: 0141 330 4600
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