Hi Stefano,
It will be interesting to see the results in your final publication.
well, same for us of course. However, this is the first time I approach
this problem, so I welcome any advice.
Especially considering that the relaxation data you observe is the
average of two states experiencing different global tumbling (the two
vectors intersect different parts of a single Brownian diffusion
tensor), but the assumption is made that they only sample one.
the dimer is perfectly symmetric in solution, in the NMR time scale, as we
observe only a single peak per residue
For dimers, unfortunately I don't have much advice I can give. The
only person who could we be the one who derives the correct
theoretical treatment of dimers in the future. You may have avoided
the issue though if you have a perfectly symmetrical dimer.
Maybe
you should perform a full analysis on one monomer, and then another
full analysis on the second, and compare.
I am not sure that I understand your suggestion, as the two monomers are
inextricably bound
It won't give much, but the bond vectors orientations are different
between two monomers. The superimposition is not perfect. But, as we
have discussed before on the list, it will not do anything for the
theoretical problem, if you indeed do have a problem. It will only
show you any small bond vector orientation artefacts.
Are you sure there are no
published theoretical treatments of such a situation?
I am aware of relaxation studies on homodimeric proteins, but I am also
quite sure that the papers do not tackle the issue of the dimer and report
the relaxation data as for a monomeric protein; again, any advice is
welcome.
I am also unaware of any theoretical treatment. If you deposit your
dynamics data for your publication in the BMRB, via the relax export
functions, then this might open a door to allow a theoretician in the
future to use real data for solving this problem. As for solving the
problem now and you are 100% sure that this is not already solved,
unless you would like to dive into quite complex theory, then there is
nothing we can do. You could make a 1 line comment about the
deficiency in the manuscript, and make the statement that this is an
unsolved problem.
Anyway, the perfect symmetry might mean that the diffusion tensor as
seen in the reference frame of each monomer is identical, so that the
bond vectors in each experience the same 5 global correlation times
and hence the standard analysis will work perfectly. If so, no
special theory is required.
Regards,
Edward
Re: dimer