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 _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
