Re: dimer
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
Re: dimer
Hi Stefano, Please see below: thinking about it, and considering that we erroneously run Relax using the full PDB for the homodimer but provided only the T1, T2 and NOE data for one monomer, as output of Dynamics Center, could you tell us how to modify the .txt files from Dynamics Center so that Relax thinks it has a full set of data for the full homodimer? The PDB that we used has residues already numbered consecutively from residue 1 to the last residue of the dimer. In this setup, relax will only look at the first monomer. We really need to change the input files for T1, T2 and NOE in order to decide which part of the protein we are looking at, but we would like to know which parts of the output files from DC should be duplicated. If you want and need it, I can send you the files in a private email to you only. There is no need to send the files. Do you have someone there who knows scripting? One option is to write a script (perl, Python, sed, etc.) which adds 147 to the residue number for all parts of the Bruker DC file. Or maybe using the script at http://thread.gmane.org/gmane.science.nmr.relax.user/1661/focus=1677 to renumber the PDB file will be sufficient. Loading the two molecules into relax and then loading the Bruker DC data might put the data into the spin containers of both molecules, as the residue numbers for both molecules will match. This would have to be very carefully checked as this is completely untested behaviour for relax. You would also need to carefully look at the log messages. If you would like me to make this last option 100% functional for relax, I would recommend creating a support request and attaching your Bruker DC files there - but they must be truncated to 1 or 2 residues. You can randomise the data slightly too for complete secrecy, if you wish. I could then use this and the PDB file to create a relax system test. Having a system test allows me to fix things in relax in ~5 to 10 minutes. The support request creation link is http://gna.org/support/?func=additemgroup=relax. 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
Re: dimer
Hi Edward, an additional question: in the output file I noticed that the last four residues at the C-terminus, for which I provided relaxation data, are not included. Any reason for it? (for the previous 9 residues we did not have the assignment because they are not observed due to intermediate exchange phenomena that broaden them too much to be visible, while the last four residues are clearly visible and they appear to be very mobile, and yet, no output from relax. Stefano ___ 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
