Dear users, I have recently carried out two seperate model-free analysis on a ~5 kDa protein with relaxation data measured at 600, 800 and 900 MHz. I used the fully automated analysis scripts for the analysis.
In the first run, I used the lowest energy structure from my 15 structure ensemble. I get an oblate diffusion tensor. When I read the results and ask for diffusion_tensor.display() in relax, I get the table with all the data which is as follows... Diffusion type spheroid tm (s) 4.63577e-09 Diso (rad/s) 3.59523e+07 Da (rad/s) -3.36136e+07 Dpar (rad/s) 1.35432e+07 Dper (rad/s) 1.35432e+07 Dratio 0.287196 theta (rad) 0.633624 phi (rad) 2.61738 Fixed flag True What is confusing me is that, even though the Dratio is 0.287196, the individual Dpar and Dper values are exactly the same! I have seen the same when I run relax on a complex of the 5 kDa protein and a 1.1 kDa peptide, where relaxation data was recorded only for the protein. I ran another run, this time using the pdb file containing all the 15 lowest energy structures. Analysis of the same relaxation data with this structure gives me an ellipsoid diffusion model with following parameters.. Diffusion type ellipsoid tm (s) 4.63094e-09 Diso (rad/s) 3.59898e+07 Da (rad/s) 2.4722e+07 Dr 0.475806 Dx (rad/s) 1.59863e+07 Dy (rad/s) 3.9512e+07 Dz (rad/s) 5.24711e+07 alpha (rad) 2.59643 beta (rad) 2.087 gamma (rad) 0.438009 Fixed flag True I remember reading an old post where Ed mentions that relax is not set up to carry out analysis for residues with multiple NH bond vectors since it lies in the model-free theory itself. In the same post it is also mentioned that if that is the case then relax should give an error. Now, about 5 residues at the N terminus and 2 at the C terminus of my 43 residue protein are unstructured and show high backbone RMSD. It would be great if i get some help regarding the understanding of why in such a case, there was no error given from relax. And also, what measures are to be taken to run relax analysis on such a protein using the 15 structure ensemble as an input structure. Is this change from oblate to ellipsoid a case of over-estimation of the diffusion properties occuring due to highly flexible termini in the protein? Regards, Vineet ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ _______________________________________________ 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
