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
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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
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