I calculated protein solution structure by NMR and now I'm doing structure refinement using RDC. My RDC values are scattered from -22 to 15.
I obtained tensor parameters using REDCAT program (Da = -7.2, R = 0.8).
Then I did structure calculation in CNS using RDC restraints as well as NOE and dihedrals.
But after that calculated RDC values were always less (by absolute value) then observed ones.
And even if I increased RDC force by 20 times, calculated RDC never exceeded 14.4 (by absolute value).
I expect, that there are some problems with tensor parameters. I tried to change Da and R, but all the times I had worse results (lots of RDC restraints were violated).
Why don't you try Xplor-NIH and see if you can reproduce the problem as well?
Mrs/Miss Mariasina,
Toward the applicability of NMR to 3D structural analysis, in general, and in particular, to proteins' determination, please consider the following review-article:
Article A stochastic dynamic mass spectrometric diffusion method and...
It deals with the capability of the combined application of the experimental mass spectrometry within the framework of our innovative stochastic dynamic theory and model formulas and the computational quantum chemistry. Therein, we have provided a correlative analysis of 3D structures obtained by our mass spectrometryc method and the single crystal X-ray diffraction data of crystals of our analytes. The chemometric data show remarkable coefficients of correlation ('r' higher than 0.99) of the mass spectrometrically and crystallographically determined geometry parameters.
Owing to the fact that both the mass spectrometry and the methods of the quantum chemistry produce exact results, the reliability of thus determining 3D structures is almost exact, as well.
Conversely, the NMR yields to error contribution to the structural 3D determination at about 4 % of the dihedral angle values. As our discussion in the shown above review-article clearly illustrates, 4 % error contribution means that NMR unable to distinguish between even not so structurally symilar molecules with respect to 3D disposition of the molecular fragments.
It would be useful, if you consider as well as the reference section to the discussed review-article, where we have discuss advantages and limitation of MS based 3D structural analyses of proteins by different from our method approaches. Despite, some critical aspects of our discussion on the different MS based methods for 3D structural analysis, the research effort so far has shown that only by mass spectrometry there is able to determine multridinentional molecular structure experimentally at high level of reliability of the analytical results in quantitative chemometric terms, in condense phases, encompassing both solid-state and solution.
The theoretical maximum of the absolute value of RDC cannot exceed 2*Da (see the dependence of the RDC on Da, R, and angles theta and phi). Therefore, for Da = 7.2, the maximum absolute value is 14.4, which is indeed observed. The only question that remains is how the program REDCAT predicts Da = -7.2 using a set of experimental data with RDC values in the interval between -22 and 15?
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