internal motions comparable to tm -- December 11, 2012 - 10:28

Dear Ed and relax users,

I have recently used relax (ver 2.0.0) to obtain the model-free dynamics of a small protein with a molecular mass of 6 kDa. In fact, it's a protein in complex with a small peptide, but only the protein is 15N isotope labelled.
R1, R2 experiments were recorded at 600, 800 and 900 MHz, and the steady-state NOE at 800 and 900 MHz. Temperature calibration was performed before running the experiments for all the fields.

I used the fully automated analysis (dauvergne_protocol.py) and that went well. At the end of the run, the selected diffusion tensor had the form of an oblate spheroid with a global rotational correlation time of 3.2 ns.

Now, I have observed that some residues display slow internal correlation times (ts) that are in the range of 1-4 ns. Considering the tm is only 3.2 ns, this would mean, that motions slower than the overall tumbling were captured. However, my understanding is and please correct me if I'm wrong, that except for Rex contributions, relaxation measurements are insensitive to motions on a time scale equal to or slower than the overall tumbling.
I'm a bit puzzled about the validity of these motions, that is to say, are they physically meaningful?
Is it possible that some of the motional models were not adequately fit and poorly chosen? Also, I've used the AICc selection method to reduce the probability of overfitting.

Cheers,

Romel Bobby
Biomolecular NMR Research Group
School of Chemical Sciences/School of Biological Sciences
The University of Auckland
+64 (09) 3737599 Ext 83157