mailVery low Tm in model-free analysis

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Posted by Pierre-Yves Savard on January 08, 2009 - 16:43:

I have some trouble using relax with my data.

I have data at 600 MHz only so I use models m0,m1,m2,m3,m9 with the
classic approach of starting with an initial estimate of the Tm, with a
modified versiion of the script which includes model
selection and diffusion tensor optimization.

The first problem is that it doesn't converge. However, the second
problem is more important in that, following the different iterations,
the Tm and S2 go down and the Rex go up to values approaching the R2.
After 35 iterations, the Tm is less than half that estimated with the
R2/R1 ratio (using quadric or tensor2) and almost all residues are
fitted with model m3... This problem starts at the second iteration.

I used this approach with success using a sample of the same protein
(136 residues) with a slightly different concentration. Using the data
from this sample (which are very close to the problematic dataset), the
converged tm was very close to the estimated tm based on the R2/R1
ratio... Moreover, S2 were much higher, with a mean value of 0.8, with
only a few Rex...

Sample one (good results): Estimated Tm = 10.1 ns, converged Tm = 10.1,
S2 = 0.88, 8 residues with Rex (mean of 2 s-1).

Sample two (problematic): Estimated Tm = 10.09 ns, Tm after 35 iteration
= 4.30, S2 = 0.48, 102 residues with Rex (mean of 10.1 s-1).

Any idea why the second sample gives rise to such annoying results ?

Thanks a lot,


Pierre-Yves Savard
Professionnel de recherche
Département de biochime et de microbiologie
Pavillon Charles-Eugène Marchand, local3252
1030 avenue de la médecine
Université Laval, Québec, Qc, G1V 0A6
Tél: 418.656.2131 #4530 Fax: 418.656.7176

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