[RASMB] Frict ratios, multiple species, and sedfit

[Peter Schuck]

Avi,

I'm not sure which model you're using in sedfit, but it doesn't sound like 
you're dealing with a self-association that is fast on the time-scale of 
sedimentation.  Assuming that you have a case where the oligomers 
equilibrate slowly enough to approximate them as essentially stable on the 
time-scale of sedimentation, which would permits the use of c(s) and c(M), 
I completely agree with you about the increasing axial ratios being 
probably the reason for the too low molar mass estimate of the higher 
oligomers.  This would be true if the monomer is the most abundant species, 
which would then govern the weight-average frictional ratio and the other 
species would be less well characterized.

Maybe one could improve this situation by using the conformational change 
model.  The strategy there would be to keep the molar mass fix at the 
monomer value for all species in the range of the monomer peak.  Then the 
f/f0 value is only governing all remaining species outside that predefined 
s-range, and therefore reflect the average f/f0 of the oligomers.  However, 
it would depend on the data quality and the population of the oligomers if 
they actually can define the f/f0 well enough to give well-defined molar 
mass values.

Peter



At 03:44 PM 6/2/03 -0400, you wrote:
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>Dear RASMB,
>
>We are using sedfit to examine a self-associating system. We find that the
>monomer molecular weight is reasonably accurate, however, the dimer weight
>is lower than expected and the tetramer weight is even lower still. Could
>this be the result of differences in the axial ratios of the oligomers,
>with the higher oligomers being more rod-like than the smaller oligomers.
>If this is the case, can the frictional ratios for different sedimenting
>species be floated in sedfit.
>
>Thanks, Avi
>
>-------------------------------------------
>Avi Chakrabartty, Ph.D., Associate Professor
>Departments of Medical Biophysics and Biochemistry,
>University of Toronto, Ontario Cancer Institute,
>610 University Avenue, Toronto, Ontario, M5G 2M9, CANADA
>
>Phone:416-946-4501 (office:ext. 4910) (lab:ext. 4915), FAX: 416-946-6529
>email: chakrab at uhnres.utoronto.ca
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