[RASMB] Equilibrium runs with small peptides, high offset values

[Erin Matthews]

Thanks everyone for suggestions on my last question about data with
negative slopes!  I have yet another question on a different system.

I did an equilbrium (absorbance optics) run on a water   
soluble  peptide of 1290 Daltons.  I had to spin at 60K rpm 
to get any reasonble data (data at lower speeds showed virtually no 
curvature).  My problem now is this: using Nonlin,  the best fit to the
data gives a lower than expected sigma (.35 instead of .46 with both the 
offset and the second virial coefficent set to 0).  There doesn't appear 
to be a higher order association.  When I fix sigma to the 'known'
value, the fit is poor, but when I then let the offset float I get a
good fit, but the offset is .1332.  Very high!  I obviously can't do an
overspeeding experiment to get an experimental measure of the depleted
meniscus absorbance.  As well, I imagine that the calculated partical
specific volume (from Durchschlag and Zipper, 1994) could be inaccurate.
Is there something more I can be doing to get an accurate fit?  Which
would be considered a more physically reasonble fit to the data--a fit
using a lower than expected sigma value or a high offset? 

Thanks,

Erin Matthews
Graduate Student, Engelman Lab, Yale University