From: Karen Fleming <kgf@mail.csb.yale.edu>
  To  : rasmb@bbri.org
  Date: Thu, 24 Jun 1999 09:37:01 -0500

re: small peptides

Hi all,

I am also in the midst of a project in which I am looking at the MW of a
small, synthetic peptide. Just this week in fact I have obtained some
useful equilibrium data which are best described (using NONLIN) by an
ideal, single species model. The statistics for the fit are quite
stellar for my machine (SRV=~4E-03 with ~900 degrees of freedom, 3
speeds at one concentration). The residuals are beautifully small and
random.

However, when I assume a "normal" vbar (~0.73) and calculate the peptide
MW from the reduced MW, I am finding that it is much smaller than I
expect. Since the ideal, single species model describes the data so
well, and since it is the simplest model, I conclude that nonideality is
probably not causing this depressed MW. (Any comments anyone??) And
actually, my first instinct is to question the value for the vbar. While
I have never seriously looked into this issue in detail, I have the
impression that the calculation of vbar from composition loses its
precision as the "protein" sample becomes small enough to be considered
a "peptide". Since I am not equipped with a precision densimeter, as a
first approach towards addressing whether the peptide vbar is anomolous
or not, I set up an H2O/D2O mixing experiment a la Edelstein and
Schachman. I do not yet have the results from this experiment, but I
would welcome any comments on this strategy.

I should also mention that fussing with the vbar value in the
calculations has been quite amusing, since I can vary my peptide MW by
+/- 100%, depending on the value I choose. I will need to get up in the
0.85 range in order for the MW to come out with reasonable agreement
with the prediction. I'm thinking that this may not be so outrageous,
since the synthetic peptide sample also contains some engineered,
organic portion. I will probably also try to calculate a vbar from the
atomic composition, taking into account the organic portion.

Comments anyone??

-Karen Fleming
Yale University
kgf@csb.yale.edu