[RASMB] Re: RASMB digest, Vol 1 #319 - 5 msgs

[Borries Demeler]

> Dear RASMB,
> 
> I attached a pdf file (distribution.pdf) containing c(s) distribution plot
> at high and low protein conecentration. The parameters are included, also
> the rmsd, f/f0, residual bitmap. p = 0.68 and the resolution is 250 (smin to
> smax is 0.1 to 25). Thanks everyone's comments and suggestion.
> 
Dear Chi-Yuan,

I am not so sure how much quantitative information you could get from
these peaks, I tried to eyeball the peak positions in both concentrations
and the peaks did not seem to match up very well between them. Here is
what I think is there:

high conc:
4.5, 6.2, 7.5, 9.0, 10.8, 13.0, 15.9, 17.3, 20.2

low conc:
4.7, 6.6, 8.7, 13.0

There is a good chance that 4.5 and 4.7 peaks are really the same species,
and 6.2 and 6.6 are as well, and so are 8.7 amd 9.0, and 13.0 seems to
be the same. However, I am concerned because 1) peaks shift, and 2) some of the
intermediates (7.5, 10.8) in the higher concentration seem to be absent
in the lower concentration, even though 13.0 is still there. I think it
would be a stretch to identify partial concentrations by peak fitting,
and I wonder how reproducible this approach would be. I think that some
of these peaks are not well enough defined to be able to classify them as
individual species present in the system.

I would recommend to use van Holde - Weischet analysis and plot the
integral distributions of each concentration in the same plot, and that
would give an immediate concentration-corrected representation of each
S-species present in the sample that is easy to compare visually and
relative amounts can be read off the ordinate directly. If you like,
send me the data and I will send you the results for this so you can
see the result.

Best regards, -Borries
---
Borries Demeler
The University of Texas Health Science Center at San Antonio
Dept. of Biochemistry, MC 7760
7703 Floyd Curl Drive, San Antonio, Texas 78229-3901
Voice: 210-567-6592, Fax: 210-567-1136, Email: demeler at biochem.uthscsa.edu