[RASMB] Frict ratios, multiple species, and sedfit

[John Philo]

Avi,

I'm guessing that you are analyzing using the c(M) distribution, and indeed
that will make the M values extremely dependent on the f/f0 ratios assumed.
I agree with Peter's remark that it sounds like you have species not in a
rapid equilibrium. However, if that is really true then it seems to me you
are basically dealing with a mixture, so if you really want a mass value to
try to identify the species then you should get away from the continuous
distribution models altogether and use a mixture model (e.g. in SEDFIT or
SVEDBERG or LAMM) instead. Then you aren't making any assumptions about the
f/f0 ratios. 

John Philo
Alliance Protein Laboratories

-----Original Message-----
From: rasmb-admin at rasmb-email.bbri.org
[mailto:rasmb-admin at rasmb-email.bbri.org] On Behalf Of Avi Chakrabartty
Sent: Monday, June 02, 2003 12:45 PM
To: rasmb at rasmb-email.bbri.org
Subject: [RASMB] Frict ratios, multiple species, and sedfit


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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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