[RASMB] time to reach equilibrium

[Arthur Rowe]

Perhaps someone could write a nice little app which would continuously
monitor at (say) hourly intervals the shift in fringe position at a radial
position near to the base of the column, and report back to the screen when
this shift either

(1) went down to below noise level, or
(2) failed to do so (i.e. system in some sort of steady state, rather than
attaining equilibrium) ?

Just to make it nice and easy for folks . . .

Arthur
-- 
*************************
Arthur Rowe
Lab at Sutton Bonington
tel: +44 115 951 6156
fax: +44 115 951 6157
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From: "John Correia" <jcorreia at biochem.umsmed.edu>
Date: Wed, 29 Sep 2004 10:31:11 -0500
To: <strauss at fmp-berlin.de>, <rasmb at server1.bbri.org>
Subject: Re: [RASMB] time to reach equilibrium


Cheers
 
We published a paper in 1977 that predicted the equilibrium distribution
from earlier scans: J.J. CORREIA, G.H. Weiss and D.A. Yphantis (1977). "An
Extrapolation Method for Reducing Equilibrium Times in Sedimentation
Equilibrium Systems,"  Biophysical J. 20, 153-168.  The point being, as
Holger just mentioned, many samples aggregate with time, or display
insolubility, instability.  Many of us have observed this with proteins like
tubulin which like to associate in polymorphic forms, and with many His
tagged proteins.  In many of these cases there is a slow loss of material
from a "stable" exponential distribution.  Information can still be
extracted, with caution.  Solutions to this problem have included change the
pH, ionic strength, etc (obvious), drop the temperature, add reducing agent
(TCEP has worked best in limiting cases), remove the His tag, go to a short
column format (which speeds up the time dramatically (16-fold for a 4-fold
reduction in column height).
 
I not only agree with Bo, I insist that you do Sed velocity before you waste
time doing sed equilibrium - I suspect most people do this - furthermore for
many systems the quantitative analysis must also come from Sed velocity -
Sedanal, Sedphat, etc make this very inviting.  In our lab sed velocity
rules, ie we have no alternative!
 
-------------------------------------------------------------------
Dr. John J. "Jack" Correia
Department of Biochemistry
University of Mississippi Medical Center
2500 North State Street
Jackson, MS  39216
(601) 984-1522     
fax (601) 984-1501 
email address: jcorreia at biochem.umsmed.edu
homepage location: http://biochemistry.umc.edu/correia.html
dept homepage location:    http://biochemistry.umc.edu/
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