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<DIV><FONT size=2>Perhaps it's time for a thread on favorite software for
equilibrium data analysis?<BR><BR>OK - I am historically a nonlin person having
been involved in all the early testing & the 1st paper describing the
method. Nonlin is great (Winnl107 is my current version) for global
analysis of sedimentation equilibrium studies of self-association.
You can mix speeds and different wavelengths and the current versions allow up
to 25 - 50 data sets in the fit. One problem with this program is the
presence of heterogeneity (dead monomers or aggregation) cannot be explicitly
fit for - instead you must infer it from a dependence of K on loading
concentration - K goes down as C increases. This is discussed in at least
two papers:</FONT></DIV>
<DIV><FONT size=2> </FONT></DIV>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT face=Tahoma><FONT
size=2><SPAN
style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-bidi-font-size: 10.0pt; mso-bidi-font-family: 'Times New Roman'">D.A
Yphantis, J.J. CORREIA, M.L. Johnson and G.‑M. Wu (1978).<SPAN
style="mso-spacerun: yes"> </SPAN>"Detection of<SPAN
style="mso-spacerun: yes"> </SPAN>Heterogeneity in Self‑Associating
Systems," in "Physical Aspects of Protein Interactions," </SPAN><?xml:namespace
prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags"
/><st1:place><SPAN
style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-bidi-font-size: 10.0pt; mso-bidi-font-family: 'Times New Roman'">N.
Catsimpoolas</SPAN></st1:place><SPAN
style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-bidi-font-size: 10.0pt; mso-bidi-font-family: 'Times New Roman'">,
ed., Elsevier, pp. 275‑303. a pdf of a scanned copy is on my web site if
you do not have access to the book!</SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-bidi-font-size: 10.0pt; mso-bidi-font-family: 'Times New Roman'"><FONT
size=2></FONT></SPAN> </P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-bidi-font-size: 10.0pt; mso-bidi-font-family: 'Times New Roman'"><?xml:namespace
prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p><FONT
size=2>Yujia Xu "Characterization of macromolecular heterogeneity by equilibrium
sedimentation techniques." <SPAN
onmouseover="AbbrLookUp(this, 'Biophys Chem.');"
title="Biophysical chemistry.">Biophys Chem.</SPAN> 2004 Mar 1;108(1-3):141-63.
</FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-bidi-font-size: 10.0pt; mso-bidi-font-family: 'Times New Roman'"><o:p><FONT
size=2></FONT></o:p></SPAN> </P>
<DIV><FONT size=2>Two new PC based packages I am familiar with (undoubtedly more
great stuff out there) now do global (essential !) hetero-association analysis
on sedimentation equilibrium (& velocity) - Stafford's SEDANAL (current
version is 397) and Cole & Lary's ready for release program (still nameless
?). I am most familiar with SEDANAL so I'll stress those details:
The best feature of SEDANAL is the fact it has a model editor that allows you to
make your own model(s) appropriate to your system. It allows up to 28
species & 27 reactions - be careful! The ability to add an aggregate
& fit for % (globally or by data set) and size is a great feature.
Pertinent to the current discussion, with monomers I often assume vbar, measure
density and fit for MW, but you can also fix MW and fit for den inc or
(1-vbar*rho) to get an idea of why you are getting an odd number. Multiple
speeds & wavelength are of course allowed. Multiple optical systems
and data weighting are also implemented. Simulation mode vs fitting mode
is just a button away. Another interesting feature that more people should
explore & think about is the ability (with velocity) to fit for kinetic on
& off rates (this by definition has no meaning for equilibrium
data). The newest SEDANAL feature for equilibrium data is the rediscovery
of Biospin, an old program developed by Dennie Roark in the Yphantis that does
sliding fits to equilibrium data to extract –, w-, z- and if you are lucky
z+1-average MW, as well nonideal moments of molecular weight to correct for
charge and size effects. Its a quick way to evaluate for aggregation,
association, nonideality and stochiometry of reaction.</FONT></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><FONT size=2>This is the short version, others will undoubtedly
have much to say, but even this requires reading for the inquiring
mind. I suggest:</FONT></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><FONT size=2><STRONG>Stafford</STRONG> WF <B>3rd</B>. <FONT
color=#990000>Graphical analysis of nonideal monomer N-mer, isodesmic, and type
II indefinite self-associating systems by equilibrium
ultracentrifugation.</FONT> <I>Biophysical Journal. 29(1):149-66, 1980
Jan</I></FONT></DIV>
<DIV><EM><FONT size=2></FONT></EM> </DIV>
<DIV><FONT size=2>Walter F. Stafford, Peter J. Sherwood "Analysis of
heterologous interacting systems by sedimentation velocity: curve fitting
algorithms for estimation of sedimentation coefficients, equilibrium and kinetic
constants Biophysical Chemistry 108 (2004) 231–243</FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=2> J Philo Method Enzymol vol 321, 100-120, 2000.
"Sedimentation Equilibrium Analysis of Mixed Association using Numerical
Constraints to Impose Mass or Signal Conservation." A thoughtful
discussion of the challenges - his program is not available but SEDANAL and
Cole's more than supplement.</FONT></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><FONT size=2>PS - These comments reflect my current usages and biases, but
be clear I am an equil opportunuity promotor of AUC methods. Lots of cool
stuff being done out there - the method has worked for 80 years - the new
analysis packages are extra perks for modern users! Take
advantage!</FONT></DIV>
<DIV><EM></EM> </DIV>
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<DIV>-------------------------------------------------------------------<BR> Dr.
John J. "Jack" Correia<BR> Department of Biochemistry<BR> University
of Mississippi Medical Center<BR> 2500 North State Street<BR> Jackson,
MS 39216<BR> (601)
984-1522
<BR> fax (601)
984-1501
<BR> email address: <A
href="mailto:jcorreia@biochem.umsmed.edu">jcorreia@biochem.umsmed.edu</A>
<BR> homepage location: <A
href="http://biochemistry.umc.edu/correia.html">http://biochemistry.umc.edu/correia.html</A><BR> dept
homepage location: <A
href="http://biochemistry.umc.edu/">http://biochemistry.umc.edu/</A><BR>-------------------------------------------------------------------<BR> <BR> <BR></DIV></FONT></BODY></HTML>