[RASMB] Origin software and vbar / Equilibrium data

[John Correia]

Perhaps it's time for a thread on favorite software for equilibrium data analysis?

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:
 
D.A Yphantis, J.J. CORREIA, M.L. Johnson and G.-M. Wu (1978).  "Detection of   Heterogeneity in Self-Associating Systems," in "Physical Aspects of Protein Interactions," N. Catsimpoolas, 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! Yujia Xu "Characterization of macromolecular heterogeneity by equilibrium sedimentation techniques." Biophys Chem. 2004 Mar 1;108(1-3):141-63.  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.
 
This is the short version, others will undoubtedly have much to say, but even this requires reading for the inquiring mind.  I suggest:
 
Stafford WF 3rd. Graphical analysis of nonideal monomer N-mer, isodesmic, and type II indefinite self-associating systems by equilibrium ultracentrifugation.  Biophysical Journal. 29(1):149-66, 1980 Jan
 
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
 
 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.
 
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!
 
 
 
 
 

 
 
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 Dr. John J. "Jack" Correia
 Department of Biochemistry
 University of Mississippi Medical Center
 2500 North State Street
 Jackson, MS  39216
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 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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