SEDANAL is a program for the analysis of data from the Beckman XL Analytical Ultracentrifuge.
It was originally written to analyze sedimentation velocity data from heterologous interacting systems of the type
A + B = C Ka = [C]/[A][B]
A + B = C K1 = [C]/[A][B]
C + B = D K2 = [D]/[C][B]
In its first incarnation, it was called ABCD_FITTER and when combined with ISODES_FITTER (which was devoted to analysis of isodesmic indefinite self-associating systems), it became ABCD_ISOFITTER. ABCD_ISOFITTER was designed to fit a two step binding reaction with isodesmic self association of component B as a side reaction.
These programs were combined and a data preprocessor with a GUI (graphical user interface) added and it was renamed SEDANAL.
Since those early days (1997-2000), SEDANAL has evolved to be able to handle any arbitrary reaction scheme with up to 28 components and/or 28 species related by up to 27 chemical reactions.
Both isodesmic and isoenthalpic indefinite self-associations are also included.
A Model Editor program is used to maintain a small database of models that are used by the main SEDANAL fitting program.
SEDANAL can process both sedimentation velocity and sedimentation equilibrium data.
- Sedimentation velocity
- Fitting with the Lamm equation
- Sedimentation equilibrium
- Fitting to sums of exponentials
Two other programs have been included within SEDANAL:
- DCDT, for the model independent analysis of sedimentation velocity data.
- DCDT processes sedimentation velocity data using the time derviative to eliminate systematic noise and produces a plot of the concentration gradient with respect to the radial axis expressed in svedbergs.
The DCDT plot [g(s*) vs s*] represents a snapshot of the sedimentation process at a particular time. It preserves diffusion information allowing accurate estimation of diffusion coefficients and, therefore, calculation of molar masses.
- Advantages of g(s*) from dc/dt
The DCDT plot [g(s*) vs s*] represents a snapshot of the boundary at a particular time.
Uses a narrow time interval.
Boundary shape is preserved.
Diffusional information is preserved allowing accuate estimates of diffusion coefficients - even for multiple overlapping boundaries - and, therefore, reliable calculation of molar masses.
Boundary spreading characteristics of interacting systems are also preserved.
- BIOSPIN, for the model independent analysis of sedimentation equilibrium data.
- BIOSPIN processes sedimentation equilibrium data to produces plots of the number, weight and z-average molar masses as a function of local cell radius and concentration.
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SEDANAL can be downloaded from the RASMB software archive
- Gelinas AD, Toth J, Bethoney KA, Stafford WF and CJ Harrison. (2004) Mutational analysis of the energetics of the GrpE.DnaK binding interface: equilibrium association constants by sedimentation velocity analytical ultracentrifugation. J Mol Biol, 339(2), 447-58.[download the pdf]
- Stafford, W. F. and P. J. Sherwood (2004). "Analysis of heterologous interacting systems by sedimentation velocity: Curve fitting algorithms for estimation of sedimentation coefficients, equilibrium and rate constants." Biophysical Chemistry,108,231-243.[download the pdf]
- Stafford, W. F. and E. H. Braswell (2004). "Sedimentation Velocity, Multi-speed Method for Analyzing Polydisperse Solutions." Biophysical Chemistry,108,273-279.[download the pdf]
- Sontag, C. A., W. F. Stafford, and J. J. Correia (2004). "A Comparison of Weight Average and Direct Boundary Fitting of Sedimentation Velocity Data for Indefinite Polymerizing Systems." Biophysical Chemistry, 108, 215-230
- Stafford, W.F. (2003) "Analytical Ultracentrifugation. Sedimentation Velocity Analysis" Current Protocols in Protein Science. 20.7.1-20.7.11, John Wiley & Sons.
- Gelinas, A. D., J. Toth, K. A. Bethoney, K. Langsetmo, W. F. Stafford, and C.J. Harrison (2003). "Thermodynamic linkage in the GrpE nucleotide exchange factor, a molecular thermosensor." Biochemistry 47(30): 9050-9.
- Stafford, W. F. (2000). "Analysis of reversibly interacting macromolecular systems by time derivative sedimentation velocity." Methods Enzymol 323, 302-325.[download the pdf]
- Rivas, G., W. F. Stafford, and A.P. Minton (1999). "Characterization of Heterologous Protein-Protein Interaction via Analytical Ultracentrifugation." Methods: A Companion to Methods in Enzymology. 19,194-212.[download the pdf]
- Laue, T. M. and W. F. Stafford (1999). "Modern applications of analytical ultracentrifugation." Annu Rev Biophys Biomol Struct 28: 75-100.
- Stafford, W.F. "Sedimentation velocity spins a new weave for an old fabric." (1997) Current Opinion in Biotechnology 8, 14-24.[download the pdf]
- Stafford, W.F. (1994) "Boundary Analysis in Sedimentation Velocity Experiments." Methods in Enzymology. Numerical Computer Methods, Part B, Orlando, Academic Press. pp. 478-501.[download the pdf]
- Stafford, W.F. (1992) "Boundary Analysis in Sedimentation Transport Experiments- A Procedure for Obtaining Sedimentation Coefficient Distributions Using the Time Derivative of the Concentration Profile." Analytical Biochem. 203, 295.[download the pdf]
As we enjoy great advantages from inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously.
Contact Walter Stafford at "stafford at sedanal dot org"
Last updated April 10, 2014