SEDANAL

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]

and

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.

SEDANAL can be downloaded from the RASMB software archive

Download SEDANAL

SEDANAL change log

Subscribe to the SEDANAL email discussion group

REFERENCES

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.
-Benjamin Franklin
Contact Walter Stafford at "stafford at bbri dot org"
Last updated May 3, 2010