SEDANAL.ORG

SEDANAL

SEDIMENTATION ANALYSIS


SEDANAL is a program for the analysis of data from the 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.

First described in:

  • Stafford, WF, (1998) "Time difference sedimentation velocity analysis of rapidly reversible interacting systems: Determination of equilibrium constants by global non-linear curve fitting procedures." Biophysical Journal,74(2),A301.

    These programs were combined and a data preprocessor with a GUI (graphical user interface) added and it was renamed SEDANAL (Stafford and Sherwood, 2004).

    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 sub-program is used to maintain a 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 Fitter (LEF) to both ideal and non-ideal, interacting and non-interacting systems.

    • Sedimentation equilibrium
      • Fitting with the Sedimentation Equilibrium Fitter (SEF) to sums of exponentials for both ideal and non-ideal, interacting and non-interacting systems

    Several other programs have been included within SEDANAL:

  • BIOSPIN, for the model independent analysis of sedimentation equilibrium data.

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    Download the lastest version of SEDANAL (has new features that may have bugs. Check the Change Logs under the Help Menu.)

    NOTE: The zip file contains the SEDANAL executable, a DDL and an online help file. They must all be installed in the Program folder.

    Download the manual for getting started and for general reference

    Be sure to peruse or search the on-line Help files from the main menu and from within each module of SEDANAL.

     
    


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    SELECTED REFERENCES

    1. Sherwood, P.J. and Stafford, W.F. (2016) "SEDANAL: Model-Dependent and Model Independent Analysis of Sedimentation Data" in Analytical Ultracentrifugation. Instrumentation, Software, and Applications, Eds. Uchiyama, S, Arisaka, F., Stafford, W.F., and Laue T.M., Springer Japan. Chapter 6, pp 81-102.

    2. Stafford, W.F. and Sherwood, P.J. (2016) "SEDANAL: Global Analysis of General Hetero- and Self-Associating Systems by Sedimentation Equilibrium" in Analytical Ultracentrifugation. Instrumentation, Software, and Applications, Eds. Uchiyama, S, Arisaka, F., Stafford, W.F., and Laue T.M., Springer Japan. Chapter 7, pp 103-118.

    3. Stafford, W.F. (2016) "Analysis of Non-deal, Interacting and Noninteracting Systems by Sedimentation Velocity Analytical Ultracentrifugation" in Analytical Ultracentrifugation. Instrumentation, Software, and Applications, Eds. Uchiyama, S, Arisaka, F., Stafford, W.F., and Laue T.M., Springer Japan. Chapter 23, pp463-482.

    4. Correia, J.J., Lyons, D.F., Sherwood, P.J. and Stafford, W.F. (2016) in Analytical Ultracentrifugation. Instrumentation, Software, and Applications, Eds. Uchiyama, S, Arisaka, F., Stafford, W.F., and Laue T.M., Springer Japan. Chapter 24, pp483-498.

    5. EunHee Lee and Walter Stafford (2015) "Interaction of Myosin Phosphatase Target Subunit (MYPT1) with Myosin Phosphatase-RhoA Interacting Protein (MRIP): A Role of Glutamic Acids in the Interaction" PLOS ONE,10(10),e0139875. link

    6. Johannes Walter, Peter J. Sherwood, Wei Lin, Doris Segets, Walter F. Stafford, and Wolfgang Peuker (2015) "Simultaneous Analysis of Hydrodynamic and Optical Properties Using Analytical Ultracentrifugation Equipped with Multiwavelength Detection", Analytical Chemistry, 87, 3396-3403. PDF

    7. Graceffa, P. and Lee, E. and Stafford, W. F. (2013) "Disulfide cross-linked antiparallel actin dimer", Biochemistry 52, 1082-1088.

    8. Stafford, W. F. and Lee, E. and Graceffa, P. (2012) "Equilibrium self-association of tropomyosin" FEBS Lett. 586, 3840-3842.

    9. Cole, J. L., Correia, J. J. and Stafford, W. F. (2011) "The use of analytical sedimentation velocity to extract thermodynamic linkage." Biophys. Chem. 159, 120-128.

    10. Correia, J. J. and Stafford, W. F. (2009) "Extracting equilibrium constants from kinetically limited reacting systems." Meth. Enzymol. 455, 419-446.

    11. Correia, J. J. and Alday, P. H. and Sherwood, P. and Stafford, W. F. (2009) "Effect of kinetics on sedimentation velocity profiles and the role of intermediates" Meth. Enzymol. 467, 135-161.

    12. 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]

    13. 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]

    14. 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]

    15. 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

    16. Stafford, W.F. (2003) "Analytical Ultracentrifugation. Sedimentation Velocity Analysis" Current Protocols in Protein Science. 20.7.1-20.7.11, John Wiley & Sons.

    17. 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.

    18. Stafford, W. F. (2000). "Analysis of reversibly interacting macromolecular systems by time derivative sedimentation velocity." Methods Enzymol 323, 302-325.[download the pdf]

    19. 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]

    20. Laue, T. M. and W. F. Stafford (1999). "Modern applications of analytical ultracentrifugation." Annu Rev Biophys Biomol Struct 28: 75-100.

    21. Stafford, W.F. "Sedimentation velocity spins a new weave for an old fabric." (1997) Current Opinion in Biotechnology 8, 14-24.[download the pdf]

    22. Liu, S. and W. Stafford (1995) "An optical thermometer for direct measurement of cell temperature in the beckman instruments XL-A analytical ultracentrifuge." Anal. Biochem. 224:199-202.

    23. 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]

    24. 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: email "stafford at sedanal dot org"

      Last updated November 6, 2016