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]
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. Up to 32 datasets, each from one centrifuge cell, can be combined in a global fit.
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:
- DCDT, for the model independent analysis of sedimentation velocity data. (Stafford, 1992)
- 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 by fitting the g(s*) vs s* function to a gaussian and extracting the diffusion coefficient from the variance of the gaussian:Here's the derivation
- 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 accurate 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.
- Multi-Wavelength Analysis (MWL) (Walter et al, 2015). SEDANAL is capable of analyzing multi-wavelength data, either by deconvoluting multi-wavelength data into component concentration distributions or by globally fitting with the Lamm Equation Fitter or the Equilibrium Fitter directly to the 4-Dimensional datasets given the spectrum of each component.SEDANAL can also acquire the spectra of well separated species using WDA.
- Wide Dstribution Analysis (WDA) (Stafford and Braswell, 2004) is also available on the DCDT/WDA menu.
- WDA can process single speed and multi-speed data allowing an extermely wide range of s values to be observed in a single run. Since all the scans from a run are used, the g(s*) distribution spans the entire run and includes all sedimenting species present in the sample, from the largest soluble aggregates to the smallest protein, spanning a range of about 250,000 S to 1.0SS in a single run, depending on the speeds chosen for a multi-speed run.
- BIOSPIN, for the model independent analysis of sedimentation equilibrium data.
- BIOSPIN (Roark and Yphantis, 1968) processes sedimentation equilibrium data to produces plots of the number, weight, and z-average molar masses as a function of local cell radius and local concentration.
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Download the lastest version of SEDANAL
Or download the current beta version (has new features that may have bugs. Check the Change Logs under the Help Menu.)
NOTE: The zip file contains the SEDANAL executable, a couple of DLLs 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.
Some handy rules of thumb for velocity and equilibrium sedimentation
Click here for a complete list of publications (searches the National Library of Medicine's PubMed database.)
- John Correia, R. T. Wright, P. J. Sherwood, W. F. Stafford (2020), "Analysis of nonideality: insights from high concentration simulations of sedimentation velocity data", European Biophysics Journal 49(8):687-700. (DOI: 10.1007/s00249-020-01474-5)
- Lee E, Salamat-Miller N, Stafford WF, Taylor K (2019) "Self-association of human beta- galactocerebrosidase: Dependence on pH, salt, and surfactant." PLoS ONE 14(12): e0226618. https:// doi.org/10.1371/journal.pone.0226618
- Maximilian J. Uttinger, Simon. E. Wawra, Tobias Guckeisen, Johannes Walter, Andreas Bear, Thaseem Thajudeen, Peter J. Sherwood, Ana Smith, Anja M. Wagemans, Walter F. Stafford, and Wolfgang Peukert (2019) "A Comprehensive Brownian Dynamics Approach for the Determination of Non-ideality Parameters from Analytical Ultracentrifugation", Langmuir 2019, 35, 11491−11502.
- Yang, DL, Correia, JJ, Stafford, WF, Roberts, CJ, Singh, S, Hayes, D, Kroe-Barrett, R,Nixon, A, Laue, TM,(2018) "Weak IgG self- and hetero-association characterized by fluorescence analytical ultracentrifugation", PROTEIN SCIENCE, 27,1334-1348.
- Robert T. Wright, David B. Hayes, Walter F. Stafford, Peter J. Sherwood, John J. Correia (2018) "Characterization of therapeutic antibodies in the presence of human serum proteins by AU-FDS analytical ultracentrifugation", Anal Biochem., 550,72-83.
- 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.
- 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.
- 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.
- Correia, J.J., Lyons, D.F., Sherwood, P.J. and Stafford, W.F. (2016) "Techniques for Dissecting the Johnston-Ogston Effect" 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.
- Bashkim Kokona, Carrie A. May, Nicole R. Cunningham, Lynn Richmond, F. Jay Garcia, Julia C. Durante, Kathleen M. Ulrich, Christine M. Roberts, Christopher D. Link, Walter F. Stafford, Thomas M. Laue, and Robert Fairman, (2016) "Studying polyglutamine aggregation in Caenorhabditis elegans using an analytical ultracentrifuge equipped with fluorescence detection," PROTEIN SCIENCE 2016 VOL 25:605—617.
- 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
- 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
- Graceffa, P. and Lee, E. and Stafford, W. F. (2013) "Disulfide cross-linked antiparallel actin dimer", Biochemistry 52, 1082-1088.
- Stafford, W. F. and Lee, E. and Graceffa, P. (2012) "Equilibrium self-association of tropomyosin" FEBS Lett. 586, 3840-3842.
- 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.
- Correia, J. J. and Stafford, W. F. (2009) "Extracting equilibrium constants from kinetically limited reacting systems." Meth. Enzymol. 455, 419-446.
- 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.
- 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.[download the pdf]
- 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]
- 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.
- 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]
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- Benjamin Franklin
Programming today is a race between software engineers striving to
build bigger and better idiot-proof programs, and the universe trying
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Contact Walter Stafford: email "stafford at sedanal dot org"
Last updated June 27, 2022