Analysis of heterologous interacting systems by sedimentation velocity: Curve fitting algorithms for estimation of sedimentation coefficients, equilibrium and kinetic constants

Biophysical Chemistry

Volumn 108, Issue 1-3, 2004, Pages 231-243

  Stafford, Walter F ^a   Sherwood, Peter J ^a  

^a BOSTON BIOMEDICAL RESEARCH INSTITUTE   (United States)

Author keywords

Analytical ultracentrifugation; Heterologous interacting systems; Kinetics; Nonlinear curve fitting; Thermodynamics; Time difference data

Indexed keywords

BUFFER; DNA; LIGAND; PROTEIN;

ALGORITHM; ANALYTICAL ERROR; ARTICLE; COMPUTER PROGRAM; CONCENTRATION (PARAMETERS); CURVE FITTING; DATA ANALYSIS; DIFFUSION COEFFICIENT; EQUILIBRIUM CONSTANT; FINITE ELEMENT ANALYSIS; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; SAMPLE; SEDIMENTATION RATE; SPECIES; SYSTEM ANALYSIS; THEORY; ULTRACENTRIFUGATION;

ALGORITHMS; DNA; KINETICS; LIGANDS; MACROMOLECULAR SUBSTANCES; MODELS, CHEMICAL; MONTE CARLO METHOD; PROTEINS; SOFTWARE; SOLUTIONS; ULTRACENTRIFUGATION;

EID: 1642368109     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2003.10.028     Document Type: Article

References (16)

1. Claverie J.M., Dreux H., Cohen R. Sedimentation of generalized systems of interacting particles. I. Solution of systems of complete Lamm equations. Biopolymers. 14:1975;1685-1700.
2. Claverie J.-M. Sedimentation of generalized systems of interacting particles III. Concentration dependent sedimentation and extension to other transport methods. Biopolymers. 15:1976;843-857.
3. Todd G.P., Haschemeyer R.H. General solution to the inverse problem of the differential equation of the ultracentrifuge. Proc. Natl. Acad. Sci. USA. 78:1981;6739-6743.
4. Demeler B., Saber H. Determination of molecular parameters by fitting sedimentation data to finite-element solutions of the Lamm equation. Biophys. J. 74:1998;444-454.
5. Schuck P. Sedimentation analysis of noninteracting and self-associating solutes using numerical solutions to the Lamm equation. Biophys. J. 75:1998;1503-1512.
6. Stafford W.F. Time difference sedimentation velocity analysis of rapidly reversible interacting systems: determination of equilibrium constants by non-linear curve fitting procedures. Biophys. J. 74:1998;A301.
7. G. Rivas, W.F. Stafford, A.P. Minton, Characterization of Heterologous Protein-Protein Interaction via Analytical Ultracentrifugation. Methods Oct. 19 (2) (1999) 194-212
8. Schuck P., Demeler B. Direct sedimentation analysis of interference optical data in analytical ultracentrifugation. Biophys. J. 76:1999;2288-2296.
9. Stafford W.F. Boundary analysis in sedimentation transport experiments: a procedure for obtaining sedimentation coefficient distributions using the time derivative of the concentration profile. Anal. Biochem. 203:1992;295-301.
10. Philo J.S. An improved function for fitting sedimentation velocity data for low-molecular-weight solutes. Biophys. J. 72:1997;435-444.
11. Sontag C.A., Stafford W.F., Correia J.J. A comparison of weight average and direct boundary fitting of sedimentation velocity data for indefinite polymerizing systems. Biophys. Chem. 1108:2004;215-230.
12. Lamm O. Die Differentialgleichung der Ultrazentrifugierung. Arkiv Math. Astron. Fysik. 21B:(2):1929;1-4.
13. Harding S.E., Johnson P. The concentration-dependence of macromolecular parameters. Biochem. J. 231:1985;543-547.
14. Nelder J.A., Mead R. A simplex method for function minimization. Comput. J. 7:1965;308-313.
15. Press W.H., Flannery B.P., Teukolsky S.A., Vetterling W.T. Richardson Extrapolation and the Bulirsch-Stoer Method. Numerical Recipes in FORTRAN: The Art of Scientific Computing. second ed. 1992;718-725 Cambridge University Press, Cambridge, England.
16. Snedecor G.W., Cochran W.G. Statistical Methods. 1967;Iowa State University Press.