Sedimentation analysis of noninteracting and self-associating solutes using numerical solutions to the Lamm equation

Biophysical Journal

Volumn 75, Issue 3, 1998, Pages 1503-1512

  Schuck, Peter ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; DIFFUSION COEFFICIENT; PROTEIN ASSEMBLY; PROTEIN CONFORMATION; SEDIMENTATION RATE;

EID: 0031688168     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)74069-X     Document Type: Article

References (40)

1. Adams, E. T. 1992. Sedimentation coefficients of self-associating species. Analysis of monomer-dimer-n-mer associations and some indefinite associations. In Analytical Ultracentrifugation in Biochemistry and Polymer Science. S. E. Harding, A. J. Rowe, and J. C. Horton, editors. The Royal Society of Chemistry, Cambridge. 407-427.
2. Beechem, J. M. 1992. Global analysis of biochemical and biophysical data. Methods Enzymol. 210:37-54.
3. Behlke, J., and O. Ristau. 1997. Molecular mass determination by sedimentation velocity experiments and direct fitting of the concentration profiles. Biophys. J. 72:428-434.
4. Bethune, J. L., and G. Kegeles. 1961a. Countercurrent distribution of chemically reacting systems. I. Polymerization. J. Phys. Chem. 65:433-438.
5. Bethune, J. L., and G. Kegeles. 1961b. Countercurrent distribution of chemically reacting systems. III. Analogs of moving boundary electrophoresis and sedimentation. J. Phys. Chem. 65:1761-1764.
6. Bevington, P. R., and D. K. Robinson. 1992. Data Reduction and Error Analysis for the Physical Sciences. McGraw-Hill, New York.
7. Cann, J. R., and G. Kegeles. 1974. Theory of sedimentation for kinetically controlled dimerization reactions. Biochemistry. 13:1868-1874.
8. Claverie, J.-M. 1976. Sedimentation of generalized systems of interacting particles. III. Concentration-dependent sedimentation and extension to other transport methods. Biopolymers. 15:843-857.
9. Claverie, J.-M., H. Dreux, and R. Cohen. 1975. Sedimentation of generalized systems of interacting particles. I. Solution of systems of complete Lamm equations. Biopolymers. 14:1685-1700.
10. Cox, D. J. 1965. Computer simulation of sedimentation in the ultracentrifuge. II. Concentration-independent sedimentation. Arch. Biochem. Biophys. 112:259-266.
11. Cox, D. J. 1966. Sedimentation of an initially skewed boundary. Science. 152:359-361.
12. Cox, D. J. 1969. Computer simulation of sedimentation in the ultracentrifuge. IV. Velocity sedimentation of self-associating solutes. Arch. Biochem. Biophys. 129:106-123.
13. Cox, D. J., and R. S. Dale. 1981. Simulation of transport experiments for interacting systems. In Protein-Protein Interactions. C. Frieden and L. W. Nichol, editors. Wiley, New York.
14. Crank, J., and P. Nicholson. 1947. A practical method for numerical evaluation of solutions of partial differential equations of the heat-conduction type. Proc. Cambridge Philos. Soc. 43:50-67.
15. Demeler, B., and H. Saber. 1998. Determination of molecular parameters by fitting sedimentation data to finite element solutions of the Lamm equation. Biophys. J. 74:444-454.
16. Dishon, M., Weiss, G. H., and D. A. Yphantis. 1966. Numerical solutions of the Lamm equation. I. Numerical procedure. Biopolymers. 4:449-455.
17. Faxén, H. 1929. Über eine Differentialgleichung aus der physikalischen Chemie. Ark. Mat. Astr. Fys. 21B:1-6.
18. Fujita, H. 1962. Mathematical Theory of Sedimentation Analysis. Academic Press, New York.
19. Fujita, H., and V. J. MacCosham. 1959. Extension of sedimentation velocity theory to molecules of intermediate sizes. J. Chem. Phys. 30:291-298.
20. Gilbert, G. A. 1955. Disc. Faraday Soc. 20:68-71.
21. Gilbert, L. M., and G. A. Gilbert. 1973. Sedimentation velocity measurement of protein association. Methods Enzymol. 27D:273-306.
22. Goad, W. B., and J. R. Cann. 1969. Theory of sedimentation of interacting systems. Ann. N.Y. Acad. Sci. 164:172-182.
23. Holladay, L. A. 1979a. An approximate solution to the Lamm equation. Biophys. Chem. 10:187-190.
24. Holladay, L. A. 1979b. Molecular weights from approach-to-sedimentation equilibrium data using nonlinear regression analysis. Biophys. Chem. 10:183-185.
25. Holladay, L. A. 1980. Simultaneous rapid estimation of sedimentation coefficient and molecular weight. Biophys. Chem. 11:303-308.
26. Lamm, O. 1929. Die Differentialgleichung der Ultrazentrifugierung. Ark. Mat. Astr. Fys. 21B:1-4.
27. MacPhee, C. E., M. A. Perugini, W. H. Sawyer, and G. J. Howlett. 1997. Trifluroethanol induces the self-association of specific amphipathic peptides. FEBS Lett. 416:265-268.
28. Marque, J. 1992. Simulation of the time course of macromolecular separations in an ultracentrifuge. II. Controlling the solute concentration. Biophys. Chem. 42:23-27.
29. Minton, A. P. 1992. Simulation of the time course of macromolecular separations in an ultracentrifuge. I. Formation of a cesium chloride density gradient at 25°C. Biophys. Chem. 42:13-21.
30. Philo, J. S. 1997. An improved function for fitting sedimentation velocity data for low-molecular-weight solutes. Biophys. J. 72:435-444.
31. Press, W. H., S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery. 1992. Numerical Recipes in C. University Press, Cambridge.
32. Sartory, W. K., H. B. Halsall, and J. P. Breillatt. 1976. Simulation of gradient and band propagation in the centrifuge. Biophys. Chem. 5:107-135.
33. Schachman, H. K. 1959. Ultracentrifugation in Biochemistry. Academic Press, New York.
34. Schuck, P., C. E. MacPhee, and G. J. Howlett. 1998. Determination of sedimentation coefficients for small proteins. Biophys. J. 74:466-474.
35. Schuck, P., and D. B. Millar. 1998. Rapid determination of molar mass in modified Archibald experiments using direct fitting of the Lamm equation. Anal. Biochem. 259:48-53.
36. 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. Anal. Biochem. 203:1-7.
37. Stafford, W. F. 1994. Boundary analysis in sedimentation velocity experiments. Methods Enzymol. 240:478-501.
38. Stafford, W. F. 1998. Time difference sedimentation velocity analysis of rapidly reversible interacting systems: determination of equilibrium constants by global non-linear curve fitting procedures. Biophys. J. 74:301a. (Abstr.).
39. Svedberg, T., and K. O. Pedersen. 1940. Die Ultrazentrifuge. Theodor Steinkopff, Dresden.
40. Zienkiewicz, O. C., and R. L. Taylor. 1991. The Finite Element Method, 4th ed, Vol. 2. McGraw-Hill, London.