SpringerProtocols: Abstract: Protein?Protein and Ligand?Protein Interactions Studied by Analytical Ultracentrifugation

4. Protein–Protein and Ligand–Protein Interactions Studied by Analytical Ultracentrifugation

By: Walter F. Stafford III²

Abstract

Full Text

Download PDF (1039K)

All biological processes involve molecular interactions that result in either binding, self-association, or hetero-associations of one form or another. It is important to understand that no interactions are completely all-or-none. Some approach all-or-none only when there is strong positive cooperativity. Examples will be given of typical biomolecular interactions and their expected dependence on concentration, in order to point out the relatively wide range of concentration over which these types of phenomena take place. This chapter is concerned both with the binding of low-molecular-weight ligands to macromolecules as well as interactions between macromolecules using analytical ultracentrifugation (AUC) as a tool for measuring association properties of these systems. The theory of sedimentation of both ideal and nonideal interacting and noninteracting systems is discussed. Examples are given of each type of system along with a discussion of how each type of system can be analyzed. Several methods of data analysis are discussed.

Affiliation(s): (2) Boston Biomedical Research Institute, Watertown, MA, USA

Book Title: Protein Structure, Stability, and Interactions

Series: Methods in Molecular Biology | Volume: 490 | Pub. Date: Mar-01-2008 | Page Range: 1-31 | DOI: 10.1007/978-1-59745-367-7_4

Subject: Protein Science

Key Words: Analytical ultracentrifugation - sedimentation - cooperativity

References

Download References

1.	Svensson, H. (1954) The second order aberrations in the interferometric measurement of concentration gradients. Optica Acta 1, 25–32.

2.	Svensson, H. (1954) The second order aberrations in the interferomentric measurement of concentration gradients. II. Experimental verification of theory. Optica Acta 1, 90–93.

3.	Svensson, H. (1956) The third order aberrations in the interferometric measurement of concentration gradients. Optica Acta 3, 164–168.

4.	Stafford, W. F. (unpublished observation).

5.	Richards, E. G., Teller, D., Schachman, H. K. (1971) Alignment of Schlieren and Rayleigh optical systems in the ultracentrifuge. I. Focusing of the camera and cylindrical lenses. Anal Biochem 41, 189–214.

6.	Richards, E. G., Teller, D. C., Hoagland, V. J., et al. (1971) Alignment of Schlieren and Rayleigh optical systems in the ultracentrifuge. II. A general procedure. Anal Biochem 41, 215–247.

7.	Richards, E. G., Bell, C. J., Kirschner, M., et al. (1972) Alignment of Schlieren and Rayleigh optical systems in the ultracentrifuge. 3. Design, construction, and placement of Rayleigh mask. Anal Biochem 46, 295–331.

8.	Casassa, E. F., Eisenberg, H. (1964) Thermodynamic analysis of multicomponent solutions. Adv Protein Chem 19, 287–395.

9.	Kar, S. R., Kingsbury, J. S., Lewis, M. S., et al. (2000) Analysis of transport experiments using pseudo-absorbance data. Anal Biochem 285, 135–142.

10.	Schuck, P., Demeler, B. (1999) Direct sedimentation analysis of interference optical data in analytical ultracentrifugation. Biophys J 76, 2288–2296.

11.	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, 295–301.

12.	Stafford, W. F., Sherwood, P. J. (2004) Analysis of heterologous interacting systems by sedimentation velocity: Curve fitting algorithms for estimation of sedimentation coefficients, equilibrium and rate constants. Biophys Chem 108, 231–243.

13.	Rivas, G., Stafford, W. F., Minton, A. P. (1999) Characterization of heterologous protein–protein interaction via analytical ultracentrifugation. Methods: A Companion to Methods in Enzymology.

14.	Stafford, W. F. (1998) Time difference sedimentation velocity analysis of rapidly reversible interacting systems: determination of equilibrium constants by non-linear curve fitting procedures. Biophys J 74, A301.

15.	Schuck, P. (1999) Sedimentation equilibrium analysis of interference optical data by systematic noise decomposition. Anal Biochem 272, 199–208.

16.	Schuck, P. (2000) Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modeling. Biophys J 78, 1606–1619.

17.	Johnson, M., Faunt, L. (1992) Parameter estimation by least-squares methods. Methods in Enzymology 210, 1–37.

18.	Johnson, M. L. (1992) Why, when, and how biochemists should use least squares, Anal Biochem 206, 215–225.

19.	Schuck, P., Perugini, M. A., Gonzales, N. R., et al. (2002) Size-distribution analysis of proteins by analytical ultracentrifugation: strategies and application to model systems, Biophys J 82, 1096–1111.

20.	Svedberg, T., Pederson, K. O. (1940) The Ultracentrifuge, Oxford University Press, New York.

21.	Schachman, H. K. (1959) . Academic Press, New York.

22.	Williams, J. W., Van Holde, K. E., Baldwin, R. L., et al. (1958) The theory of sedimentation analysis. Chem Rev 58, 715–806.

23.	Fujita, H. (1962) Mathematical Theory of Sedimentation Analysis. Academic Press, New York.

24.	Fujita, H. (1976) Foundations of Ultracentrifugal Analysis. John Wiley & Sons, New York.

25.	Tanford, C. (1961) Physical Chemistry of Macromolecules, p. 710. John Wiley & Sons, New York.

26.	Harding, S. E., Johnson, P. (1985) The concentration-dependence of macromolecular parameters, Biochem J 231, 543–547.

27.	Solovyova, A., Schuck, P., Costenaro, L., Ebel, C. (2001) Non-ideality by sedimentation velocity of halophilic malate dehydrogenase in complex solvents, Biophys J 81, 1868–1880.

28.	Roark, D. E., Yphantis, D. A. (1971) Equilibrium centrifugation of nonideal systems. The Donnan effect in self-associating systems. Biochemistry 10, 3241–328149.

29.	Lamm, O. (1929) Die Differentialgleichung der Ultrazentrifugierung. Arkiv Math. Astron. Fysik 21B, No.2, 1–4.

30.	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.

31.	Claverie, J. M., Dreux, H., Cohen, R. (1975) Sedimentation of generalized systems of interacting particles. I. Solution of systems of complete Lamm equations. Biopolymers 14, 1685–1700.

32.	Todd, G. P. Haschemeyer, R. H. (1981) General solution to the inverse problem of the differentia17l equation of the ultracentrifuge. Proc Natl Acad Sci U S A 78, 6739–6743.

33.	Todd, G., Haschemeyer, R. (1983) Generalized finite element solution to one-dimensional flux problems. Biophys Chem 17, 321–326.

34.	Holladay, L. (1980) Simultaneous rapid estimation of sedimentation coefficient and molecular weight. Biophys Chem 11, 303–308.

35.	Holladay, L. (1979) An approximate solution to the Lamm equation. Biophys Chem 10, 187–190.

36.	Philo, J. S. (1997) An improved function for fitting sedimentation velocity data for low-molecular-weight solutes. Biophys J 72, 435–444.

37.	Behlke, J., Ristau, O. (2002) A new approximate whole boundary solution of the Lamm differential equation for the analysis of sedimentation velocity experiments. Biophys Chem 95, 59–68.

38.	Gilbert, G. A. (1955) The physical chemistry of enzymes – general discussion. Discuss. Farad Soc 20, 65–77.

39.	Gilbert, G. A. (1959) Sedimentation and electrophoresis of interacting substances .1. Idealized boundary shape for a single substance aggregating reversibly. Proc R Soc A253, 377–388.

40.	Gilbert, G. A., Jenkins, R. C. (1959) Sedimentation and electrophoresis of interacting substances .2. Asymptotic boundary shape for 2 substances interacting reversibly, Proc. R Soc A253, 420–437.

41.	Schuck, P. (www.analyticalultracentrifugation.com/references.htm.).

42.	Cann, J. R. (1970) 89 Interacting Macromolecules. New York: Academic Press.

43.	Dam, J., Velikovsky, C. A., Mariuzza, R. A., et al. (2005) Sedimentation velocity analysis of heterogeneous protein–protein interactions: Lamm equation modeling and sedimentation coefficient distributions c(s), Biophys J , 619–34.

44.	Demeler, B. (2005) UltraScan A Comprehensive Data Analysis Software Package for Analytical Ultracentrifugation Experiments, in Modern Analytical Ultracentrifugation: Techniques and Methods, S.E.H.a.A.J.R. D. J. Scott, Editor. 2005, Royal Society of Chemistry, UK. p. 210–229.

Comments (Loading...)

Post comment/View all comments