Sedimentation velocity analysis of heterogeneous protein-protein interactions: Lamm equation modeling and sedimentation coefficient distributions c(s)

Biophysical Journal

Volumn 89, Issue 1, 2005, Pages 619-634

  Dam, Julie ^a   Velikovsky, Carlos A ^a   Mariuzza, Roy A ^a   Urbanke, Claus ^b   Schuck, Peter ^c  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^b HANNOVER MEDICAL SCHOOL   (Germany)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; DIFFUSION; EQUILIBRIUM CONSTANT; LAMM EQUATION MODELING; LIGAND BINDING; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MOLECULAR INTERACTION; PROBLEM SOLVING; PROTEIN PROTEIN INTERACTION; QUANTITATIVE ANALYSIS; REACTION ANALYSIS; SEDIMENTATION COEFFICIENT DISTRIBUTION; SEDIMENTATION RATE; ULTRACENTRIFUGATION;

EID: 20444380585     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.059568     Document Type: Article

References (56)

1. Svedberg, T., and K. O. Pedersen. 1940. The Ultracentrifuge. Oxford University Press, London, UK.
2. Lamm, O. 1929. Die Differentialgleichung der Ultrazentrifugierung. Ark. Mat. Astr. Fys. 21B:1-4. [in German].
3. Holladay, L. A. 1979. An approximate solution to the Lamm equation. Biophys. Chem. 10:187-190.
4. Gilbert, G. A., and L. M. Gilbert. 1980. Ultracentrifuge studies of interactions and equilibria: impact of interactive computer modelling. Biochem. Soc. Trans. 8:520-522.
5. Urbanke, C., B. Ziegler, and K. Stieglitz. 1980. Complete evaluation of sedimentation velocity experiments in the analytical ultracentrifuge. Fresenius Z. Anal. Chem. 301:139-140.
6. 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, NY.
7. Philo, J. S. 1997. An improved function for fitting sedimentation velocity data for low molecular weight solutes. Biophys. J. 72:435-444.
8. Kindler, B. 1997. Akkuprog: Auswertung von Messungen chemischer Reaktionsgeschwindigkeit und Analyse von Biopolymeren in der Ultrazentrifuge. University of Hannover, Hannover, Germany, [in German].
9. Schuck, P. 1998. Sedimentation analysis of noninteracting and self-associating solutes using numerical solutions to the Lamm equation. Biophys. J. 75:1503-1512.
10. Demeler, B., J. Behlke, and O. Ristau. 2000. Determination of molecular parameters from sedimentation velocity experiments: whole boundary fitting using approximate and numerical solutions of the Lamm equation. Methods Enzymol. 321:36-66.
11. Stafford, W. F., and P. J. Sherwood. 2004. Analysis of heterologous interacting systems by 36 sedimentation velocity: curve fitting algorithms for estimation of sedimentation coefficients, equilibrium and kinetic constants. Biophys. Chem. 108:231-243.
12. Cole, J. L., and J. C. Hansen. 1999. Analytical ultracentrifugation as a contemporary biomolecular research tool. J. Biomol. Tech. 10:163-176.
13. Arisaka, F. 1999. Applications and future perspectives of analytical ultracentrifugation. Tanpakushitsu Kakusan Koso. 44:82-91.
14. Laue, T. M., and W. F. I. Stafford. 1999. Modem applications of analytical ultracentrifugation. Annu. Rev. Biophys. Biomol. Struct. 28:75-100.
15. Rivas, G., W. Stafford, and A. P. Minton. 1999. Characterization of heterologous protein-protein interactions via analytical ultracentrifugation. Methods. 19:194-212.
16. Lebowitz, J., M. S. Lewis, and P. Schuck. 2002. Modem analytical ultracentrifugation in protein science: a tutorial review. Protein Sci. 11:2067-2079.
17. Scott, D. J., and P. Schuck. 2005. A brief introduction to the analytical ultracentrifugation of proteins for beginners. In Modem Analytical Ultracentrifugation: Techniques and Methods. D. J. Scott, S. E. Harding, and A. J. Rowe, editors. The Royal Society of Chemistry, Cambridge, UK. In press.
18. Balbo, A., and P. Schuck. 2005. Analytical ultracentrifugation in the study of protein self-association and heterogeneous protein-protein interactions. In Protein-Protein Interactions. E. Golemis and P. D. Adams, editors. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, NY. In press.
19. Balbo, A., K. H. Minor, C. A. Velikovsky, R. Mariuzza, C. B. Peterson, and P. Schuck. 2005. Studying multi-protein complexes by multi-signal sedimentation velocity analytical ultracentrifugation. Proc. Natl. Acad. Sci. USA. 102:81-86.
20. van Holde, K. E., and W. O. Weischet. 1978. Boundary analysis of sedimentation velocity experiments with monodisperse and paucidisperse solutes. Biopolymers. 17:1387-1403.
21. Demeler, B., H. Saber, and J. C. Hansen. 1997. Identification and interpretation of complexity in sedimentation velocity boundaries. Biophys. J. 72:397-407.
22. 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.
23. Schuck, P., and P. Rossmanith. 2000. Determination of the sedimentation coefficient distribution by least-squares boundary modeling. Biopolymers. 54:328-341.
24. Schuck, P. 2000. Size distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modeling. Biophys. J. 78:1606-1619.
25. Gilbert, G. A. 1955. Faraday Discuss. 20:68-71.
26. Gilbert, G. A., and R. C. Jenkins. 1956. Boundary problems in the sedimentation and electrophoresis of complex systems in rapid reversible equilibrium. Nature. 177:853-854.
27. Steiner, R. F. 1954. Reversible association processes of globular proteins. V. The study of associating systems by the methods of macromolecular physics. Arch. Biochem. Biophys. 49:400-416.
28. Fujita, H. 1975. Foundations of Ultracentrifugal Analysis. John Wiley & Sons, New York, NY.
29. Goad, W. B., and J. R. Cann. 1969. Theory of sedimentation of interacting systems. Ann. N. Y. Acad. Sci. 164:172-182.
30. 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.
31. Schuck, P. 2003. On the analysis of protein self-association by sedimentation velocity analytical ultracentrifugation. Anal. Biochem. 320:104-124.
32. Krauss, G., A. Pingoud, D. Boehme, D. Riesner, F. Peters, and G. Maass. 1975. Equivalent and nonequivalent binding sites for tRNA on aminoacyl-tRNA synthetases. Eur. J. Biochem. 55:517-529.
33. Urbanke, C., G. Witte, and U. Curth. 2005. A sedimentation velocity method in the analytical ultracentrifuge for the study of protein-protein interactions. In Protein-Ligand Interactions: Methods and Applications. G. U. Nienhaus, editor. Humana Press, Totowa, NJ. 101-113.
34. Machner, M. P., C. Urbanke, M. Barzik, S. Otten, A. S. Sechi, J. Wehland, and D. W. Heinz. 2001. ActA from Listeria monocytogenes can interact with up to four Ena/VASP homology 1 domains simultaneously. J. Biol. Chem. 276:40096-40103.
35. J. Dam, and P. Schuck. 2005. Sedimentation velocity analysis of protein-protein interactions: sedimentation coefficient distributions c(s) and asymptotic boundary profiles from Gilbert-Jenkins theory. Biophys. J. 89:651-666.
36. Fujita, H. 1962. Mathematical Theory of Sedimentation Analysis. Academic Press, New York, NY.
37. 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.
38. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery. 1992. Numerical Recipes in C. Cambridge University Press, Cambridge, UK.
39. Schuck, P., M. A. Perugini, N. R. Gonzales, G. J. Howlett, and D. Schubert. 2002. Size-distribution analysis of proteins by analytical ultracentrifugation: strategies and application to model systems. Biophys. J. 82:1096-1111.
40. Amato, U., and W. Hughes. 1991. Maximum entropy regularization of Fredholm integral equations of the first kind. Inverse problems 7:793-808.
41. Schuck, P., and B. Demeler. 1999. Direct sedimentation analysis of interference optical data in analytical ultracentrifugation. Biophys. J. 76:2288-2296.
42. Dam, J., and P. Schuck. 2004. Calculating sedimentation coefficient distributions by direct modeling of sedimentation velocity profiles. Methods Enzymol 384:185-212.
43. Cox, D. J. 1969. Computer simulation of sedimentation in the ultracentrifuge. IV. Velocity sedimentation of self-associating solutes. Arch. Biochem. Biophys. 129:106-123.
44. Dam, J., R. Guan, K. Natarajan, N. Dimasi, L. K. Chlewicki, D. M. Kranz, P. Schuck, D. H. Margulies, and R. A. Mariuzza. 2003. Variable MHC class I engagement by Ly49 NK cell receptors revealed by the crystal structure of Ly49C bound to H-2Kb. Nat. Immunol. 4:1213-1222.
45. Samelson, L. E. 2002. Signal transduction mediated by the T cell antigen receptor: the role of adapter proteins. Annu. Rev. Immunol. 20:371-394.
46. Houtman, J. C., Y. Higashimoto, N. Dimasi, S. Cho, H. Yamaguchi, B. Bowden, C. Regan, E. L. Malchiodi, R. Mariuzza, P. Schuck, E. Appella, and L. E. Samelson. 2004. Binding specificity of multiprotein signaling complexes is determined by both cooperative interactions and affinity preferences. Biochemistry. 43:4170-4178.
47. Bethune, J. L., and G. Kegeles. 1961. Countercurrent distribution of chemically reacting systems. III. Analogs of moving boundary electrophoresis and sedimentation. J. Phys. Chem. 65:1761-1764.
48. Dishon, M., G. H. Weiss, and D. A. Yphantis. 1967. Numerical simulations of the Lamm equation. III. Velocity centrifugation. Biopolymers. 5:697-713.
49. Cann, J. R., and D. C. Dates. 1973. Theory of electrophoresis and sedimentation for some kinetically controlled interactions. Biochemistry. 12:1112-1119.
50. Cann, J. R. 1985. Effects of diffusion on the electrophoretic behavior of associating systems: the Gilbert-Jenkins theory revisited. Arch. Biochem. Biophys. 240:489-499.
51. 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.
52. Cann, J. R., and G. Kegeles. 1974. Theory of sedimentation for kinetically controlled dimerization reactions. Biochemistry. 13:1868-1874.
53. Cann, J. R. 1982. Theory of sedimentation for antigen-antibody reactions effect of antibody heterogeneity on the shape of the pattern. Mol. Immunol. 19:505-514.
54. Revzin, A., and P. H. von Hippel. 1977. Direct measurement of association constants for the binding of Escherichia coli lac repressor to non-operator DNA. Biochemistry. 16:4769-4776.
55. Cann, J. R. 1986. Effects of microheterogeneity on sedimentation patterns of interacting proteins and the sedimentation behavior of systems involving two ligands. Methods Enzymol. 130:19-35.
56. Wemer, W. E., and H. K. Schachman. 1989. Analysis of the ligand-promoted global conformational change in aspartate trans-carbamoylase. Evidence for a two-state transition from boundary spreading in sedimentation velocity experiments. J. Mol. Biol. 206:221-230.