Abstract
The analytical ultracentrifuge has had wide application in the characterization of the structure, interaction and function of macromolecules in solution. This includes the determination of molecular weight, the characterization of shape, the determination of subunit stoichiometry, the quantification of ligand binding, the quantification of ligand-binding-promoted conformational changes and the characterization of macromolecular assembly processes (Schachman, 1992). In recent years, however, other technologies have been developed which can make some of the relevent measurements with equal or greater precision, often using less material. For instance, molecular weight can now be routinely determined by gene or protein sequencing and by mass spectroscopic methods, especially electrospray (ES) and matrix-assisted laser-desorption (MALD) MS (Carr, et al, 1991). Ligand binding can be quantified by classical spectroscopic and radiochemical methods as well as by microcalorimetry (Freire, et al, 1990). Ligand binding promoted conformational changes can be characterized by time- resolved fluorescence anisotropy (Lakowicz, 1983; Beechem, et al, 1986; Waxman, et al, 1994) although, the centrifuge still has a major impact in this area (Kirschner and Schachman, 1973a; Kirschner and Schachman, 1973b; Howlett and Schachman, 1977; Eisenstein, et al, 1990) The thermodynamic characterization of macromolecular assembly processes, however, is an area where the analytical ultracentrifuge has few rivals (Adams and Lewis, 1968; Roark and Yphantis, 1969; Hensley, et al, 1975b; Blackburn and Noltman, 1981; Minton and Lewis, 1981; Wilf and Minton, 1981; Correia, et al, 1985; Duong, et al., 1986; Hensley, et al, 1986; Lewis and Youle, 1986; Chatelier and Minton, 1987; Ross, et al, 1991; Rivas, et al, 1992).
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References
Adams, E. T. J. and Lewis, M. S. (1968): Sedimentation equilibrium in reacting systems. VI. Some applications to indefinite self-associations. Studies with beta-lactoglobulin A, Biochemistry 7, 1044–53.
Bates, D. M. and Watts, D. G. (1988): Nonlinear Regression Analysis and Its Applications, New York, Wiley Interscience.
Bates, D. M. and Watts, D. G. (1991): Model building in chemistry using profile t and trace plots., Chemometrics and Intelligent Laboratory Systems 10, 107–116.
Beechem, J. M., Knutson, J. R., and Brand, L. (1986): Global analysis of multiple dye fluorescence anisotropy experiments on proteins, Biochem Soc Trans 14, 832–5.
Bevington, P. R. (1969): Data Reduction and Error Analysis for the Physical Sciences, New York, McGraw Hill Book Company.
Blackburn, M. N. and Noltman, E. A. (1981): Evidence for an intermediate in the denaturation and assembly of phosphoglucose isomerase., Archives of Biochemistry and Biophysics 212, 162–169.
Brooks, I., Watts, D. G., Soneson, K. K., and Hensley, P. (1994a): Determining the Confidence Intervals of Parameters from Analysis of Equilibrium Analytical Ultracentrifuge Data. In: Methods in Enzymology, L. Brand and M. L. Johnson, ed. s, New York, Academic Press, (in press).
Brooks, I., Wetzel, R., Chan, W., Lee, G., Watts, D. G., Soneson, K. K., and Hensley, P. (1994b): A Mutational Analysis of the Relation Between Domain-Domain Interactions in Solution, Inclusion Body and Fibril Formation in vitro for REI, an Immunoglobulin VL(Bence-Jones) Domain Expressed in E. coli, (submitted).
Buxbaum, J. (1992): Mechanisms of disease: Monoclonal immunoglobulin deposition, Hemat. Oncol. Clin. North America 6, 323–346.
Cantor, C. R. and Schimmel, P. R. (1980): Biophysical chemistry, pt. 2: Techniques for the study of biological structure and function., San Francisco, W.H. Freeman and Co.
Carr, S. A., Hemling, M. E., Bean, M. F., and Roberts, G. D. (1991): Integration of mass spectrometry in analytical biotechnology, Analytical Chemistry 63, 2802–2824.
Chan, W., Hensley, P., Lee, G., and Wetzel, R. (1993): Secretion into the Escherichia coli periplasm of the immunoglobulin VL domain REI: inclusion body formation, purification, and dimerization of a series of point mutants, Ms. in preparation.
Chatelier, R. C. and Minton, A. P. (1987): Sedimentation equilibrium in macromolecular solutions of arbitrary concentration. I. Self-associating proteins, Biopolymers 26, 507–24.
Correia, J. J., Shire, S., Yphantis, D. A., and Schuster, T. M. (1985): Sedimentation equilibrium measurements of the intermediate-size tobacco mosaic virus protein polymers, Biochemistry 24, 3292–7.
Creighton, T. E. (1984): Proteins: Structures and Molecular Properties, New York, W. H. Freeman.
Draper, N. and Smith, H. (1981): Applied Regression Analysis, Second Edition, New York, Wiley-Interscience.
Duong, L. T., Eisenstein, E., Green, S. M., Ornberg, R. L., and Hensley, P. (1986): The quaternary structure of ornithine transcarbamoylase and arginase from Saccharomyces cerevisiae, J Biol Chem 261, 12807–13.
Eisenstein, E., Markby, D. W., and Schachman, H. K. (1990): Heterotopic effectors promote a global conformational change in aspartate transcarbamoylase, Biochemistry 29, 3724–31.
Epp, O., Colman, P., Fehlhammer, H., Bode, W., Schiffer, M., Huber, R., and Palm, W. (1974): Crystal and molecular structure of a dimer composed of the variable portions of the Bence-Jones protein REI, Eur. J. Biochem. 45, 513–524.
Freire, E., Mayorga, O. L., and Straume, M. (1990): Isothermal Titration Calorimetry, Analytical Chemistry 62, 950A–959A.
Helms, L. R. and Wetzel, R. (1994): Dramatic reduction in domain folding stability by a point mutation, Asp82 to Val82, associated with light chain deposition disease., (submitted).
Hensley, P., Edelstein, S. J., Wharton, D. C., and Gibson, Q. H. (1975b): Conformation and spin state in methemoglobin, J Biol Chem 250, 952–60.
Hensley, P., Moffat, K., and Edelstein, S. J. (1975a): Influence of inositol hexaphosphate binding on subunit dissociation in methemoglobin, J Biol Chem 250, 9391–6.
Hensley, P., O., Keefe, M. C., Spangler, C. J., Osborne, J. C. J., and Vogel, C. W. (1986): The effects of metal ions and temperature on the interaction of cobra venom factor and human complement factor B, J Biol Chem 261, 11038–44.
Howlett, G. J. and Schachman, H. K. (1977): Allosteric regulation of aspartate transcarbamoylase. Changes in the sedimentation coefficient promoted by the bisubstrate analogue N-(phosphonacetyl)-L-aspartate, Biochemistry 16, 5077–83.
Johnson, M. L. and Faunt, L. M. (1992): Parameter estimation by least-squares methods. In: Methods Enzymol, L. Brand and M. L. Johnson, ed. s, New York, Academic Press, 1–37.
Johnson, M. L. and Staume, M. (1994): Comments on the Analysis of Sedimentation Equilbrium Experiments. In: Modern Analytical Ultracentrifugation: Acquisition and Interpretation of Data for Biological and Synthetic Polymer Systems, T. M. Schuster and T. M. Laue, ed. s, Boston, MA, Birkhauser Boston, Inc., (this volume).
Kirschner, M. W. and Schachman, H. K. (1973a): Local and gross conformational changes in aspartate transcarbamylase, Biochemistry 12, 2997–3004.
Kirschner, M. W. and Schachman, H. K. (1973b): Conformational studies on the nitrated catalytic subunit of aspartate transcarbamylase, Biochemistry 12, 2987–97.
Kosaka, M., Iishi, Y., Okagawa, K., Saito, S., Sugihara, J., and Muto, Y. (1989): Tetrameric Bence-Jones protein in the immunoproliferative diseases, Am. J. Clin. Path. 91, 639–646.
Kratky, O., Leopold, H., and Stabinger, H. (1973): Determination of the partial specific volume of proteins by the mechanical oscillator tecnhique. In: Methods in Enzymology. Enzyme Structure, part D, C. H. W. Hirs and S. N. Timasheff, ed. s, New York, Academic Press, 98–110.
Lakowicz, J. R. (1983): Principles of Fluorescence Spectroscopy, New York, Plenum. Association of REI Immunoglobulin Light Chain VL Domains
Laue, T. M., Shah, B. D., Ridgeway, T. M., and Pelletier, S. L. (1992): Computer-Aided Interpretation of Analytical Sedimentation Data for Proteins. In: Analytical Ultracentrifugation in Biochemistry and Polymer Science, S. E. Harding, A. J. Rowe and J. C. Horton, ed. s, Cambridge, Great Britain, The Royal Society of Chemistry, 90–125.
Lee, G., Chan, W., Hurle, M. R., DesJarlais, R. L., Watson, F., Sathe, G. M., and Wetzel, R. (1993): Strong inhibition of fibrinogen binding to platelet receptor allbßlllby RGD sequences installed into a presentation scaffold, Protein Engineering 6, 745–754.
Lewis, M. S. and Youle, R. J. (1986): Ricin subunit association. Thermodynamics and the role of the disulfide bond in toxicity, J Biol Chem 261, 11571–7.
Minton, A. P. (1994): Conservation of signal: a new algorithm for the elimination of reference concentration as an independent parameter in the analysis of sedimentation equilbrium data. In: Modern Analytical Ultracentrifugation: Acquisition and Interpretation of Data for Biological and Synthetic Polymer Systems, T. M. Shuster and T. M. Laue, ed. s, Boston, MA, Birkhauser Boston, Inc., (This volume).
Minton, A. P. and Lewis, M. S. (1981): Self-association in highly concentrated solutions of myoglobin: a novel analysis of sedimentation equilibrium of highly nonideal solutions, Biophys Chem 14,317–24. Press, W. H., Flannery, B. P., Teukolsky, S. A., and Vetterling, W. T. ( 1986 ): Numerical Recipies — The Art of Scientific Computing, New York, Cambridge University Press.
Rivas, G., Ingham, K. C., and Minton, A. P. (1992): Calcium-linked self- association of human complement C1s, Biochemistry 31, 11707–12.
Roark, D. E. and Yphantis, D. A. (1969): Studies of self-associating systems by equilibrium ultracentrifugation, Ann NY. Acad. Sci. 164, 245–78.
Ross, P. D., Howard, F. B., and Lewis, M. S. (1991): Thermodynamics of antiparallel hairpin-double helix equilibria in DNA oligonucleotides from equilibrium ultracentrifugation, Biochemistry 30, 6269–75.
Schachman, H. K. (1992): Is There a Future for the Ultracentrifuge? In: Analytical Ultracentrifugation in Biochemistry and Polymer Science, S. E. Harding, A. J. Rowe and J. C. Horton, ed. s, Cambridge, Great Britain, The Royal Society of Chemistry, 3–15.
Stevens, F. J., Westholm, F. A., Solomon, A., and Schiffer, M. (1980): Self- association of human immunoglobulin kI light chains: Role of the third hypervariable region, Proc. Natl Acad. Sci. USA 77, 1144–1148.
Straume, M. and Johnson, M. L. (1992): Monte Carlo method for determining complete confidence probability distributions of estimated model parameters. In: Methods Enzymol, L. Brand and M. L. Johnson, ed. s, New York, Academic Press, 117–29.
Watts, D. G. (1991): Model building in chemistry using profile t and trace plots., Chemometrics and intelligent laboratory systems 10, 107–116.
Watts, D. G. (1994): How good are parameter estimates from nonlinear models? In: Methods in Enzymology, L. Brand and M. L. Johnson, ed. s, New York, NY, Academic Press, (in press).
Waxman, E., Laws, W. R., Laue, T. M., and Ross, J. B. A. (1994): Refining Hydrodynamic Shapes of Proteins: The Combination of Data from Analytical Ultracentrifugation and Time-Resolved Fluorescence Anisotropy Decay. In: Modern Analytical Ultracentrifugation: Acquisition and Interpretation of Data for Biological and Synthetic Polymer Systems, T. M. Schuster and T. M. Laue, ed. s, Boston, MA, Birkhouser Boston, Inc, (This Volume).
Wetzel, R. (1992): Protein aggregation in vivo: Bacterial inclusion bodies and mammalian amyloid. In: Stability of Protein Pharmaceuticals: In Vivo Pathways of Degradation and Strategies for Protein Stabilization, T. J. Ahern and M. C. Manning, ed. s, New York, Plenum Press, 43–88.
Wetzel, R. (1994): Aggregation - The Dark Side of Protein Folding, Trends in Biotechnology 12, (in press).
Wetzel, R., Hurle, M. R., Li, L., Helms, L., and Chan, W. (1993): Molecular basis of sequence effects in light chain amyloidosis and light chain deposition disease, Submitted.
Wilf, J. and Minton, A. P. (1981): Evidence for protein self-association induced by excluded volume. Myoglobin in the presence of globular proteins, Biochim Biophys Acta 670, 316–22.
Zimyatnin, A. A. (1972): Protein volume in solution., Prog. Biophys. Mol. Biol. 24, 109–123.
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Brooks, I. et al. (1994). Association of Rei Immunoglobulin Light Chain VL Domains: The Functional Linearity Of Parameters in Equilibrium Analytical Ultracentrifuge Models for Self-Associating Systems. In: Schuster, T.M., Laue, T.M. (eds) Modern Analytical Ultracentrifugation. Emerging Biochemical and Biophysical Techniques. Birkhäuser Boston. https://doi.org/10.1007/978-1-4684-6828-1_2
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