Analytical ultracentrifugation as a contemporary biomolecular research tool

Journal of Biomolecular Techniques

Volumn 10, Issue 4, 1999, Pages 163-176

  Cole, James L ^a   Hansen, Jeffrey C ^b  

^a MERCK RESEARCH LABORATORIES   (United States)

^b UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT SAN ANTONIO   (United States)

Author keywords

Centrifugation; Conformational changes; Sedimentation equilibrium; Sedimentation velocity; Solution interactions

Indexed keywords

EID: 0001209134     PISSN: 15240215     EISSN: 19434731     Source Type: Journal    
DOI: None     Document Type: Review

References (98)

1. Schachman HK. Is there a future for the ultracentrifuge? In Harding SE, Rowe AJ, Horton JC (ed): Analytical Ultracentrifugation in Biochemistry and Polymer Science, Cambridge, UK: Royal Society of Chemistry, 1992:3-15.
2. van Holde KE, Hansen JC. Analytical ultracentrifugation from 1924 to the present: a remarkable history. Chemtracts Biochem Mol Biol 1998;11:933-943.
3. Schuster TM, Toedt JM. New revolutions in the evolution of analytical ultracentrifugation. Curr Opin Struct Biol 1996;6:650-658.
4. Hensley P. Defining the structure and stability of macromolecular assemblies in solution: the re-emergence of analytical ultracentrifugation as a practical tool. Structure 1996;4:367-373.
5. Hansen JC, Lebowitz J, Demeler B. Analytical ultracentrifugation of complex macromolecular systems. Biochemistry 1994;33:13155-13163.
6. Giebeler R. The optima XL-A: a new analytical ultracentrifuge with a novel precision absorption optical system. In Harding SE, Rowe AJ, Horton JC (ed): Analytical Ultracentrifugation in Biochemistry and Polymer Science. Cambridge, UK Royal Society of Chemistry, 1992:16-25.
7. Laue TM. Choosing Which Optical System of the Optima XL-I Analytical Centrifuge to Use. Beckman Coulter Application Information, number A-1821-A,1996(URL: http://www.beckman.com/Beckman/biorsrch/prodinfo/xla/a_1821a.asp).
8. Furst A. analytical ultracentrifuge with Rayleigh interference optics. Eur J Biochem 1997;35:307-310.
9. Yphantis DA, Lary JW, Stafford WF, et al. On-line data acquisition for the Rayleigh interference optical system of the analytical ultracentrifuge. In Shuster TM, Laue TM (ed): Modern Analytical Ultracentrifugation. Boston: Birkhauser, 1994:209-226.
10. Lewis MS, Shrager RI, Kim S-J. Analysis of proteinnucleic acid and protein-protein interactions using multi-wavelength scans from the XL-A analytical centrifuge. In Shuster TM, Laue TM (eds): Modern Analytical Ultracentrifugation, Boston: Birkhauser, 1994: 94-115.
11. Howlett GJ. Analysis of hetero-associating systems by sedimentation equilibrium. Chemtracts Biochem Mol Biol 1998;11:950-959.
12. Gray RA, Stern A, Bewley T, Shire SJ. Rapid Determination of Spectrophotometric Absorptivity by Analytical Ultracentrifugation. Beckman Coulter Application Information, number A-1815-A, 1995 (URL: http://www.beckman.com/beckman/biorsrch/prodinfo/xla/pdf/a_1815a.pdf).
13. Cantor CR, Schimmel PR. Biophysical Chemistry, part II. San Francisco: WH Freeman, 1980.
14. Ralston G. Introduction to Analytical Ultracentrifugation. Fullerton, CA: Beckman Instruments, 1993.
15. Schachman HK. Ultracentrifugation in Biochemistry. New York: Academic Press, 1959.
16. Tanford C. Physical Chemistry of Macromolecules. New York: John Wiley and Sons, 1961.
17. van Holde KE. Sedimentation analysis of proteins. In Neurath H, Hill RH (ed): The Proteins, I. New York: Academic Press, 1975:225-291.
18. van Holde KE. Physical Biochemistry, 2nd ed. Englewood Cliffs, NJ: Prentice-Hall, 1985.
19. Johnson ML, Correia JJ, Yphantis DA, Halvorson HR. Analysis of data from the analytical ultracentrifuge by nonlinear least squares techniques. Biophys J 1981;36: 575-588.
20. McRorie DK, Voelker PJ. Self-Associating Systems in the Analytical Ultracentrifuge. Fullerton, CA: Beckman Instruments, 1993.
21. Fujita H. Foundations of Ultracentrifugal Analysis. New York: Wiley, 1975.
22. van Holde KE, Weischet WO. Boundary analysis of sedimentation-velocity experiments with monodisperse and paucidisperse solutes. Biopolymers 1978;17:1387-1403.
23. Demeler B, Saber H, Hansen JC. Identification and interpretation of complexity in sedimentation velocity boundaries. Biophys J 1997;72:397-407.
24. Carruthers LC, Schirf V, Demeler B, Hansen JC. Sedimentation velocity analysis of macromolecular assemblies. Methods Enzymol 1999 (in press).
25. Stafford WF. Boundary analysis in sedimentation transport experiments: a procedure for obtaining sedimentation coefficient distributions using the time derivative of the concentration profile. Anal Biochem 1992;203: 295-301.
26. Stafford WF. Methods for obtaining sedimentation coefficient distributions. In Harding SE, Rowe AJ, Horton JC (ed): Analytical Ultracentrifugation in Biochemistry and Polymer Science. Cambridge, UK: Royal Society of Chemistry, 1992:359-393.
27. Stafford WF. Sedimentation boundary analysis of interacting systems: use of the apparent sedimentation coefficient distribution function. In Shuster TM, Laue TM (ed): Modern Analytical Ultracentrifugation. Boston: Birkhauser, 1994:119-137.
28. Stafford WF. Boundary analysis in sedimentation velocity experiments. Methods Enzymol 1994;240:478-501.
29. Stafford WF. Sedimentation velocity spins a new weave for an old fabric. Curr Opin Biotechnol 1997;8:14-24.
30. Holladay LA. Simultaneous rapid estimation of sedimentation coefficient and molecular weight. Biophys Chem 1980;303-308.
31. Holladay LA. An approximate solution to the Lammequation. Biophys Chem 1979;10:187-190.
32. Philo JS. Measuring sedimentation, diffusion, and molecular weights of small molecules by direct fitting of sedimentation velocity concentration profiles. In Shuster TM, Laue TM (ed): Modern Analytical Ultracentrifugation. Boston: Birkhauser, 1994:156-170.
33. Philo JS. An improved function for fitting sedimentation velocity data for low-molecular-weight solutes. Biophys J 1997;72:435-44.
34. Behlke J, Ristau O. Molecular mass determination by sedimentation velocity experiments and direct fitting of the concentration profiles. Biophys J 1997;72:428-434.
35. Demeler B, Saber H. Determination of molecular parameters by fitting sedimentation data to finite-element solutions of the Lamm equation. Biophys J 1998;74: 444-454.
36. Schuck P. Sedimentation analysis of noninteracting and self-associating solutes using numerical solutions to the Lamm equation. Biophys J 1998;75:1503-1512.
37. Johnson ML, Straume M. Comments on the analysis of sedimentation equilibrium experiments In Shuster TM, Laue TM (ed): Modern Analytical Ultracentrifugation. Boston: Birkhauser, 1994:37-65.
38. Johnson ML, Faunt LM. Parameter estimation by leastsquares methods. Methods Enzymol 1992;210:1-37.
39. Milthorpe BK, Jeffrey PD, Nichol LW. The direct analysis of sedimentation equilibrium results obtained with polymerising systems. Biophys Chem 1975;3:169-176.
40. van Holde KE, Baldwin RL. Rapid attainment of sedimentation equilibrium. J Phys Chem 1958;62:734-743.
41. Yphantis DA. Rapid determination of molecular weights of proteins and peptides. Ann NY Acad Sci 1960;88: 586-601.
42. Laue TM. Short Column Sedimentation Equilibrium Analysis for Rapid Characterization of Macromolecules in Solution. Beckman Coulter Application Information DS-835, 1992 (URL: http://www.beckman.com/Beckman/articles/ds835/ds835.asp).
43. Minton AP. Alternative strategies for the characterization of associations in muticomponent solutions via measurements of sedimentation equilibrium. Prog Colloid Polymer Sci 1997;107:11-19.
44. Philo JS. Improving sedimentation equilibrium analysis of mixed associations using numerical constraints to impose mass or signal conservation. Methods Enzymol 1999 (in press).
45. Minton AP. Analytical centrifugation with preparative ultracentrifuges. Biophys Biochem 1989;176:209-216.
46. Darawshe S, Rivas G, Minton AP. Rapid and accurate microfractionation of the contents of small centrifuge tubes: application in the measurement of molecular weight of proteins via sedimentation equilibrium. Biophys Biochem 1993;209:130-135.
47. Winzor DJ, Jacobsen MP, Wills PR. Direct analysis of sedimentation equilibrium distributions reflecting complex formation between dissimilar reactants. Biochemistry 1998;37:2226-2233.
48. Garcia de la Torre J, Navarro S, Lopez Martinez MC, Diaz FG, Lopez Cascales JJ. HYDRO: a computer program for the prediction of hydrodynamic properties of macromolecules. Biophys J 1994;67:530-531.
49. Byron O. Construction of hydrodynamic bead models from high-resolution x-ray crystallographic or nuclear magnetic resonance data. Biophys J 1997;72:408-415.
50. Carruthers LM, Bednar J, Woodcock CL, Hansen JC. Linker histones stabilize the intrinsic salt-dependent folding of nucleosomal arrays: mechanistic ramifications for higher-order chromatin folding. Biochemistry 1998;37:14776-14787.
51. Rogers DP, Roberts LM, Lebowitz J, et al. The lipidfree structure of apolipoprotein A-I: effects of aminoterminal deletions. Biochemistry 1998;37:11714-11725.
52. Fleming KG, Hohl TM, Yu RC, et al. A revised model for the oligomeric state of the N-ethylmaleimidesensitive fusion protein, NSF. J Biol Chem 1998;273: 15675-15681.
53. Rippe K, Mucke N, Schulz A. Association states of the transcription activator protein NtrC from E. coli determined by analytical ultracentrifugation. J Mol Biol 1998; 278:915-933.
54. Rosenfeld RD, Zeni L, Welcher AA, et al. Biochemical, biophysical, and pharmacological characterization of bacterially expressed human agouti-related protein. Biochemistry 1998;37:16041-15052.
55. Zubrzycki IZ, Frankel LK, Russo PS, Bricker TM. Hydrodynamic studies on the manganese-stabilizing protein of photosystem II. Biochemistry 1998;37:13553-13558.
56. Rich RL, Demeler B, Ashby K, et al. Domain structure of the Staphylococcus aureus collagen adhesin. Biochemistry 1998;37:15423-15433.
57. Tse C, Fletcher TM, Hansen JC. Enhanced transcription factor access to arrays of histone H3/H4 tetramer-DNA complexes in vitro: implications for replication and transcription. Proc Natl Acad Sci USA 1998;95:12169-12173.
58. Fless GM, Kirk EW, Klezovitch O, et al. Effect of phospholipase A2 digestion on the conformation and lysine/fibrinogen binding properties of human lipoprotein[ a]. J Lipid Res 1999;40:583-592.
59. Wagschal K, Tripet B, Hodges RS. De novo design of a model peptide sequence to examine the effects of single amino acid substitutions in the hydrophobic core on both stability and oligomerization state of coiledcoils. J Mol Biol 1999;285:785-803.
60. Gutierrez MM, Tsai SW, Phillips ML, et al. Studying low-density lipoprotein-monoclonal antibody complexes using dynamic laser light scattering and analytical ultracentrifugation. Biochemistry 1999;38:1284-1292.
61. Tse C, Hansen JC. Hybrid trypsinized nucleosomal arrays: identification of multiple functional roles of the H2A/H2B and H3/H4 N-termini in chromatin fiber compaction. Biochemistry 1997;36:11381-11388.
62. Bullard JM, Demeler B, Spremulli LL. Expression and characterization of a human mitochondrial phenylalanyl- tRNA synthetase. Biochemistry 1999;38:2716-2724.
63. Tse C, Sera T, Wolffe AP, Hansen JC. Acetylationinduced decondensation of nucleosomal arrays dramatically facilitates transcription by RNA polymerase III. Mol Cell Biol 1998;18:4629-4638.
64. Logie C, Tse C, Hansen JC, Peterson CL. The core histone N-terminal domains are required for multiple rounds of catalytic chromatin remodeling by the SWI/SNF and RSC complexes. Biochemistry 1999;38: 2514-2522.
65. Kar SR, Adams AC, Lebowitz J, Taylor KB, Hall LM. The cyanobacterial repressor SmtB is predominantly a dimer and binds two Zn2 ions per subunit. Biochemistry 1997;36:15343-15348.
66. Fletcher TM, Serwer P, Hansen JC. Quantitative analysis of macromolecular conformational changes using agarose gel electrophoresis: application to chromatin folding. Biochemistry 1994;33:10859-10863.
67. Fletcher TM, Hansen JC. Core histone tail domains mediate oligonucleosome folding and nucleosomal DNA organization through distinct molecular mechanisms. J Biol Chem 1995;270:25359-25362.
68. Behal RH, DeBuysere MS, Demeler B, Hansen JC, Olson MS. Pyruvate dehydrogenase multienzyme complex. Characterization of assembly intermediates by sedimentation velocity analysis. J Biol Chem 1994;269: 31372-31377.
69. Mendoza JA, Demeler B, Horowitz PM. Alteration of the quaternary structure of cpn60 modulates chaperonin- assisted folding: implications for the mechanism of chaperonin action. J Biol Chem 1994;269:2447-2451.
70. Musatov A, Robinson NC. Detergent-solubilized monomeric and dimeric cytochrome bc1 isolated from bovine heart. Biochemistry 1994;33:13005-130012.
71. Anant JS, Desnoyers L, Machius M, et al. Mechanism of Rab geranylgeranylation: formation of the catalytic ternary complex. Biochemistry 1998;37:12559-12568.
72. Liu J, Laue TM, Choi HU, Tang LH, Rosenberg L. The self-association of biglycan from bovine articular cartilage. J Biol Chem 1994;269:28366-28373.
73. McLachlin DT, Bestard JA, Dunn SD. The beta and delta subunits of the Escherichia coli ATP synthase interact via residues in their C-terminal regions. J Biol Chem 1998;273:15162-15168.
74. Toedt JM, Braswell EH, Schuster TM, et al. Biophysical characterization of a designed TMV coat protein mutant, R46G, that elicits a moderate hypersensitivity response in Nicotiana sylvestris. Protein Sci 1999;8:261-270.
75. Hsu YR, Nybo R, Sullivan JK, et al. Heparin is essential for a single keratinocyte growth factor molecule to bind and form a complex with two molecules of the extracellular domain of its receptor. Biochemistry 1999; 38:2523-2534.
76. Fujita T, Ralston GB, Morris MB. Biophysical properties of human erythrocyte spectrin at alkaline pH: implications for spectrin structure, function, and association. Biochemistry 1998;37:264-271.
77. Leroux MR, Melki R, Gordon B, Batelier G, Candido EP. Structure-function studies on small heat shock protein oligomeric assembly and interaction with unfolded polypeptides. J Biol Chem 1997;272:24646-24656.
78. Fletcher TM, Krishnan U, Serwer P, Hansen JC. Quantitative agarose gel electrophoresis of chromatin: nucleosome-dependent changes in charge, sharp, and deformability at low ionic strength. Biochemistry 1994;33:2226-2233.
79. Schwarz PM, Felthauser A, Fletcher TM, Hansen JC. Reversible oligonucleosome self-association: dependence on divalent cations and core histone tail domains. Biochemistry 1996;35:4009-4015.
80. Syto R, Murgolo NJ, Braswell EH, et al. Structural and biological stability of the human interleukin 10 homodimer. Biochemistry 1998;37:16943-16951.
81. Saez C, Thielens NM, Bjes ES, Esser AF. Association of terminal complement proteins in solution and modulation by suramin. Biochemistry 1999;38:6807-6816.
82. Tennyson RB, Lindsley JE. Type II DNA topoisomerase from Saccharomyces cerevisiae is a stable dimer. Biochemistry 1997;36:6107-6114.
83. Wu X, Spiro C, Owen WG, McMurray CT. CAMP response element-binding protein monomers cooperatively assemble to form dimers on DNA. J Biol Chem 1998;273:20820-20827.
84. Zhong M, Kim SJ, Wu C. Sensitivity of Drosophila heat shock transcription factor to low pH. J Biol Chem 1999; 274:3135-3140.
85. Daugherty MA, Brenowitz M, Fried MG. The TATAbinding protein from Saccharomyces cerevisiae oligomerizes in solution at micromolar concentrations to form tetramers and octamers. J Mol Biol 1999;285: 1389-1399.
86. Cole JL. Characterization of human cytomegalovirus protease dimerization by analytical centrifugation. Biochemistry 1996;35:15601-15610.
87. Steinmetzer K, Behlke J, Brantl S. Plasmid pIP501 encoded transcriptional repressor CopR binds to its target DNA as a dimer. J Mol Biol 1998;283:595-603.
88. Rusinova E, Ross JBA, Laue TM, Sowers LC, Senear DF. Linkage between operator binding and dimer to octamer self-assembly of bacteriophage lambda cI repressor. Biochemistry 1997;36:12994-3003.
89. Parker MH, Stafford WF 3rd, Prevelige PE Jr. Bacteriophage P22 scaffolding protein forms oligomers in solution. J Mol Biol 1997;268:655-665.
90. Abril AM, Salas M, Andreu JM, Hermoso JM, Rivas G. Phage ø29 protein p6 is in a monomer-dimer equilibrium that shifts to higher association states at the millimolar concentrations found in vivo. Biochemistry 1997; 36:11901-11908.
91. Begg GE, Morris MB, Ralston GB. Comparison of the salt-dependent self-association of brain and erythroid spectrin. Biochemistry 1997;36:6977-6985.
92. Vulevic B, Lobert S, Correia JJ. Role of guanine nucleotides in the vinblastine-induced self-association of tubulin: effects of guanosine α, β-methylenetriphosphate and guanosine α, β -methylenediphosphate. Biochemistry 1997;36:12828-12835.
93. Lobert S, Ingram JW, Hill BT, Correia JJ. A comparison of thermodynamic parameters for vinorelbine- and vinflunine- induced tubulin self-association by sedimentation velocity. Mol Pharmacol 1998;53:908-915.
94. Shi J, Ghirlando R, Beavil RL, et al. Interaction of the low-affinity receptor CD23/Fc epsilonRII lectin domain with the Fc epsilon3-4 fragment of human immunoglobulin E. Biochemistry 1997;36:2112-2122.
95. Darawshe S, Millar DB, Ahmed SA, Miles EW, Minton AP. Dissociation equilibria of the tryptophan synthase alpha 2 beta 2 complex in saline buffer and guanidine isothiocyanate, as studied by sedimentation equilibrium. Biophys Chem 1997;69:53-62.
96. Cole JL, Carroll SS, Blue ES, Viscount T, Kuo LC. Activation of RNase L by 2',5'-oligoadenylates. Biophysical characterization. J Biol Chem 1997;272:19187-19192.
97. Beernink HT, Morrical SW. The uvsY recombination protein of bacteriophage T4 forms hexamers in the presence and absence of single-stranded DNA. Biochemistry 1998;37:5673-5681.
98. Laue TM, Stafford WF. Modern applications of the analytical ultracentrifuge. Annu Rev Biophys Biomol Struct 1999;28:75-100.