Studying Protein Folding and Aggregation by Laser Light Scattering

Protein Folding Handbook

Volumn 2, Issue , 2008, Pages 673-709

  Gast, Klaus ^a   Modler, Andreas J ^a  

^a UNIVERSITY OF POTSDAM   (Germany)

Author keywords

Instruments; Laser light; Light scattering; Macromolecules; Stress

Indexed keywords

EID: 84888203982     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527619498.ch19     Document Type: Chapter

References (87)

1. Jakeman, E., Pusey, P. N. & Vaughan, J. M. (1976). Intensity fluctuation light-scattering spectroscopy using a conventional source. Optics Commun. 17, 305-308.
2. Huglin, M. (1972). Light Scattering from Polymer Solutions, Academic Press, New York.
3. Kratochvil, P. (1987). Classical Light Scattering from Polymer Solutions, Elsevier, Amsterdam.
4. Schmitz, K. S. (1990). An Introduction to Dynamic Light Scattering by Macromolecules. Academic Press, New York.
5. Chu, B. (1991). Laser Light Scattering. Academic Press, New York.
6. Brown, W. (1993). Dynamic Light Scattering. Claredon Press, Oxford.
7. Berne, B. J. & Pecora, R. (2000). Dynamic Light Scattering with Applications to Chemistry, Biology, and Physics. Dover Publications, Mineola, New York.
8. Provencher, S. W. (1982). CONTIN -a general-purpose constrained regularization program for inverting noisy linear algebraic and integralequations. 2 Phys. Commun. 27, 229-242.
9. Koppel, D. E. (1972). Analysis of macromolecular polydispersity in intensity correlation spectroscopy: the method of cumulants. 2 Chem. Phys. 57, 4814-4820.
10. Harding, S. E. & Johnson, P. (1985). The concentration dependence of macromolecular parameters. 2 J. 231, 543-547.
11. Garcia Bernal, J. M. & De La Torre, J. G. (1981). Transport-properties of oligomeric subunit structuresBiopolymers.20, 129-139.
12. Claes, P., Dunford, M., Kenney, A. & Penny, V. (1992). An on-line dynamic light scattering instrument for macromolecular characterization. In Laser Light Scattering in Biochemistry (Harding, S. E., Sattelle, D. B. & Bloomfield, V. A., eds), pp. 66-76. Royal Society of Chemistry, Cambridge.
13. Nicoli, D. F. & Benedek, G. B. (1976). Study of the thermal denaturation of lysozyme and other globular proteins by light-scattering spectroscopyBiopolymers 15, 2421-2437.
14. Gast, K., Zirwer, D., Damaschun, H., Hahn, U., Müller-Frohne, M., Wirth, M. & Damaschun, G. (1997). Ribonuclease T1 has different dimensions in the thermally and chemically denatured states: a dynamic light scattering study. FEBS Lett. 403, 245-248.
15. Fabian, H., Fälber, K., Gast, K., Reinstadler, D., Rogov, V. V., Naumann, D., Zamyatkin, D. F. & Filimonov, V. V. (1999). Secondary structure and oligomerization behavior of equilibrium unfolding intermediates of the lambda Cro repressorBiochemistry 38, 5633-5642.
16. Privalov, P. L. (1990). Cold denaturation of proteins. 2 Rev. Biochem. Mol. Biol. 25, 281-305.
17. Griko, Y. V., Venyaminov, S. Y. & Privalov, P. L. (1989). Heat and cold denaturation of phosphoglycerate kinase (interaction of domains). FEBS Lett. 244, 276-278.
18. Damaschun, G., Damaschun, H., Gast, K., Misselwitz, R., Müller, J. J., Pfeil, W. & Zirwer, D. (1993). Cold denaturation-induced conformational changes in phosphoglycerate kinase from yeast.Biochemistry32, 7739-7746.
19. Agashe, V. R., Udgaonkar, J. B. (1995). Thermodynamics of denaturation of barstar: evidence for cold denaturation and evaluation of the interaction with guanidine hydrochloride.Biochemistry.34, 3286-3299.
20. Wong, K. B., Freund, S. M. V. & Fersht, A. R. (1996). Cold denaturation of barstar: H-1, N-15 and C-13 NMR assignment and characterisation of residual structure. 2 Mol. Biol. 259, 805-818.
21. Tanford, C. (1968). Protein denaturation. 2 Protein Chem. 23, 121-282.
22. Dubin, S. B., Feher, G. & Benedek, G. B. (1973). Study of the chemical denaturation of lysozyme by optical mixing spectroscopy.Biochemistry.12, 714-719.
23. Nöppert, A., Gast, K., Müller-Frohne, M., Zirwer, D. & Damaschun, G. (1996). Reduceddenatured ribonuclease A is not in a compact state. FEBS Lett. 380, 179-182.
24. Fink, A. L., Calciano, L. J., Goto, Y., Kurotsu, T. & Palleros, D. R. (1994). Classification of acid denaturation of proteins: intermediates and unfolded states.Biochemistry.33, 12504-12511.
25. Barrick, D., Hughson, F. M. & Baldwin, R. L. (1994). Molecular mechanism of acid denaturation-the role of histidine-residues in the partial unfolding of apomyoglobin. 2 Mol. Biol. 237, 588-601.
26. Ptitsyn, O. B. (1995). Molten globule and protein folding. 2 Protein Chem. 47, 83-229.
27. Arai, M. & Kuwajima, K. (2000). Role of the molten globule state in protein folding. 2 Protein Chem. 53, 209-282.
28. Kuwajima, K. & Arai, M. (2000). The molten globule state: the physical picture and biological significance. In Mechanisms of Protein Folding (Pain, R. H., ed.), pp. 138-174. Oxford University Press, Oxford.
29. Gast, K., Zirwer, D., Müller-Frohne, M. & Damaschun, G. (1998). Compactness of the kinetic molten globule of bovine alphalactalbumin: a dynamic light scattering study. Protein Sci. 7, 2004-2011.
30. Gast, K., Damaschun, H., Misselwitz, R., Müller-Frohne, M., Zirwer, D. & Damaschun, G. (1994). Compactness of protein molten globules: temperature-induced structural changes of the apomyoglobin folding intermediate. 2 Biophys. J. 23, 297-305.
31. Kataoka, M., Kuwajima, K., Tokunaga, F. & Goto, Y. (1997). Structural characterization of the molten globule of alpha-lactalbumin by solution x-ray scattering. Protein Sci. 23, 422-430.
32. Kataoka, M., Nishii, I., Fujisawa, T., Ueki, T., Tokunaga, F. & Goto, Y. (1995). Structural characterization of the molten globule and native states of apomyoglobin by solution X-ray scattering. 2 Mol. Biol. 249, 215-228.
33. Gast, K., Zirwer, D., Müller-Frohne, M. & Damaschun, G. (1999). Trifluoroethanol-induced conformational transitions of proteins: insights gained from the differences between alpha-lactalbumin and ribonuclease A. Protein Sci. 8, 625-634.
34. Damaschun, G., Damaschun, H., Gast, K. & Zirwer, D. (1999). Proteins can adopt totally different folded conformations. 2 Mol. Biol. 291, 715-725.
35. Wright, P. E. & Dyson, H. J. (1999). Intrinsically unstructured proteins: Re-assessing the protein structurefunction paradigm. 2 Mol. Biol. 293, 321-331.
36. Gast, K., Damaschun, H., Eckert, K., Schulze-Forster, K., Maurer, H. R., Muller, F. M., Zirwer, D., Czarnecki, J. & Damaschun, G. (1995). Prothymosin alpha: A biologically active protein with random coil conformation.Biochemistry.34, 13211-13218.
37. Damaschun, G., Damaschun, H., Gast, K., Misselwitz, R., Zirwer, D., Gührs, K. H., Hartmann, M., Schlott, B., Triebel, H. & Behnke, D. (1993). Physical and conformational properties of staphylokinase in solution. Biochim. Biophys.Acta. 1161, 244-248.
38. Uversky, V. N. (1993). Use of fast protein size-exclusion liquidchromatography to study the unfolding of proteins which denature through the molten globule.Biochemistry.32, 13288-13298.
39. Wilkins, D. K., Grimshaw, S. B., Receveur, V., Dobson, C. M., Jones, J. A. & Smith, L. J. (1999). Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques.Biochemistry.38, 16424-16431.
40. Flory, P. J. (1969). Statistical Mechanics of Chain Molecules. John Wiley & Sons, New York.
41. Baldwin, R. L. & Zimm, B. H. (2000). Are denatured proteins ever random coils? Proc. Natl Acad. Sci.USA.97, 12391-12392.
42. Zhou, H. X. (2002). Dimensions of denatured protein chains from hydrodynamic data. 2 Phys. Chem. 106, 5769-5775.
43. Tanford, C., Kawahara, K. & Lapanje, S. (1966). Proteins in 6 M guanidine hydrochloride. 2 J. Biol. Chem. 241, 1923-1921.
44. Damaschun, G., Damaschun, H., Gast, K. & Zirwer, D. (1998). Denatured states of yeast phosphoglycerate kinase. Biochemistry (Moscow) 63, 259-275.
45. Byron, O. (2000). Hydrodynamic bead modeling of biological macromolecules. Methods Enzymol. 278, 304-.
46. Garcia De La Torre, J., Huertas, M. L. & Carrasco, B. (2000). Calculation of hydrodynamic properties of globular proteins from their atomiclevel structure. 2 J. 78, 719-730.
47. Harding, S. E. (2001). The hydration problem in solution biophysics: an introduction. 2 Chem. 93, 87-91.
48. Halle, B. & Davidovic, M. (2003). Biomolecular hydration: From water dynamics to hydrodynamics. Proc. Natl Acad. Sci.USA.100, 12135-12140.
49. Garcia De La Torre, J. (2001). Hydration from hydrodynamics. 2 Biophys. Chem. 159, 170-.
50. Feng, H. P. & Widom, J. (1994). Kinetics of compaction during lysozyme refolding studied by continuous-flow quasielastic light scattering.Biochemistry.33, 13382-13390.
51. Gast, K., Zirwer, D. & Damaschun, G. (2000). Time-resolved dynamic light scattering as a method to monitor compaction during protein folding. In Data Evaluation in Light Scattering of Polymers (Helmstedt, M. & Gast, K., eds), pp. 205-220. Wiley-VCH, Weinheim.
52. Shastry, M. C. R., Luck, S. D. & Roder, H. (1998). A continuous-flow capillary mixing method to monitor reactions on the microsecond time scale. 2 Biophys J. 74, 2714-2721.
53. Segel, D. J., Bachmann, A., Hofrichter, J., Hodgson, K. O., Doniach, S. & Kiefhaber, T. (1999). Characterization of transient intermediates in lysozyme folding with time-resolved small-angle X-ray scattering. 2 Mol. Biol. , 489-499.
54. Pollack, L., Tate, M. W., Darnton, N. C., Knight, J. B., Gruner, S. M., Eaton, W. A. & Austin, R. H. (1999). Compactness of the denatured state of a fast-folding protein measured by submillisecond small-angle x-ray scattering. Proc. Natl Acad. Sci.USA.96, 10115-10117.
55. Arai, M., Ito, K., Inobe, T., Nakao, M., Maki, K., Kamagata, K., Kihara, H., Amemiya, Y. & Kuwajima, K. (2002). Fast compaction of alphalactalbumin during folding studied by stopped-flow X-ray scattering. 2 Mol. Biol. 321, 121-132.
56. Nöppert, A., Gast, K., Zirwer, D. & Damaschun, G. (1998). Initial hydrophobic collapse is not necessary for folding RNase A. Folding Des. 3, 213-221.
57. Jaenicke, R. & Seckler, R. (1997). Protein misassembly in vitro. 2 Protein Chem. 50, 1-59.
58. De Young, L. R., Dill, K. A. & Fink, A. L. (1993). Aggregation of globular proteins. 2 Chem. Res. 26, 614-620.
59. Zettlmeissl, G., Rudolph, R. & Jaenicke, R. (1979). Reconstitution of lactic dehydrogenase. Noncovalent aggregation vs. reactivation. 1. Physical properties and kinetics of aggregation. Biochemistry.18, 5567-5571.
60. Finke, J. M., Roy, M., Zimm, B. H. & Jennings, P. A. (2000). Aggregation events occur prior to stable intermediate formation during refolding of interleukin 1 beta.Biochemistry.39, 575-583.
61. Jossang, T., Feder, J. & Rosenqvist, E. (1985). Heat aggregation kinetics of human IgG. 2 Chem. Phys. 82, 574-589.
62. Smoluchowski, M. v. (1917). Versuch einer mathematischen Theorie der Koagulationskinetik kolloider Lösungen. 2 Phys. Chem. 92, 129-168.
63. Aymard, P., Nicolai, T., Durand, D. & Clark, A. (1999). Static and dynamic scattering of betalactoglobulin aggregates formed after heat-induced denaturation at pH 2.Macromolecules.32, 2542-2552.
64. Le Bon, C., Nicolai, T. & Durand, D. (1999). Kinetics of aggregation and gelation of globular proteins after heat-induced denaturation.Macromolecules.32, 6120-6127.
65. Bauer, R., Carrotta, R., Rischel, C. & Ogendal, L. (2000). Characterization and isolation of intermediates in beta-lactoglobulin heat aggregation at high pH. 2 J. 79, 1030-1038.
66. Bernocco, S., Ferri, F., Profumo, A., Cuniberti, C. & Rocco, M. (2000). Polymerization of rod-like macromolecular monomers studied by stopped-flow, multiangle light scattering: Set-up, data processing, and application to fibrin formation. 2 J. 79, 561-583.
67. Buchner, J., Schmidt, M., Fuchs, M., Jaenicke, R., Rudolph, R., Schmid, F. X. & Kiefhaber, T. (1991). GroE facilitates refolding of citrate synthase by suppressing aggregation.Biochemistry.30, 1586-1591.
68. Fezoui, Y., Hartley, D. M., Harper, J. D., Khurana, R., Walsh, D. M., Condron, M. M., Selkoe, D. J., Lansbury, P. T., Fink, A. L. & Teplow, D. B. (2000). An improved method of preparing the amyloid betaprotein for fibrillogenesis and neurotoxicity experiments.Amyloid.7, 166-178.
69. Lomakin, A., Benedek, G. B. & Teplow, D. B. (1999). Monitoring protein assembly using quasielastic light scattering spectroscopy. Methods Enzymol. 309, 429-459.
70. Tomski, S. J. & Murphy, R. M. (1992). Kinetics of aggregation of synthetic beta-amyloid peptide. 2 Biochem. Biophys. 294, 630-638.
71. Murphy, R. M. & Pallitto, M. R. (2000). Probing the kinetics of betaamyloid self-association. 2 Struct. Biol. 130, 109-122.
72. Lomakin, A., Chung, D. S., Benedek, G. B., Kirschner, D. A. & Teplow, D. B. (1996). On the nucleation and growth of amyloid beta-protein fibrils: Detection of nuclei and quantitation of rate constants. Proc. Natl Acad. Sci.USA.93, 1125-1129.
73. Lomakin, A., Teplow, D. B., Kirschner, D. A. & Benedek, G. B. (1997). Kinetic theory of fibrillogenesis of amyloid beta-protein. Proc. Natl Acad. Sci.USA.94, 7942-7947.
74. Kusumoto, Y., Lomakin, A., Teplow, D. B. & Benedek, G. B. (1998). Temperature dependence of amyloid beta-protein fibrillization. Proc. Natl Acad. Sci.USA.95, 12277-12282.
75. Modler, A. J., Gast, K., Lutsch, G. & Damaschun, G. (2003). Assembly of amyloid protofibrils via critical oligomers -a novel pathway of amyloid formation. 2 Mol. Biol. 325, 135-148.
76. Hornemann, S. & Glockshuber, R. (1998). A scrapie-like unfolding intermediate of the prion protein domain PrP(121-231) induced by acidic pH. Proc. Natl Acad. Sci.USA.95, 6010-6014.
77. Morillas, M., Vanik, D. L. & Surewicz, W. K. (2001). On the mechanism of alpha-helix to betasheet transition in the recombinant prion protein.Biochemistry.40, 6982-6987.
78. Baskakov, I. V., Legname, G., Baldwin, M. A., Prusiner, S. B. & Cohen, F. E. (2002). Pathway complexity of prion protein assembly into amyloid. 2 Biol. Chem. 277, 21140-21148.
79. Sokolowski, F., Modler, A. J., Masuch, R., Zirwer, D., Baier, M., Lutsch, G., Moss, D. A., Gast, K. & Naumann, D. (2003). Formation of critical oligomers is a key event during conformational transition of recombinant Syrian hamster prion protein. 2 Biol. Chem. 278, 40481-40492.
80. Richardson, J. S. & Richardson, D. C. (2002). Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc. Natl Acad. Sci.USA.99, 2754-2759.
81. Flory, P. J. (1953). Principles of Polymer Chemistry. Cornell University Press, Ithaca.
82. Oosawa, F. & Asakura, S. (1975). Thermodynamics of the Polymerization of Protein. Academic Press, London.
83. Eaton, W. A. & Hofrichter, J. (1990). Sickle cell hemoglobin polymerization. 2 Protein Chem. 40, 63-279.
84. Jarrett, J. T. & Lansbury, P. T., Jr. (1993). Seeding ''one-dimensional crystallization'' of amyloid: a pathogenic mechanism in Alzheimer's disease and scrapie? Cell 73, 1055-1058.
85. Serio, T. R., Cashikar, A. G., Kowal, A. S., Sawicki, G. J., Moslehi, J. J., Serpell, L., Arnsdorf, M. F. & Lindquist, S. L. (2000). Nucleated conformational conversion and the replication of conformational information by a prion determinant.Science.289, 1317-1321.
86. Theisen, A., Johann, C., Deacon, M. P. & Harding, S. E. (2000). Refractive Increment Data-book. Nottingham University Press, Nottingham.
87. Gast, K., Modler, A. J., Damaschun, H., Kröber, R., Lutsch, G., Zirwer, D., Golbik, R. & Damaschun, G. (2003). Effect of environmental conditions on aggregation and fibril formation of barstar. 2 Biophys. J. 32, 710-723.