Distinguishing crystal-like amyloid fibrils and glass-like amorphous aggregates from their kinetics of formation

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 36, 2012, Pages 14446-14451

  Yoshimura, Yuichi ^a   Lin, Yuxi ^a   Yagi, Hisashi ^a   Lee, Young Ho ^a   Kitayama, Hiroki ^a   Sakurai, Kazumasa ^a   So, Masatomo ^a   Ogi, Hirotsugu ^a   Naiki, Hironobu ^b   Goto, Yuji ^a  

^a OSAKA UNIVERSITY   (Japan)

^b UNIVERSITY OF FUKUI   (Japan)

Author keywords

Glass transition; Metastability; Protein aggregation; Ultrasonication

Indexed keywords

8 ANILINO 1 NAPHTHALENESULFONIC ACID; AMYLOID; THIOFLAVINE;

ARTICLE; CRYSTAL STRUCTURE; FLUORESCENCE ANALYSIS; KINETICS; LIGHT SCATTERING; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN FOLDING; PROTEIN STRUCTURE; SOLUBILITY; ULTRASOUND;

AMYLOID; ANILINO NAPHTHALENESULFONATES; BETA 2-MICROGLOBULIN; ESCHERICHIA COLI; FLUORESCENCE; HUMANS; HYDROGEN-ION CONCENTRATION; KINETICS; MICROSCOPY, ELECTRON; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEOSTASIS DEFICIENCIES; SODIUM CHLORIDE; THIAZOLES; ULTRASONICS;

EID: 84865957943     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1208228109     Document Type: Article

References (46)

1. Chiti F, Dobson CM (2006) Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 75:333-366. (Pubitemid 44118036)
2. Andersson A, et al. (2008) Amyloid deposition in transplanted human pancreatic islets: A conceivable cause of their long-term failure. Exp Diabetes Res 2008:562985.
3. Sugiyama M, et al. (2010) SAXS and SANS observations of abnormal aggregation of human α-crystallin. Chem Biodiversity 7:1380-1388.
4. Truscott RJ (2005) Age-related nuclear cataract-oxidation is the key. Exp Eye Res 80:709-725.
5. Dobson CM (2003) Protein folding and misfolding. Nature 426:884-890.
6. Wang L, Maji SK, Sawaya MR, Eisenberg D, Riek R (2008) Bacterial inclusion bodies contain amyloid-like structure. PLoS Biol 6:1791-1801.
7. de Groot NS, Sabate R, Ventura S (2009) Amyloids in bacterial inclusion bodies. Trends Biochem Sci 34:408-416.
8. Niwa T, et al. (2009) Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins. Proc Natl Acad Sci USA 106:4201-4206.
9. Agostini F, Vendruscolo M, Tartaglia GG (2012) Sequence-based prediction of protein solubility. J Mol Biol 421:237-241.
10. Stranks SD, et al. (2009) Model for amorphous aggregation processes. Phys Rev E 80:051907.
11. Kelly JW (1996) Alternative conformations of amyloidogenic proteins govern their behavior. Curr Opin Struct Biol 6:11-17.
12. 2-microglobulin and amyloid formation in vitro. Biochemistry 39:8735-8746. (Pubitemid 30602783)
13. Khurana R, et al. (2001) Partially folded intermediates as critical precursors of light chain amyloid fibrils and amorphous aggregates. Biochemistry 40:3525-3535. (Pubitemid 32242809)
14. Uversky VN, Li J, Fink AL (2001) Evidence for a partially folded intermediate in α-synuclein fibril formation. J Biol Chem 276:10737-10744. (Pubitemid 38089246)
15. Sluzky V, Tamada JA, Klibanov AM, Langer R (1991) Kinetics of insulin aggregation in aqueous solutions upon agitation in the presence of hydrophobic surfaces. Proc Natl Acad Sci USA 88:9377-9381. (Pubitemid 21915634)
16. Giehm L, Otzen DE (2010) Strategies to increase the reproducibility of protein fibrillization in plate reader assays. Anal Biochem 400:270-281.
17. Stathopulos PB, et al. (2004) Sonication of proteins causes formation of aggregates that resemble amyloid. Protein Sci 13:3017-3027. (Pubitemid 39431263)
18. Ohhashi Y, Kihara M, Naiki H, Goto Y (2005) Ultrasonication-induced amyloid fibril formation of β2 -microglobulin. J Biol Chem 280:32843-32848. (Pubitemid 41368332)
19. Yamaguchi K, Matsumoto T, Kuwata K (2008) Critical region for amyloid fibril formation of mouse prion protein: Unusual amyloidogenic properties of the helix 2 peptide. Biochemistry 47:13242-13251.
20. Chatani E, et al. (2009) Ultrasonication-dependent production and breakdown lead to minimum-sized amyloid fibrils. Proc Natl Acad Sci USA 106:11119-11124.
21. So M, et al. (2011) Ultrasonication-dependent acceleration of amyloid fibril formation. J Mol Biol 412:568- 577.
22. Jarrett JT, Lansbury PT, Jr (1993) Seeding "one-dimensional crystallization"of amyloid: A pathogenic mechanism in Alzheimer's disease and scrapie? Cell 73:1055-1058. (Pubitemid 23180480)
23. Come JH, Fraser PE, Lansbury PT, Jr (1993) A kinetic model for amyloid formation in the prion diseases: Importance of seeding. Proc Natl Acad Sci USA 90:5959-5963. (Pubitemid 23191433)
24. Cabriolu R, Kashchiev D, Auer S (2010) Atomistic theory of amyloid fibril nucleation. J Chem Phys 133:225101.
25. Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG (1995) Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins 21:167- 195.
26. Nymeyer H, Garcia AE, Onuchic JN (1998) Folding funnels and frustration in off-lattice minimalist protein landscapes. Proc Natl Acad Sci USA 95:5921-5928. (Pubitemid 28248940)
27. Wolynes PG (2005) Energy landscapes and solved protein-folding problems. Philos Trans R Soc A 363:453- 467.
28. Yamamoto S, Gejyo F (2005) Historical background and clinical treatment of dialysis-related amyloidosis. Biochim Biophys Acta 1753:4-10. (Pubitemid 41597426)
29. 2-microglobulin amyloid fibril growth and stability. Biochemistry 44:1288-1299. (Pubitemid 40209008)
30. Naiki H, Higuchi K, Hosokawa M, Takeda T (1989) Fluorometric determination of amyloid fibrils in vitro using the fluorescent dye, thioflavin T. Anal Biochem 177:244-249. (Pubitemid 19088253)
31. LeVine H, 3rd (1999) Quantification of β-sheet amyloid fibril structures with thioflavin T. Methods Enzymol 309:274-284.
32. Nielsen L, et al. (2001) Effect of environmental factors on the kinetics of insulin fibril formation: Elucidation of the molecular mechanism. Biochemistry 40:6036-6046. (Pubitemid 32466306)
33. Naiki H, Gejyo F (1999) Kinetic analysis of amyloid fibril formation. Methods Enzymol 309:305-318. (Pubitemid 29446457)
34. Morris AM, Watzky MA, Agar JN, Finke RG (2008) Fitting neurological protein aggregation kinetic data via a 2-step, minimal/"Ockham's razor" model: The Finke-Watzky mechanism of nucleation followed by autocatalytic surface growth. Biochemistry 47:2413-2427. (Pubitemid 351304547)
35. Bergfors T (2003) Seeds to crystals. J Struct Biol 142:66-76.
36. Jarrett JT, Lansbury PT, Jr (1992) Amyloid fibril formation requires a chemically discriminating nucleation event: Studies of an amyloidogenic sequence from the bacterial protein OsmB. Biochemistry 31:12345-12352. (Pubitemid 23163109)
37. Dima RI, Thirumalai D (2002) Exploring protein aggregation and self-propagation using lattice models: Phase diagram and kinetics. Protein Sci 11:1036-1049. (Pubitemid 34441223)
38. Crespo R, Martins PM, Gales L, Rocha F, Damas AM (2010) Potential use of ultrasound to promote protein crystallization. J Appl Crystallogr 43:1419-1425.
39. Goto Y, Calciano LJ, Fink AL (1990) Acid-induced folding of proteins. Proc Natl Acad Sci USA 87:573-577.
40. Auer S, et al. (2007) Importance of metastable states in the free energy landscapes of polypeptide chains. Phys Rev Lett 99:178104.
41. De Simone A, et al. (2011) Experimental free energy surfaces reveal the mechanisms of maintenance of protein solubility. Proc Natl Acad Sci USA 108:21057-21062.
42. Jarrett JT, Berger EP, Lansbury PT, Jr (1993) The carboxy terminus of the β amyloid protein is critical for the seeding of amyloid formation: Implications for the pathogenesis of Alzheimer's disease. Biochemistry 32:4693-4697. (Pubitemid 23162022)
43. Ogi H, Tomiyama Y, Shoji Y, Mizugaki T, Hirao M (2006) Effects of dissolved and ambient gases on sonochemical degradation of methylene blue in high-amplitude resonant mode. Jpn J Appl Phys 45:4678-4683. (Pubitemid 43800131)
44. Yanagi K, et al. (2011) Hexafluoroisopropanol induces amyloid fibrils of islet amyloid polypeptide by enhancing both hydrophobic and electrostatic interactions. J Biol Chem 286:23959-23966.
45. Nelson R, et al. (2005) Structure of the cross-β spine of amyloid-like fibrils. Nature 435:773-778. (Pubitemid 40839722)
46. Sawaya MR, et al. (2007) Atomic structures of amyloid cross-β spines reveal varied steric zippers. Nature 447:453-457. (Pubitemid 46816731)