Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Amyloid formation by globular proteins under native conditions

Abstract

The conversion of proteins from their soluble states into well-organized fibrillar aggregates is associated with a wide range of pathological conditions, including neurodegenerative diseases and systemic amyloidoses. In this review, we discuss the mechanism of aggregation of globular proteins under conditions in which they are initially folded. Although a conformational change of the native state is generally necessary to initiate aggregation, we show that a transition across the major energy barrier for unfolding is not essential and that aggregation may well be initiated from locally unfolded states that become accessible, for example, via thermal fluctuations occurring under physiological conditions. We review recent evidence on this topic and discuss its significance for understanding the onset and potential inhibition of protein aggregation in the context of diseases.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: The process of protein folding.
Figure 2: Proposed process of fibril formation for human lysozyme.
Figure 3: Proposed process of aggregation for Sso AcP.
Figure 4: Proposed process of fibril formation for S134N SOD1.
Figure 5: Proposed process of fibril formation for human TTR.
Figure 6: Superposition of β2m crystallographic structures.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

References

  1. Selkoe, D.J. Folding proteins in fatal ways. Nature 426, 900–904 (2003).

    Article  CAS  Google Scholar 

  2. Westermark, P. et al. Amyloid: toward terminology clarification. Report from the Nomenclature Committee of the International Society of Amyloidosis. Amyloid 12, 1–4 (2005).

    Article  CAS  Google Scholar 

  3. Chiti, F. & Dobson, C.M. Protein misfolding, functional amyloid, and human disease. Annu. Rev. Biochem. 75, 333–366 (2006).

    Article  CAS  Google Scholar 

  4. Bemporad, F. et al. Sequence and structural determinants of amyloid fibril formation. Acc. Chem. Res. 39, 620–627 (2006).

    Article  CAS  Google Scholar 

  5. Guijarro, J.I., Sunde, M., Jones, J.A., Campbell, I.D. & Dobson, C.M. Amyloid fibril formation by an SH3 domain. Proc. Natl. Acad. Sci. USA 95, 4224–4228 (1998).

    Article  CAS  Google Scholar 

  6. McParland, V.J. et al. Partially unfolded states of beta(2)-microglobulin and amyloid formation in vitro. Biochemistry 39, 8735–8746 (2000).

    Article  CAS  Google Scholar 

  7. Litvinovich, S.V. et al. Formation of amyloid-like fibrils by self-association of a partially unfolded fibronectin type III module. J. Mol. Biol. 280, 245–258 (1998).

    Article  CAS  Google Scholar 

  8. Fändrich, M., Fletcher, M.A. & Dobson, C.M. Amyloid fibrils from muscle myoglobin. Nature 410, 165–166 (2001).

    Article  Google Scholar 

  9. Ferrão-Gonzales, A.D., Souto, S.O., Silva, J.L. & Foguel, D. The preaggregated state of an amyloidogenic protein: hydrostatic pressure converts native transthyretin into the amyloidogenic state. Proc. Natl. Acad. Sci. USA 97, 6445–6450 (2000).

    Article  Google Scholar 

  10. De Felice, F.G. et al. Formation of amyloid aggregates from human lysozyme and its disease-associated variants using hydrostatic pressure. FASEB J. 18, 1099–1101 (2004).

    Article  CAS  Google Scholar 

  11. Chiti, F. et al. Designing conditions for in vitro formation of amyloid protofilaments and fibrils. Proc. Natl. Acad. Sci. USA 96, 3590–3594 (1999).

    Article  CAS  Google Scholar 

  12. Schmittschmitt, J.P. & Scholtz, J.M. The role of protein stability, solubility, and net charge in amyloid fibril formation. Protein Sci. 12, 2374–2378 (2003).

    Article  CAS  Google Scholar 

  13. Booth, D.R. et al. Instability, unfolding and aggregation of human lysozyme variants underlying amyloid fibrillogenesis. Nature 385, 787–793 (1997).

    Article  CAS  Google Scholar 

  14. Raffen, R. et al. Physicochemical consequences of amino acid variations that contribute to fibril formation by immunoglobulin light chains. Protein Sci. 8, 509–517 (1999).

    Article  CAS  Google Scholar 

  15. Stathopulos, P.B. et al. Cu/Zn superoxide dismutase mutants associated with amyotrophic lateral sclerosis show enhanced formation of aggregates in vitro. Proc. Natl. Acad. Sci. USA 100, 7021–7026 (2003).

    Article  CAS  Google Scholar 

  16. Sekijima, Y. et al. The biological and chemical basis for tissue-selective amyloid disease. Cell 121, 73–85 (2005).

    Article  CAS  Google Scholar 

  17. Kelly, J.W. Alternative conformations of amyloidogenic proteins govern their behavior. Curr. Opin. Struct. Biol. 6, 11–17 (1996).

    Article  CAS  Google Scholar 

  18. Dobson, C.M. Protein misfolding, evolution and disease. Trends Biochem. Sci. 24, 329–332 (1999).

    Article  CAS  Google Scholar 

  19. Frauenfelder, H., Sligar, S.G. & Wolynes, P.G. The energy landscapes and motions of proteins. Science 254, 1598–1603 (1991).

    Article  CAS  Google Scholar 

  20. Karplus, M. & McCammon, J.A. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9, 646–652 (2002).

    Article  CAS  Google Scholar 

  21. Roder, H., Elove, G.A. & Shastry, M.C.R. in Mechanisms of Protein Folding 2nd edn. (ed. Pain, R.) 70–72 (Oxford University Press, Oxford, 2000).

    Google Scholar 

  22. Pepys, M.B. et al. Human lysozyme gene mutations cause hereditary systemic amyloidosis. Nature 362, 553–557 (1993).

    Article  CAS  Google Scholar 

  23. Valleix, S. Hereditary renal amyloidosis caused by a new variant lysozyme W64R in a French family. Kidney Int. 61, 907–912 (2002).

    Article  CAS  Google Scholar 

  24. Yazaki, M., Farrell, S.A. & Benson, M.D. A novel lysozyme mutation Phe57Ile associated with hereditary renal amyloidosis. Kidney Int. 63, 1652–1657 (2003).

    Article  CAS  Google Scholar 

  25. Röcken, C. et al. ALys amyloidosis caused by compound heterozygosity in exon 2 (Thr70Asn) and exon 4 (Trp112Arg) of the lysozyme gene. Hum. Mutat. 27, 119–120 (2006).

    Article  Google Scholar 

  26. Canet, D. et al. Local cooperativity in the unfolding of an amyloidogenic variant of human lysozyme. Nat. Struct. Biol. 9, 308–315 (2002).

    Article  CAS  Google Scholar 

  27. Dumoulin, M. et al. Reduced global cooperativity is a common feature underlying the amyloidogenicity of pathogenic lysozyme mutations. J. Mol. Biol. 346, 773–788 (2005).

    Article  CAS  Google Scholar 

  28. Canet, D. et al. Mechanistic studies of the folding of human lysozyme and the origin of amyloidogenic behavior in its disease-related variants. Biochemistry 38, 6419–6427 (1999).

    Article  CAS  Google Scholar 

  29. Frare, E. et al. Identification of the core structure of lysozyme amyloid fibrils by proteolysis. J. Mol. Biol. 361, 551–561 (2006).

    Article  CAS  Google Scholar 

  30. Johnson, R.J. et al. Rationalising lysozyme amyloidosis: insights from the structure and solution dynamics of T70N lysozyme. J. Mol. Biol. 352, 823–836 (2005).

    Article  CAS  Google Scholar 

  31. Dumoulin, M., Kumita, J.R. & Dobson, C.M. Normal and aberrant biological self-assembly: insights from studies of human lysozyme and its amyloidogenic variants. Acc. Chem. Res. 39, 603–610 (2006).

    Article  CAS  Google Scholar 

  32. Plakoutsi, G., Taddei, N., Stefani, M. & Chiti, F. Aggregation of the acylphosphatase from Sulfolobus solfataricus: the folded and partially unfolded states can both be precursors for amyloid formation. J. Biol. Chem. 279, 14111–14119 (2004).

    Article  CAS  Google Scholar 

  33. Plakoutsi, G. et al. Evidence for a mechanism of amyloid formation involving molecular reorganisation within native-like precursor aggregates. J. Mol. Biol. 351, 910–922 (2005).

    Article  CAS  Google Scholar 

  34. Plakoutsi, G. et al. Exploring the mechanism of formation of native-like and precursor amyloid oligomers for the native acylphosphatase from Sulfolobus solfataricus. Structure 14, 993–1001 (2006).

    Article  CAS  Google Scholar 

  35. Soldi, G., Bemporad, F. & Chiti, F. The degree of structural protection at the edge β-strands determines the pathway of amyloid formation in globular proteins. J. Am. Chem. Soc. 130, 4295–4302 (2008).

    Article  CAS  Google Scholar 

  36. Bemporad, F., Vannocci, T., Varela, L., Azuaga, A.I. & Chiti, F. A model for the aggregation of the acylphosphatase from Sulfolobus solfataricus in its native-like state. Biochim. Biophys. Acta 1784, 1986–1996 (2008).

    Article  CAS  Google Scholar 

  37. Watanabe, M. et al. A novel missense point mutation (S134N) of the Cu/Zn superoxide dismutase gene in a patient with familial motor neuron disease. Hum. Mutat. 9, 69–71 (1997).

    Article  CAS  Google Scholar 

  38. Elam, J.S. et al. Amyloid-like filaments and water-filled nanotubes formed by SOD1 mutant proteins linked to familial ALS. Nat. Struct. Biol. 10, 461–467 (2003).

    Article  CAS  Google Scholar 

  39. Banci, L. et al. Fully metallated S134N Cu,Zn-superoxide dismutase displays abnormal mobility and intermolecular contacts in solution. J. Biol. Chem. 280, 35815–35821 (2005).

    Article  CAS  Google Scholar 

  40. Antonyuk, S. et al. Structural consequences of the familial amyotrophic lateral sclerosis SOD1 mutant His46Arg. Protein Sci. 14, 1201–1213 (2005).

    Article  CAS  Google Scholar 

  41. Cao, X. et al. Structures of the G85R variant of SOD1 in familial amyotrophic lateral sclerosis. J. Biol. Chem. 283, 16169–16177 (2008).

    Article  CAS  Google Scholar 

  42. Wang, Q., Johnson, J.L., Agar, N.Y. & Agar, J.N. Protein aggregation and protein instability govern familial amyotrophic lateral sclerosis patient survival. PLoS Biol. 6, e170 (2008).

    Article  Google Scholar 

  43. Nordlund, A. & Oliveberg, M. Folding of Cu/Zn superoxide dismutase suggests structural hotspots for gain of neurotoxic function in ALS: parallels to precursors in amyloid disease. Proc. Natl. Acad. Sci. USA 103, 10218–10223 (2006).

    Article  CAS  Google Scholar 

  44. Benson, M.D. & Kincaid, J.S. The molecular biology and clinical features of amyloid neuropathy. Muscle Nerve 36, 411–423 (2007).

    Article  CAS  Google Scholar 

  45. Blake, C.C., Burridge, J.M. & Oatley, S.J. X-ray analysis of thyroid hormone binding to prealbumin. Biochem. Soc. Trans. 6, 1114–1118 (1978).

    Article  CAS  Google Scholar 

  46. Colon, W. & Kelly, J.W. Partial denaturation of transthyretin is sufficient for amyloid fibril formation in vitro. Biochemistry 31, 8654–8660 (1992).

    Article  CAS  Google Scholar 

  47. Lai, Z., Colón, W. & Kelly, J.W. The acid-mediated denaturation pathway of transthyretin yields a conformational intermediate that can self-assemble into amyloid. Biochemistry 35, 6470–6482 (1996).

    Article  CAS  Google Scholar 

  48. Quintas, A., Vaz, D.C., Cardoso, I., Saraiva, M.J. & Brito, R.M. Tetramer dissociation and monomer partial unfolding precedes protofibril formation in amyloidogenic transthyretin variants. J. Biol. Chem. 276, 27207–27213 (2001).

    Article  CAS  Google Scholar 

  49. Liu, K. et al. Deuterium-proton exchange on the native wild-type transthyretin tetramer identifies the stable core of the individual subunits and indicates mobility at the subunit interface. J. Mol. Biol. 303, 555–565 (2000).

    Article  CAS  Google Scholar 

  50. Liu, K., Cho, H.S., Lashuel, H.A., Kelly, J.W. & Wemmer, D.E. A glimpse of a possible amyloidogenic intermediate of transthyretin. Nat. Struct. Biol. 7, 754–757 (2000).

    Article  CAS  Google Scholar 

  51. Hörnberg, A., Olofsson, A., Eneqvist, T., Lundgren, E. & Sauer-Eriksson, A.E. The β-strand D of transthyretin trapped in two discrete conformations. Biochim. Biophys. Acta 1700, 93–104 (2004).

    Article  Google Scholar 

  52. Serag, A.A., Altenbach, C., Gingery, M., Hubbell, W.L. & Yeates, T.O. Identification of a subunit interface in transthyretin amyloid fibrils: evidence for self-assembly from oligomeric building blocks. Biochemistry 40, 9089–9096 (2001).

    Article  CAS  Google Scholar 

  53. Serag, A.A., Altenbach, C., Gingery, M., Hubbell, W.L. & Yeates, T.O. Arrangement of subunits and ordering of β-strands in an amyloid sheet. Nat. Struct. Biol. 9, 734–739 (2002).

    Article  CAS  Google Scholar 

  54. Olofsson, A., Ippel, J.H., Wijmenga, S.S., Lundgren, E. & Ohman, A. Probing solvent accessibility of transthyretin amyloid by solution NMR spectroscopy. J. Biol. Chem. 279, 5699–5707 (2004).

    Article  CAS  Google Scholar 

  55. Gejyo, F. et al. A new form of amyloid protein associated with chronic hemodialysis was identified as β2-microglobulin. Biochem. Biophys. Res. Commun. 129, 701–706 (1985).

    Article  CAS  Google Scholar 

  56. Esposito, G. et al. Removal of the N-terminal hexapeptide from human β2-microglobulin facilitates protein aggregation and fibril formation. Protein Sci. 9, 831–845 (2000).

    Article  CAS  Google Scholar 

  57. Chiti, F. et al. Detection of two partially structured species in the folding process of the amyloidogenic protein β 2-microglobulin. J. Mol. Biol. 307, 379–391 (2001).

    Article  CAS  Google Scholar 

  58. Kameda, A. et al. Nuclear magnetic resonance characterization of the refolding intermediate of β2-microglobulin trapped by non-native prolyl peptide bond. J. Mol. Biol. 348, 383–397 (2005).

    Article  CAS  Google Scholar 

  59. Jahn, T.R., Parker, M.J., Homans, S.W. & Radford, S.E. Amyloid formation under physiological conditions proceeds via a native-like folding intermediate. Nat. Struct. Mol. Biol. 13, 195–201 (2006).

    Article  CAS  Google Scholar 

  60. Chiti, F. et al. A partially structured species of β 2-microglobulin is significantly populated under physiological conditions and involved in fibrillogenesis. J. Biol. Chem. 276, 46714–46721 (2001).

    Article  CAS  Google Scholar 

  61. Eakin, C.M., Attenello, F.J., Morgan, C.J. & Miranker, A.D. Oligomeric assembly of native-like precursors precedes amyloid formation by β-2 microglobulin. Biochemistry 43, 7808–7815 (2004).

    Article  CAS  Google Scholar 

  62. Eakin, C.M., Berman, A.J. & Miranker, A.D. A native to amyloidogenic transition regulated by a backbone trigger. Nat. Struct. Mol. Biol. 13, 202–208 (2006).

    Article  CAS  Google Scholar 

  63. Verdone, G. et al. The solution structure of human β2-microglobulin reveals the prodromes of its amyloid transition. Protein Sci. 11, 487–499 (2002).

    Article  CAS  Google Scholar 

  64. Eakin, C.M., Knight, J.D., Morgan, C.J., Gelfand, M.A. & Miranker, A.D. Formation of a copper specific binding site in non-native states of β-2-microglobulin. Biochemistry 41, 10646–10656 (2002).

    Article  CAS  Google Scholar 

  65. Calabrese, M.F. & Miranker, A.D. Formation of a stable oligomer of β-2 microglobulin requires only transient encounter with Cu(II). J. Mol. Biol. 367, 1–7 (2007).

    Article  CAS  Google Scholar 

  66. Calabrese, M.F., Eakin, C.M., Wang, J.M. & Miranker, A.D. A regulatable switch mediates self-association in an immunoglobulin fold. Nat. Struct. Mol. Biol. advance online publication, doi:10.1038/nsmb.1483 (August 2008).

  67. Kameda, A. et al. Nuclear magnetic resonance characterization of the refolding intermediate of β2-microglobulin trapped by non-native prolyl peptide bond. J. Mol. Biol. 348, 383–397 (2005).

    Article  CAS  Google Scholar 

  68. Esposito, G. et al. The controlling roles of Trp60 and Trp95 in β2-microglobulin function, folding and amyloid aggregation properties. J. Mol. Biol. 378, 887–897.

    Article  Google Scholar 

  69. Johnson, S.M. et al. Native state kinetic stabilization as a strategy to ameliorate protein misfolding diseases: a focus on the transthyretin amyloidoses. Acc. Chem. Res. 38, 911–921 (2005).

    Article  CAS  Google Scholar 

  70. Ray, S.S., Nowak, R.J., Brown, R.H. Jr. & Lansbury, P.T. Jr. Small-molecule-mediated stabilization of familial amyotrophic lateral sclerosis-linked superoxide dismutase mutants against unfolding and aggregation. Proc. Natl. Acad. Sci. USA 102, 3639–3644 (2005).

    Article  CAS  Google Scholar 

  71. Soldi, G., Plakoutsi, G., Taddei, N. & Chiti, F. Stabilization of a native protein mediated by ligand binding inhibits amyloid formation independently of the aggregation pathway. J. Med. Chem. 49, 6057–6064 (2006).

    Article  CAS  Google Scholar 

  72. Dumoulin, M. et al. A camelid antibody fragment inhibits the formation of amyloid fibrils by human lysozyme. Nature 424, 783–788 (2003).

    Article  CAS  Google Scholar 

  73. Bouchard, M., Zurdo, J., Nettleton, E.J., Dobson, C.M. & Robinson, C.V. Formation of insulin amyloid fibrils followed by FTIR simultaneously with CD and electron microscopy. Protein Sci. 9, 1960–1967 (2000).

    Article  CAS  Google Scholar 

  74. Pedersen, J.S., Christensen, G. & Otzen, D.E. Modulation of S6 fibrillation by unfolding rates and gatekeeper residues. J. Mol. Biol. 341, 575–588 (2004).

    Article  CAS  Google Scholar 

  75. Chow, M.K., Ellisdon, A.M., Cabrita, L.D. & Bottomley, S.P. Polyglutamine expansion in ataxin-3 does not affect protein stability: implications for misfolding and disease. J. Biol. Chem. 279, 47643–47651 (2004).

    Article  CAS  Google Scholar 

  76. Soldi, G. et al. Amyloid formation of a protein in the absence of initial unfolding and destabilization of the native state. Biophys. J. 89, 4234–4244 (2005).

    Article  CAS  Google Scholar 

  77. Iannuzzi, C., Vilasi, S., Portaccio, M., Irace, G. & Sirangelo, I. Heme binding inhibits the fibrillization of amyloidogenic apomyoglobin and determines lack of aggregate cytotoxicity. Protein Sci. 16, 507–516 (2007).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Fabrizio Chiti or Christopher M Dobson.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Chiti, F., Dobson, C. Amyloid formation by globular proteins under native conditions. Nat Chem Biol 5, 15–22 (2009). https://doi.org/10.1038/nchembio.131

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchembio.131

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing