Location via proxy:   [ UP ]  
[Report a bug]   [Manage cookies]                
Skip to main content

Advertisement

Protein folding and misfolding

  • Review Article
  • Published:

From Nature

View current issue Submit your manuscript

Abstract

The manner in which a newly synthesized chain of amino acids transforms itself into a perfectly folded protein depends both on the intrinsic properties of the amino-acid sequence and on multiple contributing influences from the crowded cellular milieu. Folding and unfolding are crucial ways of regulating biological activity and targeting proteins to different cellular locations. Aggregation of misfolded proteins that escape the cellular quality-control mechanisms is a common feature of a wide range of highly debilitating and increasingly prevalent diseases.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Figure 1: A schematic energy landscape for protein folding.
Figure 2: Regulation of protein folding in the ER.
Figure 3: A schematic representation of the general mechanism of aggregation to form amyloid fibrils.
Figure 4: A unified view of some of the types of structure that can be formed by polypeptide chains.

Similar content being viewed by others

References

  1. Vendruscolo, M., Zurdo, J., MacPhee, C. E. & Dobson, C. M. Protein folding and misfolding: a paradigm of self-assembly and regulation in complex biological systems. Phil. Trans. R. Soc. Lond. 361, 1205–1222 (2003).

    Article  ADS  MathSciNet  CAS  Google Scholar 

  2. Radford, S. E. & Dobson, C. M. From computer simulations to human disease: emerging themes in protein folding. Cell 97, 291–298 (1999).

    Article  CAS  Google Scholar 

  3. Dobson, C. M., Sali, A. & Karplus, M. Protein folding: a perspective from theory and experiment. Angew. Chem. Int. Ed. Eng. 37, 868–893 (1998).

    Article  Google Scholar 

  4. Wolynes, P. G., Onuchic, J. N. & Thirumalai, D. Navigating the folding routes. Science 267, 1619–1620 (1995).

    Article  ADS  CAS  Google Scholar 

  5. Dill, K. A. & Chan, H. S. From Levinthal to pathways to funnels. Nature Struct. Biol. 4, 10–19 (1997).

    Article  CAS  Google Scholar 

  6. Dinner, A. R., Sali, A., Smith, L. J., Dobson, C. M. & Karplus, M. Understanding protein folding via free energy surfaces from theory and experiment. Trends Biochem. Sci. 25, 331–339 (2000).

    Article  CAS  Google Scholar 

  7. Baldwin, R. L. Protein folding: matching speed and stability. Nature 369, 183–184 (1994).

    Article  ADS  CAS  Google Scholar 

  8. Eaton, W. A., Munoz, V., Thompson, P. A., Henry, E. R. & Hofrichter, J. Kinetics and dynamics of loops, α-helices, β-hairpins, and fast-folding proteins. Acc. Chem. Res. 31, 745–753 (1998).

    Article  CAS  Google Scholar 

  9. Snow, C. D., Nguyen, H., Pande, V. S. & Gruebele, M. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 420, 102–106 (2002).

    Article  ADS  CAS  Google Scholar 

  10. Yang, W. Y. & Gruebele, M. Folding at the speed limit. Nature 423, 193–197 (2003).

    Article  ADS  CAS  Google Scholar 

  11. Mayor, U. et al. The complete folding pathway of a protein from nanoseconds to microseconds. Nature 421, 863–867 (2003).

    Article  ADS  CAS  Google Scholar 

  12. Plaxco, K. W., Simons, K. T. & Baker, D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277, 985–994 (1998).

    Article  CAS  Google Scholar 

  13. Schuler, B., Lipman, E. A. & Eaton, W. A. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature 419, 743–747 (2002).

    Article  ADS  CAS  Google Scholar 

  14. Fersht, A. R. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding (W.H. Freeman, New York, 1999).

    Google Scholar 

  15. Fersht, A. R. Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism. Proc. Natl Acad. Sci. USA 97, 1525–1529 (2000).

    Article  ADS  CAS  Google Scholar 

  16. Shea, J. E. & Brooks, C. L. From folding surfaces to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. Annu. Rev. Phys. Chem. 52, 499–535 (2001).

    Article  ADS  CAS  Google Scholar 

  17. Fersht, A. R. & Daggett, V. Protein folding and unfolding at atomic resolution. Cell 108, 573–582 (2002).

    Article  CAS  Google Scholar 

  18. Vendruscolo, M., Paci, E., Dobson, C. M. & Karplus, M. Three key residues form a critical contact network in a transition state for protein folding. Nature 409, 641–646 (2001).

    Article  ADS  CAS  Google Scholar 

  19. Makarov, D. E. & Plaxco, K. W. The topomer search model: a simple, quantitative theory of two-state protein folding kinetics. Protein Sci. 12, 17–26 (2003).

    Article  CAS  Google Scholar 

  20. Baker, D. A surprising simplicity to protein folding. Nature 405, 39–42 (2000).

    Article  ADS  CAS  Google Scholar 

  21. Roder, H. & Colon, W. Kinetic role of early intermediates in protein folding. Curr. Opin. Struct. Biol. 7, 15–28 (1997).

    Article  CAS  Google Scholar 

  22. Sanchez, I. E. & Kiefhaber, T. Evidence for sequential barriers and obligatory intermediates in apparent two-state protein folding. J. Mol. Biol. 325, 367–376 (2003).

    Article  CAS  Google Scholar 

  23. Khan, F., Chuang, J. I., Gianni, S. & Fersht, A. R. The kinetic pathway of folding of barnase. J. Mol. Biol. 333, 169–186 (2003).

    Article  CAS  Google Scholar 

  24. Vendruscolo, M., Paci, E., Karplus, M. & Dobson, C. M. Structures and relative free energies of partially folded states of proteins. Proc. Natl Acad. Sci. USA 100, 14817–14821 (2003).

    Article  ADS  CAS  Google Scholar 

  25. Cheung, M. S., Garcia, A. E. & Onuchic, J. N. Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc. Natl Acad. Sci. USA 99, 685–690 (2002).

    Article  ADS  CAS  Google Scholar 

  26. Hardesty, B. & Kramer, G. Folding of a nascent peptide on the ribosome. Prog. Nucleic Acid Res. Mol. Biol. 66, 41–66 (2001).

    Article  CAS  Google Scholar 

  27. Bukau, B. & Horwich, A. L. The Hsp70 and Hsp60 chaperone machines. Cell 92, 351–366 (1998).

    Article  CAS  Google Scholar 

  28. Hartl, F. U. & Hayer-Hartl, M. Molecular chaperones in the cytosol: from nascent chain to folded protein. Science 295, 1852–1858 (2002).

    Article  ADS  CAS  Google Scholar 

  29. Ellis, R. J. Macromolecular crowding: an important but neglected aspect of the intracellular environment. Curr. Opin. Struct. Biol. 11, 114–119 (2001).

    Article  CAS  Google Scholar 

  30. Schiene, C. & Fischer, G. Enzymes that catalyse the restructuring of proteins. Curr. Opin. Struct. Biol. 10, 40–45 (2000).

    Article  CAS  Google Scholar 

  31. Hammon, C. & Helenius, A. Quality control in the secretory pathway. Curr. Opin. Cell. Biol. 7, 523–529 (1995).

    Article  Google Scholar 

  32. Kaufman, R. J. et al. The unfolded protein response in nutrient sensing and differentiation. Nature Rev. Mol. Cell Biol. 3, 411–421 (2002).

    Article  CAS  Google Scholar 

  33. Wilson, M. R. & Easterbrook Smith, S. B. Clusterin is a secreted mammalian chaperone. Trends Biochem. Sci. 25, 95–98 (2000).

    Article  CAS  Google Scholar 

  34. Schubert, U. et al. Rapid degradation of a large fraction of newly synthesized proteins by proteasomes. Nature 404, 770–774 (2000).

    Article  ADS  CAS  Google Scholar 

  35. Bence, N. F., Sampat, R. M. & Kopito, R. R. Impairment of the ubiquitin–proteasome system by protein aggregation. Science 292, 1552–1555 (2001).

    Article  ADS  CAS  Google Scholar 

  36. Thomas, P. J., Qu, B. H. & Pedersen, P. L. Defective protein folding as a basis of human disease. Trends Biochem. Sci. 20, 456–459 (1995).

    Article  CAS  Google Scholar 

  37. Dobson, C. M. The structural basis of protein folding and its links with human disease. Phil. Trans. R. Soc. Lond. B 356, 133–145 (2001).

    Article  CAS  Google Scholar 

  38. Horwich, A. Protein aggregation in disease: a role for folding intermediates forming specific multimeric interactions. J. Clin. Invest. 110, 1221–1232 (2002).

    Article  CAS  Google Scholar 

  39. Bullock, A. N. & Fersht, A. R. Rescuing the functions of mutant p53. Nature Rev. Cancer 1, 68–76 (2001).

    Article  CAS  Google Scholar 

  40. Tan, S. Y. & Pepys, M. B. Amyloidosis. Histopathology 25, 403–414 (1994).

    Article  CAS  Google Scholar 

  41. Kelly, J. W. Alternative conformation of amyloidogenic proteins and their multi-step assembly pathways. Curr. Opin. Struct. Biol. 8, 101–106 (1998).

    Article  CAS  Google Scholar 

  42. Sunde, M. & Blake, C. C. F. The structure of amyloid fibrils by electron microscopy and X-ray diffraction. Adv. Protein Chem. 50, 123–159 (1997).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  44. Fändrich, M. & Dobson, C. M. The behaviour of polyamino acids reveals an inverse side-chain effect in amyloid structure formation. EMBO J. 21, 5682–5690 (2002).

    Article  Google Scholar 

  45. Jiménez, J. L. et al. Cryo-electron microscopy of an SH3 amyloid fibril and model of the molecular packing. EMBO J. 18, 815–821 (1999).

    Article  Google Scholar 

  46. Petkova, A. T. et al. A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR. Proc. Natl Acad. Sci. USA 99, 16742–16747 (2002).

    Article  ADS  CAS  Google Scholar 

  47. Chiti, F., Stefani, M., Taddei, N., Ramponi, G. & Dobson, C. M. Rationalization of mutational effects on protein aggregation rates. Nature 424, 805–808 (2003).

    Article  ADS  CAS  Google Scholar 

  48. Caughey, B. & Lansbury, P. T. Jr. Protofibrils, pores, fibrils, and neurodegeneration: separating the responsible protein aggregates from the innocent bystanders. Annu. Rev. Neurosci. 26, 267–298 (2003).

    Article  CAS  Google Scholar 

  49. Bitan, G. et al. Amyloid β-protein (Aβ) assembly: Aβ40 and Aβ42 oligomerize through distinct pathways. Proc. Natl Acad. Sci. USA 100, 330–335 (2003).

    Article  ADS  CAS  Google Scholar 

  50. Nilsson, M. R., Driscoll, M. & Raleigh, D. P. Low levels of asparagine deamidation can have a dramatic effect on aggregation of amyloidogenic peptides: implications for the study of amyloid formation. Protein Sci. 11, 342–349 (2002).

    Article  CAS  Google Scholar 

  51. Schlunegger, M. P., Bennett, M. J. & Eisenberg, D. Oligomer formation by 3D domain swapping: a model for protein assembly and misassembly. Adv. Protein Chem. 50, 61–122 (1997).

    Article  CAS  Google Scholar 

  52. Bucciantini, M. et al. Inherent cytotoxicity of aggregates implies a common origin for protein misfolding diseases. Nature 416, 507–511 (2002).

    Article  ADS  CAS  Google Scholar 

  53. Lashuel, H. A., Hartley, D., Petre, B. M., Walz, T. & Lansbury, P. T. Jr. Neurodegenerative disease: amyloid pores from pathogenic mutations. Nature 418, 291 (2002).

    Article  ADS  CAS  Google Scholar 

  54. Dobson, C. M. Protein folding and disease: a view from the First Horizon Symposium. Nature Rev. Drug Discov. 2, 154–160 (2003).

    Article  CAS  Google Scholar 

  55. True, H. L. & Lindquist, S. L. A yeast prion provides a mechanism for genetic variation and phenotypic diversity. Nature 407, 477–483 (2000).

    Article  ADS  CAS  Google Scholar 

  56. Chapman, M. R. et al. Role of Escherichia coli curli operons in directing amyloid fiber formation. Science 295, 851–855 (2002).

    Article  ADS  CAS  Google Scholar 

  57. Kelly, J. W. & Balch, W. E. Amyloid as a natural product. J. Cell Biol. 161, 461–462 (2003).

    Article  CAS  Google Scholar 

  58. Broome, B. M. & Hecht, M. H. Nature disfavours sequences of alternating polar and non-polar amino acids: implications for amyloidogenesis. J. Mol. Biol. 296, 961–968 (2000).

    Article  CAS  Google Scholar 

  59. Chiti, F. et al. Kinetic partitioning of protein folding and aggregation. Nature Struct. Biol. 9, 137–143 (2002).

    Article  CAS  Google Scholar 

  60. Macario, A. J. L. & Macario, E. C. Sick chaperones and ageing: a perspective. Ageing Res. Rev. 1, 295–311 (2002).

    Article  CAS  Google Scholar 

  61. Ramirez-Alvarado, M., Merkel, J. S. & Regan, L. A systematic exploration of the influence of the protein stability on amyloid fibril formation in vitro. Proc. Natl Acad. Sci. USA 97, 8979–8984 (2000).

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  63. Prusiner, S. B. Prion diseases and the BSE crisis. Science 278, 245–251 (1997).

    Article  CAS  Google Scholar 

  64. Taylor, J. P., Hardy, J. & Fischbeck, K. H. Toxic proteins in neurodegenerative disease. Science 296, 1991–1995 (2002).

    Article  ADS  CAS  Google Scholar 

  65. Walsh, D. M. et al. Naturally secreted oligomers of amyloid β protein potently inhibit hippocampal long-term potentiation in vivo. Nature 416, 535–539 (2002).

    Article  ADS  CAS  Google Scholar 

  66. Kayed, R. et al. Common structure of soluble amyloid oligomers implies common mechanisms of pathogenesis. Science 300, 486–489 (2003).

    Article  ADS  CAS  Google Scholar 

  67. Stefani, M. & Dobson, C. M. Protein aggregation and aggregate toxicity: new insights into protein folding, misfolding diseases and biological evolution. J. Mol. Med. 81, 678–699 (2003).

    Article  CAS  Google Scholar 

  68. Sherman, M. Y. & Goldberg, A. L. Cellular defenses against unfolded proteins: a cell biologist thinks about neurodegenerative diseases. Neuron 29, 15–32 (2001).

    Article  CAS  Google Scholar 

  69. Muchowski, P. J. et al. Hsp70 and Hsp40 chaperones can inhibit self-assembly of polyglutamine proteins into amyloid-like fibrils. Proc. Natl Acad. Sci. USA 97, 7841–7846 (2000).

    Article  ADS  CAS  Google Scholar 

  70. Csermely, P. Chaperone overload is a possible contributor to 'civilization diseases'. Trends Genet. 17, 701–704 (2001).

    Article  CAS  Google Scholar 

  71. Dobson, C. M. Getting out of shape—protein misfolding diseases. Nature 418, 729–730 (2002).

    Article  ADS  CAS  Google Scholar 

Download references

Acknowledgements

I should like to thank in particular the Wellcome Trust, the Leverhulme Trust and the UK Research Councils for generous support over many years, without whom my own research activities in this area of science could not have been carried out.

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Dobson, C. Protein folding and misfolding. Nature 426, 884–890 (2003). https://doi.org/10.1038/nature02261

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature02261

  • Springer Nature Limited

This article is cited by