Protein folding and misfolding: From atoms to organisms

Physical Biology: From Atoms to Medicine

Volumn , Issue , 2008, Pages 289-335

  Dobson, Christopher M ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84967361708     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1142/9781848162013_013     Document Type: Chapter

References (95)

1. Vendruscolo M, Zurdo J, MacPhee CE, Dobson CM. (2003) Protein folding and misfolding: A paradigm of self-assembly and regulation in complex biological systems. Phil Trans R Soc Lond A361: 1205- 1222.
2. Dobson CM. (2003) Protein folding and misfolding. Nature 426: 884- 890.
3. Chiti F, Dobson CM. (2006) Protein misfolding, functional amyloid and human disease. Annu Rev Biochem 75: 333-366.
4. Dobson CM, Sali A, Karplus M. (1998) Protein folding: A perspective from theory and experiment. Angew Chem Int Ed Eng 37: 868-893.
5. Wolynes PG, Onuchic JN, Thirumalai D. (1995) Navigating the folding routes. Science 267: 1619-1620.
6. Dill KA, Chan HS. (1997) From Levinthal to pathways to funnels. Nature Struct Biol 4: 10-19.
7. Dinner AR, Sali A, Smith LJ, Dobson CM, Karplus M. (2000) Understanding protein folding via free energy surfaces from theory and experiment. Trends Biochem Sci 25: 331-339.
8. Baldwin RL. (1994) Protein folding: Matching speed and stability. Nature 369: 183-184.
9. Schuler B, Lipman EA, Eaton WA. (2002) Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature 419: 743-737.
10. Fersht AR. (1999) Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. W.H. Freeman, New York.
11. Shea JE, Brooks CL. (2001) From folding surfaces to folding proteins: A review and assessment of simulation studies of protein folding and unfolding. Ann Rev Phys Chem 52: 499-535.
12. Fersht AR, Daggett V. (2002) Protein folding and unfolding at atomic resolution Cell 108: 573-582.
13. Vendruscolo M, Paci E, Dobson CM, Karplus M. (2001) Three key residues form a critical contact network in a transition state for protein folding. Nature 409: 641-646.
14. Paci E, Lindorff-Larsen K, Dobson CM, Karplus M, Vendruscolo M. (2005) Transition state contact orders correlate with protein folding rates. J Mol Biol 352: 495-500.
15. Radford SE, Dobson CM, Evans PA. (1992) The folding of hen lysozyme involves partially structured intermediates and multiple pathways. Nature 358: 302-307.
16. Hooke SD, Radford SE, Dobson CM. (1994) The refolding of human lysozyme: A comparison with the structurally homologous hen lysozyme. Biochemistry 33: 5867-5876.
17. IJ-values. Proc Natl Acad Sci USA 102: 12389-12394.
18. Vendruscolo M, Paci E, Karplus M, Dobson CM. (2003) Structure and relative free energies of partially folded states of proteins. Proc Natl Acad Sci USA 100: 14817-14821.
19. Cheung MS, Garcia AE, Onuchic JN. (2002) 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.
20. Hardesty B, Kramer G. (2001) Folding of a nascent peptide on the ribosome. Prog Nucl Acid Res Mol Biol 66: 41-66.
21. Hartl FU, Hayer-Hartl M. (2002) Molecular chaperones in the cytosol: From nascent chain to folded protein. Science 295: 1852-1858.
22. Hsu ST, Fucini P, Cabrita LD, Launay H, Dobson CM, Christodoulou J. (2007) Structure and dynamics of a ribosome-bound nascent chain by NMR spectroscopy. Proc Natl Acad Sci USA 104: 16516-16521.
23. Ellis RJ. (2001) Macromolecular crowding: An important but neglected aspect of the intracellular environment. Curr Opin Struct Biol 11: 114- 119.
24. Kerner MJ, Naylor DJ, Ishihama Y, Maier T, Chang JC, Stines AP et al. (2005) Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell 122: 209-220.
25. Gaetano GG, Hartl FU, Dobson CM, Vendruscolo M. Unpublished data.
26. Hammon C, Helenius A. (1995) Quality control in the secretory pathway. Curr Opin Cell Biol 7: 523.
27. Kaufman RJ, Scheuner D, Schröder M, Shen X, Lee K, Liu CY, Arnold SM. (2002) The unfolded protein response in nutrient sensing and differentiation. Nature Rev Mol Cell Biol 3: 411-421.
28. Bence NF, Sampat RM, Kopito RR. (2001) Impairment of the ubiquitinproteosome system by protein aggregation. Science 292: 1552-1555.
29. Wilson MR, Easterbrook Smith SB. (2000) Clusterin is a secreted mammalian chaperone. Trends Biochem Sci 25: 95-98.
30. Kumita JR, Poon S, Caddy GL, Hagan CL, Dumoulin M, Yerbury JJ, Stewart EM, Robinson CV, Wilson MR, Dobson CM. (2007) The extracellular chaperone clusterin potently inhibits human lysozyme amyloid formation by interacting with prefibrillar species. J Mol Biol 369: 157-167.
31. Thomas PJ, Qu BH, Pedersen PL. (1995) Defective protein folding as a basis of human disease. Trends Biochem Sci 20: 456-459.
32. Dobson CM. (2001) The structural basis of protein folding and its links with human disease. Phil Trans R Soc Lond B356: 133-145.
33. Horwich A. (2002) Protein aggregation in disease: A role for folding intermediates forming specific multimeric interactions. J Clin Invest 110: 1221-1232.
34. Bullock AN, Fersht AR. (2001) Rescuing the functions of mutant p53. Nature Rev Cancer 1: 68-76.
35. Tan SY, Pepys MB. (1994) Amyloidosis. Histophathology 25: 403- 414.
36. Kelly JW. (1998) Alternative conformation of amyloidogenic proteins and their multi-step assembly pathways. Curr Opin Struct Biol 8: 101- 106.
37. Sunde M, Blake CCF. (1997) The structure of amyloid fibrils by electron microscopy and X-ray diffraction. Adv Protein Chem 50: 123-159.
38. Dobson CM. (1999) Protein misfolding, evolution and disease. Trends Biochem Sci 24: 329-332.
39. Fändrich M, Fletcher MA, Dobson CM. (2001) Amyloid fibrils from muscle myoglobin. Nature 410: 165-166.
40. Fändrich M, Dobson CM. (2002) The behaviour of polyamino acids reveals an inverse side-chain effect in amyloid structure formation. EMBO J 21: 5682-5690.
41. Auer S, Dobson CM, Vendruscolo M. (2007) Revealing the nucleation barriers for protein aggregation and amyloid formation. HFSP J 1: 137-146.
42. Jaroniec CP, MacPhee CE, Bajaj VS, McMahon MT, Dobson CM, Griffin RG. (2004) High resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy. Proc Natl Acad Sci USA 101: 711-716.
43. Jiménez JL, Guijarro JI, Orlova E, Zurdo J, Dobson CM, Sunde M, Saibil HR. (1999) Cryo-electron microscopy structure of an SH3 amyloid fibril and model of the molecular packing. EMBO J 18: 815- 821.
44. Nelson R, Sawaya MR, Balbirnie M, Madsen AO, Riekel C, Grothe R, Eisenberg D. (2005) Structure of the cross-beta spine of amyloid-like fibrils. Nature 435: 773-778.
45. Knowles TP, Fitzpatrick AW, Meehan S, Mott HR, Vendruscolo M, Dobson CM, Welland ME. (2007) Role of intermolecular forces in defining material properties of protein nanofibrils. Science 318: 1900- 1903.
46. Chiti F, Stefani M, Taddei N, Ramponi G, Dobson CM. (2003) Rationalisation of mutational effects on protein aggregation rates. Nature 424: 805-808.
47. Pawar AP, DuBay KF, Zurdo J, Chiti F, Vendruscolo M, Dobson CM. (2005) Prediction of ‘aggregation-prone’ and ‘aggregation-susceptible’ regions in proteins associated with neurodegenerative diseases. J Mol Biol 350: 379-392.
48. Booth DR, Sunde M, Bellotti V, Robinson CV, Hutchinson WL, Fraser PE, Hawkins PN, Dobson CM, Radford SE, Blake CCF, Pepys MB. (1997) Instability, unfolding and aggregation of human lysozyme variants underlying amyloid fibrillogenesis. Nature 385: 787-793.
49. Dumoulin M, Kumita JR, Dobson CM. (2006) Normal and aberrant biological self-assembly: Insights from studies of human lysozyme and its amyloidogenic variants. Accts Chem Res 39: 603-610.
50. Dumoulin M, Last AM, Desmyter A, Decanniere K, Canet D, Spencer A, Archer DB, Muyldermans S, Wyns L, Matagne A, Redfield C, Robinson CV, Dobson CM. (2003) A camelid antibody fragment inhibits amyloid fibril formation by human lysozyme. Nature 424: 783-788.
51. Caughey B, Lansbury Jr, PT. (2003) Protofibrils, pores, fibrils, and neurodegeneration: Separating the responsible protein aggregates from the innocent bystanders. Annu Rev Neurosci 26: 267-298.
52. Bitan G, Kirkitadze MD, Lomakin A, Vollers SS, Benedek GB, Teplow DB. (2003) Amyloid beta-protein (Abeta) assembly: Abeta 40 and Abeta 42 oligomerize through distinct pathways. Proc Natl Acad Sci USA 100: 330-335.
53. Smith JF, Knowles TP, Dobson CM, MacPhee CE, Welland ME. (2006) Characterization of the nanoscale properties of individual amyloid fibrils. Proc Natl Acad Sci USA 103: 15806-15811.
54. Tanaka M, Collins SR, Toyama BH, Weissman JS. (2006) The physical basis of how prion conformations determine strain phenotypes. Nature 442: 585-589.
55. Nilsson MR, Driscoll M, Raleigh DP. (2002) 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.
56. Schlunegger MP, Bennett MJ, Eisenberg D. (1997) Oligomer formation by 3D domain swapping: A model for protein assembly and misassembly. Adv Protein Chem 50: 61-122.
57. Morozova-Roche LA, Zamotin V, Malisauskas M, Ohman A, Chertkova R, Lavrikova MA, Kostanyan IA, Dolgikh DA, Kirpichnikov MP. (2004) Fibrillation of carrier protein albebetia and its biologically active constructs: Multiple aligomeric intermediates and pathways. Biochemistry 43: 9610-9619.
58. Lashuel HA, Hartley D, Petre BM, Walz T, Lansbury Jr, PT. (2002) Neurodegenerative disease: Amyloid pores from pathogenic mutations. Nature 418: 291.
59. Dobson CM. (2003) Protein folding and disease: A view from the first horizon symposium. Nature Rev Drug Disc 2: 154-160.
60. Krebs MR, MacPhee CE, Miller AF, Dunlop IE, Dobson CM, Donald AM. (2004) The formation of sperulites by amyloid fibrils of bovine insulin. Proc Natl Acad Sci USA 101: 14420-14424.
61. True HL, Lindquist SL. (2000) A yeast prion provides a mechanism for genetic variation and phenotypic diversity. Nature 407: 477-483.
62. Chapman MR, Robinson LS, Pinkner JS, Roth R, Heuser J, Hammar M, Normark S, Hultgren SJ. (2002) Role of Escherichia coli curli operons in directing amyloid fiber formation. Science 295: 851-855.
63. Kelly JW, Balch WE. (2003) Amyloid as a natural product. J Cell Biol 161: 461-462.
64. Broome BM, Hecht MH. (2000) Nature disfavours sequences of alternative polar and non-polar amino acids: Implications for amyloidogenesis. J Mol Biol 296: 961-968.
65. Chiti F, Taddei N, Baroni F, Capanni C, Stefani M, Ramponi G, Dobson CM. (2002) Kinetic partitioning of protein folding and aggregation. Nature Struct Biol 9: 137-143.
66. Macario AJL, Macario EC. (2002) Sick chaperones and ageing: A perspective. Ageing Res Rev 1: 295-311.
67. Ramirez-Alvarado M, Merkel JS, Regan L. (2000) A systematic exploration of the influence of the protein stability on amyloid fibril formation in vitro. Proc Natl Acad Sci USA 97: 8979-8984.
68. Prusiner SB. (1997) Prion diseases and the BSE crisis. Science 278: 245-251.
69. Taylor JP, Hardy J, Fischbeck KH. (2002) Toxic proteins in neurodegenerative disease. Science 296: 1991-1995.
70. Walsh DM, Klyubin I, Fadeeva JV, Cullen WK, Anwyl R, Wolfe MS, Rowan MJ, Selkoe DJ. (2002) Naturally secreted oligomers of amyloid beta protein potently inhibit hippocampal long-term potentiation in vivo. Nature 416: 535-539.
71. Bucciantini M, Giannoni E, Chiti F, Baroni F, Formigli L, Zurdo J, Taddei N, Ramponi G, Dobson CM, Stefani M. (2002) Inherent cytotoxicity of aggregates implies a common origin for protein misfolding diseases. Nature 416: 507-511.
72. Baglioni S, Casamenti F, Bucciantini M, Luheshi L, Taddei N, Chiti F, Dobson CM, Stefani M. (2006) Pre-fibrillar amyloid aggregates could be generic toxins in higher organisms. J Neurosci 26: 8160-8167.
73. Kayed R, Head E, Thompson JL, McIntire TM, Milton SC, Cotman, CW, Glabe CG. (2003) Common structure of soluble amyloid oligomrs implies common mechanisms of pathogenesis. Science 300: 486-489.
74. Kayed R, Glabe CG. (2006) Conformation-dependent anti-amyloid oligomer antibodies. Methods Enzymol 413: 326-344.
75. Stefani M, Dobson CM. (2003) Protein aggregation and aggregate toxicity: New insights into protein folding, misfolding diseases and biological evolution. J Mol Med 81: 678-699.
76. Sherman MY, Goldberg AL. (2001) Cellular defenses against unfolded proteins: A cell biologist thinks about neurodegenerative diseases, Neuron 29: 15-32.
77. Muchowski PJ, Schaffar G, Sittler A, Wanker EE, Hayer-Hartl MK, Hartl FU. (2000) Hsp70 and Hsp40 chaperones can inhibit selfassembly of polyglutamine proteins into amyloid-like fibrils. Proc Natl Acad Sci USA 97: 7841-7846.
78. Csermely P. (2001) Chaperone overload is a possible contributor to “civilization diseases”. Trends Gen 17: 701-704.
79. Dobson CM. (2002) Getting out of shape - protein misfolding diseases. Nature 418: 729-730.
80. Tartaglia GG, Pechmann S, Dobson CM, Vendruscolo M. (2007) Life on the edge: A link between gene expression levels and aggregation rates of human proteins. Trends Biochem Sci 32: 204-206.
81. Bilen J, Bonini NM. (2005) Drosophila as a model for human neurodegenerative disease. Annu Rev Genet 39: 153-171.
82. Finelli A, Kelkar A, Song HJ, Yang H, Konsolaki M. (2004) A model for studying Alzheimer’s Abeta42-induced toxicity in Drosophila melanogaster. Mol Cell Neurosci 26: 365-375.
83. Crowther DC, Kinghorn KJ, Miranda E, Pase R, Curry JA, Duthie FA, Gubb DC, Lomar DA. (2005) Intraneuronal Abeta, non-amyloid aggregates and neurodegeneration in a Drosophila model of Alzheimer’s disease. Neuroscience 132: 123-135.
84. Iijima K, Liu HP, Chiang AS, Hearn SA, Konsolaki M, Zhong Y. (2004) Dissecting the pathological effects of human Abeta40 and Abeta42 in Drosophila: A potential model for Alzheimer’s disease. Proc Natl Acad Sci USA 101: 6623-6628.
85. Luheshi LM, Tartaglia GG, Brorsson AC, Pawar AP, Watson IE, Chiti F, Vendruscolo M, Lomas DA, Dobson CM, Crowther DC. (2007) Systematic in vivo analysis of the intrinsic determinants of amyloidbeta pathogenicity. PLoS Biol 5: e290.
86. Dodart JC, Bales KR, Gannon KS, Greene SJ, DeMattos RB et al. (2002) Immunization reverses memory deficits without reducing brain Abeta burden in Alheimer’s disease model. Nature Neurosci 5: 452- 457.
87. Westerman MA, Cooper-Blacketer D, Mariash A, Kotilinek L, Kawarabayashi T, Yourkin LH, Carlson GA, Yourkin SG, Ashe KH. (2002) The relationship between Abeta and memory in the Tg2576 mouse model of Alzheimer’s disease. J Neurosci 22: 1858-1867.
88. Cohen E, Bieschke J, Perciavalle RM, Kelly JW, Dillon A. (2006) Opposing activities protect against age-onset proteotoxicity. Science 313: 1604-1610.
89. Lansbury PT. (1999) Evolution of amyloid: What normal protein folding may tell us about fibrillogenesis and disease. Proc Natl Acad Sci USA 96: 3342-3344.
90. Luheshi LM, Crowther DC, Dobson CM. (2008) Protein misfolding and disease: From the test tube to the organism. Curr Opin Chem Biol 12: 25-31.
91. Dobson CM. (2006) An accidental breach of a protein’s natural defences. Nature Struct Mol Biol 13: 295-297.
92. Cohen FE, Kelly JW. (2003) Nature 426: 905-909.
93. Dobson CM. (2004) In the footsteps of alchemists. Science 304: 1259- 1262.
94. Schenck D. (2003) Amyloid-beta immunotherapy for Alzheimer’s disease: The end of the beginning. Nature Rev Neurosci 4: 49-60.
95. Dumoulin M, Dobson CM. (2005) Probing the origins, diagnosis and treatment of amyloid disease using antibodies. Biochimie 86: 589- 600.