A generic mechanism of emergence of amyloid protofilaments from disordered oligomeric aggregates

PLoS Computational Biology

Volumn 4, Issue 11, 2008, Pages

  Auer, Stefan ^a   Meersman, Filip ^b   Dobson, Christopher M ^c   Vendruscolo, Michele ^c  

^a UNIVERSITY OF LEEDS   (United Kingdom)

^b UNIVERSITY OF LEUVEN   (Belgium)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOPROTEINS; HYDROGEN BONDS; NEURODEGENERATIVE DISEASES; OLIGOMERS;

ALZHEIMERS DISEASE; AMYLOID FORMATION; CHAIN AGGREGATES; CONDITION; GENERIC MECHANISM; METASTABLES; NEURODEGENERATIVE; PARKINSON'S DISEASE; POLYPEPTIDES CHAINS; PROTOFILAMENTS;

AGGREGATES;

AMYLOID; PEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; BETA SHEET; HYDROGEN BOND; HYDROPHOBICITY; PHASE TRANSITION; STRUCTURE ANALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; METABOLISM; PROTEIN QUATERNARY STRUCTURE; PROTEIN SECONDARY STRUCTURE;

AMYLOID; COMPUTER SIMULATION; MODELS, MOLECULAR; PEPTIDES; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY;

EID: 57149102288     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000222     Document Type: Article

References (40)

1. Chiti F, Dobson CM (2006) Protein misfolding, functional amyloid and human disease. Annu Rev Biochem 75: 333-366.
2. Jahn T, Radford SE (2008) Folding versus aggregation: Polypeptide conformations on competing pathways. Arch Biochem Biophys 469: 100-117.
3. Makin OS, Atkins E, Sikorski P, Johansson J, Serpell LC (2005) Molecular basis for amyloid fibril formation and stability. Proc Natl Acad Sci U S A 102: 315-320.
4. Dobson CM (1999) Protein misfolding, evolution and disease. Trends Biochem Sci 24: 329-332.
5. Selkoe DJ (2003) Folding proteins in fatal ways. Nature 426: 900-904.
6. 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.
7. Harper JD, Lieber CM, Lansbury PT (1997) Atomic force microscopic imaging of seeded fibril formation and fibril branching by the Alzheimer's disease amyloid-beta protein. Chem Biol 4: 951-959.
8. 1-42 are potent central nervous system neurotoxins. Proc Natl Acad Sci U S A 95: 6448-6453.
9. Serio TR, Cashikar AG, Kowal AS, Sawicki GJ, Moslehi JJ, et al. (2000) Nucleated conformational conversion and the replication of conformational information by a prion determinant. Science 289: 1317-1321.
10. Haass C, Selkoe DJ (2007) Soluble protein oligomers in neurodegeneration: lessons from the Alzheimer's amyloid β-peptide. Nat Rev Mol Cell Biol 8: 101-112.
11. 10-35): sequence effects. Proc Natl Acad Sci U S A 99: 14126-14131.
12. Hwang W, Zhang S, Kamm R, Karplus M (2004) Kinetic control of dimer structure formation in amyloid fibrillogenesis. Proc Natl Acad Sci U S A 101: 12916-12921.
13. Buchete N, Tycko R, Hummer G (2005) Molecular dynamics simulations of Alzheimer's β-amyloid protofilaments. J Mol Biol 353: 804-821.
14. Hills RD, Brooks CL (2007) Hydrophobic cooperativity as a mechanism for amyloid nucleation. J Mol Biol 368: 894-901.
15. Nguyen PH, Li MS, Stock G, Straub JE, Thirumalai D (2007) Monomer adds to preformed structured oligomers of Aβ-peptides by a two-stage dock-lock mechanism. Proc Natl Acad Sci U S A 104: 111-116.
16. Cheon M, Chang I, Mohanty S, Luheshi LM, Dobson CM, et al. (2007) Structural reorganisation and potential toxicity of oligomeric species formed during the assembly of amyloid fibrils. PLoS Comp Biol 3: e173. doi:10.1371/journal.pcbi.0030173.
17. Cheon M, Favrin G, Chang I, Dobson CM, Vendruscolo M (2008) Calculation of the free energy barriers in the oligomerisation of Ab peptide fragments. Front Biosci 13: 5614-5622.
18. Nguyen HD, Hall CK (2004) Molecular dynanmics simulations of spontaneous fibril formation by random-coil peptides. Proc Natl Acad Sci U S A 101: 16180-16185.
19. Urbanc B, Cruz L, Yun S, Buldyrev SV, Bitan G, et al. (2004) In silico study of amyloid β-protein folding and oligomerization. Proc Natl Acad Sci U S A 101: 17345-17350.
20. Pellarin R, Caflisch A (2006) Interpreting the aggregation kinetics of amyloid peptides. J Mol Biol 360: 882-892.
21. Pellarin R, Guarnera E, Caflisch A (2007) Pathways and intermediates of amyloid fibril formation. J Mol Biol 374: 917-924.
22. Derreumaux P, Mousseau N (2007) Coarse-grained protein molecular dynamics simulations. J Chem Phys 126: 025101.
23. Luheshi LM, Tartaglia GG, Brorsson AC, Pawar AP, Watson IE, et al. (2007) Systematic in vivo analysis of the intrinsic determinants of amyloid b pathogenicity. PLoS Biol 5: e290. doi:10.1371/journal.pbio.0050290.
24. Hoang TX, Trovato A, Seno F, Banavar JR, Maritan A (2004) Geometry and symmetry presculpt the free-energy landscape of proteins. Proc Natl Acad Sci U S A 101: 7960-7964.
25. Hoang TX, Marsella L, Trovato A, Seno F, Banavar JR, et al. (2006) Common attributes of native-state structures of proteins, disordered proteins, and amyloid. Proc Natl Acad Sci U S A 103: 6883-6888.
26. Banavar JR, Maritan A (2007) Physics of proteins. Annu Rev Biophys Biomol Struct 36: 261-280.
27. Auer S, Miller M, Krivov SV, Dobson CM, Karplus M, et al. (2007) Generic properties of the free energy landscapes of proteins. Phys Rev Lett 99: 178104.
28. Auer S, Dobson CM, Vendruscolo M (2007) Characterization of the nucleation barriers for protein aggregation and amyloid formation. HFSP J 1: 137-146.
29. Kammerer RA, Kostrewa D, Zurdo J, Detken A, Garcia-Echeverria C, et al. (2004) Exploring amyloid formation by a de novo design. Proc Natl Acad Sci U S A 101: 4435-4440.
30. Fandrich M, Dobson CM (2002) The behaviour of polyamino acids reveals an inverse side chain effect in amyloid structure formation. EMBO J 21: 5682-5690.
31. Knowles TP, Fitzpatrick AW, Mott H, Meehan S, Vendruscolo M, et al. (2007) Self-assembling protein fibrils represent a novel class of high performance nanoscale biomaterials. Science 318: 1900-1903.
32. Turner MS, Briehl RW, Ferrone FA, Josephs R (2003) Twisted protein aggregates and disease: the stability of sickle hemoglobin fibers. Phys Rev Lett 90: 128103.
33. 105-115, but not the mature amyloid fibrils. J Mol Biol 349: 903-909.
34. Petty SA, Decatur SM (2005) Intersheet rearrangement of polypeptides during nucleation of β-sheet aggregates. Proc Natl Acad Sci U S A 102: 14272-14277.
35. Knowles TPJ, Shu W, Devlin GL, Meehan S, Auer S, et al. (2007) Kinetics and thermodynamics of amyloid formation. Proc Natl Acad Sci U S A 104: 10016-10021.
36. Serio TR, Cashikar AG, Kowal AS, Sawicki GJ, Moslehi JJ, et al. (2000) Nucleated conformational conversion and the replication of conformational information by a prion determinant. Science 289: 1317-1321.
37. Zhu M, Souillac PO, Ionescu-Zanetti C, Carter SA, Fink AL (2002) Surface-catalyzed amyloid fibril formation. J Biol Chem 277: 50914-50922.
38. Auer S, Frenkel D (2004) Quantitative prediction of crystal-nucleation rates for spherical colloids. Annu Rev Phys Chem 55: 333-361.
39. Kayed R, Head E, Thompson JL, McIntire TM, Milton SC, et al. (2003) Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis. Science 300: 486-489.
40. Fersht AR, Shi JP, Knill-Jones J, Lowe DM, Wilkinson AJ, et al. (1985) Hydrogen bonding and biological specificity analyzed by protein engineering. Nature 314: 235-238.