Insight into the structure of amyloid fibrils from the analysis of globular proteins

PLoS Computational Biology

Volumn 2, Issue 12, 2006, Pages 1608-1618

  Trovato, Antonio ^a,b   Chiti, Fabrizio ^c   Maritan, Amos ^a,b,d   Seno, Flavio ^a,b,d  

^a Unità di Padova ^*  (Italy)

^b UNIVERSITY OF PADOVA   (Italy)

^c UNIVERSITY OF FLORENCE   (Italy)

^d SEZIONE DI PADOVA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CHAINS; GLYCOPROTEINS; POLYPEPTIDES;

AMYLOID FIBRIL; AMYLOID STRUCTURES; FIBRILLAR AGGREGATES; GENERIC FEATURES; GLOBULAR PROTEINS; POLYPEPTIDES CHAINS; PROPERTY; PROTEIN MOLECULES; SELF-PROPAGATING; SOLUBLE STATE;

PEPTIDES;

ALPHA SYNUCLEIN; AMYLIN; DNA FRAGMENT; GLOBULAR PROTEIN; PEPTIDE DERIVATIVE; TAU PROTEIN; AMYLOID; MULTIPROTEIN COMPLEX;

AMINO ACID SEQUENCE; ARTICLE; CELL HETEROGENEITY; PODOSPORA ANSERINA; PRION; PROTEIN AGGREGATION; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; METHODOLOGY; MOLECULAR GENETICS; SEQUENCE ANALYSIS; ULTRASTRUCTURE;

AMINO ACID SEQUENCE; AMYLOID; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MULTIPROTEIN COMPLEXES; SEQUENCE ANALYSIS, PROTEIN;

EID: 33845978790     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0020170     Document Type: Article

References (59)

1. Selkoe DJ (2003) Folding proteins in fatal ways. Nature 426: 900-904.
2. Chiti F, Dobson CM (2006) Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 75: 333-366.
3. Westermark P, Benson MD, Buxbaum JN, Cohen AS, Frangione B, et al. (2005) Amyloid: Toward terminology clarification. Amyloid 12: 1-4.
4. 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.
5. Uversky VN, Fink AL (2004) Conformational constraints for amyloid formation fibrillation: The importance of being unfolded. Biochim Biophys Acta 1698: 131-153.
6. 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.
7. Barnhart MM, Chapman MR, Robinson (2006) Curli biogenesis and function. Annu Rev Microbiol 60: 131-147.
8. Fowler DM, Koulov AV, Alory-Jost C, Marks MS, Balch WE, et al. (2006) Functional amyloid formation within mammalian tissue. PLoS Biol 4(1): 100-107.
9. Talbot NJ (2003) Aerial morphogenesis: Enter the chaplins. Curr Biol 13: R696-R698.
10. Chien P, Weissman JS, DePace AH (2004) Emerging principles of conformation-based prion inheritance. Annu Rev Biochem 73: 617-656.
11. Sunde M, Blake C (1997) The structure of amyloid fibrils by electron microscopy and X-ray diffraction. Adv Protein Chem 50: 123-159.
12. Serpell LC, Sunde M, Benson MD, Tennent GA, Pepys MB, et al. (2000) The protofilament substructure of amyloid fibrils. J Mol Biol 300: 1033-1039.
13. Bauer HH, Aebi U, Haner M, Hermann R, Muller M, et al. (1995) Architecture and polymorphism of fibrillar supramolecular assemblies produced by in vitro aggregation of human calcitonin. J Struct Biol 115: 1-15.
14. Saiki M, Honda S, Kawasaki K, Zhou D, Kaito A, et al. (2005) Higher-order molecular packing in amyloid-like constructed with linear arrangements of hydrophobic and hydrogen-bonding side-chains. J Mol Biol 348: 983-998.
15. Pedersen JS, Dikov D, Flink JL, Hjuler HA, Christiansen G, et al. (2006) The changing face of glucagon fibrillation: Structural polymorphism and conformational imprinting. J Mol Biol 355: 501-523.
16. Jaroniec CP, MacPhee CE, Astrof NS, Dobson CM, Griffin RG (2002) Molecular conformation of a peptide fragment of transthyretin in an amyloid fibril. Proc Natl Acad Sci U S A 99: 16748-16753.
17. Petkova AT, Ishii Y, Balbach JJ, Antzutkin ON, Leapman RD, et al. (2002) A structural model for Alzheimer's beta-amyloid fibrils based on experimental constraints from solid state NMR. Proc Natl Acad Sci U S A 99: 16742-16747.
18. Torok M, Milton S, Kayed R, Wu P, McIntire T, et al. (2002) Structural and dynamic features of Alzheimer's Abeta peptide in amyloid fibrils studied by site-directed spin labeling. J Biol Chem 277: 40810-40815.
19. Der-Sarkissian A, Jao CC, Chen J, Langen R (2003) Structural organization of alpha-synuclein fibrils studied by site-directed spin labeling. J Biol Chem 278: 37530-37535.
20. Jayasinghe SA, Langen R (2004) Identifying structural features of fibrillar islet amyloid polypeptide using site-directed spin labeling. J Biol Chem 279: 48420-48425.
21. Margittai M, Langen R (2004) Template-assisted filament growth by parallel stacking of tau. Proc Natl Acad Sci U S A 101: 10278-10283.
22. Del Mar C, Greenbaum EA, Mayne L, Englander SW, Woods VL Jr (2005) Structure and properties of alpha-synuclein and other amyloids determined at the amino acid level. Proc Natl Acad Sci U S A 102: 15477-15482.
23. Heise H, Hoyer W, Becker S, Andronesi OC, Riedel D, et al. (2005) Molecular-level secondary structure, polymorphism, and dynamics of fulllength alpha-synuclein fibrils studied by solid-state NMR. Proc Natl Acad Sci U S A 102: 15871-15876.
24. Kajava AV, Aebi U, Steven AC (2005) The parallel superpleated betastructure as a model for amyloid fibrils of human amylin. J Mol Biol 348: 247-252.
25. Krishnan R, Lindquist SL (2005) Structural insights into a yeast prion illuminate nucleation and strain diversity. Nature 435: 765-772.
26. Lührs T, Ritter C, Adrian M, Riek-Loher D, Bohrmann B, et al. (2005) 3D structure of Alzheimer's amyloid-beta(1-42) fibrils. Proc Natl Acad Sci U S A 102: 17342-17347.
27. 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.
28. Nelson R, Sawaya MR, Balbirnie M, Madsen AO, Riekel C, et al. (2005) Structure of the cross-beta spine of amyloid-like fibrils. Nature 435: 773-778.
29. Ritter C, Maddelein ML, Siemer AB, Luhrs T, Ernst M, et al. (2005) Correlation of structural elements and infectivity of the HET-s prion. Nature 435: 844-848.
30. Petkova AT, Buntkowsky G, Dyda F, Leapman RD, Yau WM, et al. (2004) Solid state NMR reveals a pH-dependent antiparallel beta-sheet registry in fibrils formed by a beta-amyloid peptide. J Mol Biol 335: 247-260.
31. Chiti F, Stefani M, Taddei N, Ramponi G, Dobson CM (2003) Rationalization of the effects of mutations on peptide and protein aggregation rates. Nature 424: 805-808.
32. Yoon S, Welsh SJ (2004) Detecting hidden sequence propensity for amyloid fibril formation. Protein Sci 13: 2149-2160.
33. Fernandez-Escamilla AM, Rousseau F, Schymkowitz J, Serrano L (2004) Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol 22: 1302-1306.
34. Pawar AP, DuBay KF, Zurdo J, Chiti F, Vendruscolo M, et al. (2005) Prediction of "aggregation-prone" and "aggregation- susceptible" regions in proteins associated with neurodegenerative diseases. J Mol Biol 350: 379-392.
35. Tartaglia GG, Cavalli A, Pellarin R, Caflisch A (2005) Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences. Protein Sci 14: 2723-2734.
36. Galzitskaya OV, Garbuzynskiy SO, Lobanov MY (2006) Is it possible to predict amyloidogenic regions from sequence alone? J Bioinform Comp Biol 4: 373-388.
37. Galzitskaya OV, Garbuzynskiy SO, Lobanov MY (2006) Prediction of amyloidogenic and disordered regions in protein chains. PLoS Comput Biol 2(12): e177. doi:10.1371/journal.pcbi.0020177.eor
38. Khare SD, Wilcox KC, Gong P, Dokholyan NV (2005) Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation. Proteins 61: 617-632.
39. Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, et al. (2006) The 3D profile method for identifying fibril-forming segments of proteins. Proc Natl Acad Sci U S A 103: 4074-4078.
40. 16-22, a seven-residue fragment of the Alzheimer's β-amyloid peptide, and structural characterization by solid state NMR. Biochemistry 39: 13748-13759.
41. Bemporad F, Calloni G, Campioni S, Plakoutsi G, Taddei N, et al. (2006) Sequence and structural determinants of amyloid fibril formation. Acc Chem Res 39: 620-627.
42. Wood SJ, Wetzel R, Martin JD, Hurle MR (1995) Prolines and amyloidogenicity in fragments of the Alzheimer's peptide beta/A4. Biochemistry 34: 724-730.
43. Tjernberg LO, Callaway DJ, Tjernberg A, Hahne S, Lilliehook C, et al. (1999) A molecular model of Alzheimer amyloid beta-peptide fibril formation. J Biol Chem 274: 12619-12625.
44. Bodles AM, Guthrie DJ, Harriott P, Campbell P, Irvine GB (2000) Toxicity of non-Abeta component of Alzheimer's disease amyloid, and N-terminal fragments thereof, correlates to formation of beta-sheet structure and fibrils. Eur J Biochem 267: 2186-2194.
45. Bodles AM, Guthrie DJ, Greer B, Irvine GB (2001) Identification of the region of non-A beta component (NAC) of Alzheimer's disease amyloid responsible for its aggregation and toxicity. J Neurochem 78: 384-395.
46. von Bergen M, Friedhoff P, Biernat J, Heberle J, Mandelkow EM, et al. (2000) Assembly of tau protein into Alzheimer paired helical filaments depends on a local sequence motif ((306)VQIVYK(311)) forming beta structure. Proc Natl Acad Sci U S A 97: 5129-5134.
47. Coustou V, Deleu C, Saupe S, Begueret J (1997) The protein product of the het-s heterokaryon incompatibility gene of the fungus Podospora anserina behaves as a prion analog. Proc Natl Acad Sci U S A 94: 9773-9778.
48. Saupe SJ (2000) Molecular genetics of heterokaryon incompatibility in filamentous ascomycetes. Microbiol Mol Biol Rev 64: 489-502.
49. Balguerie A, Dos Reis S, Ritter C, Chaignepain S, Coulary-Salin B, et al. (2003) Domain organization and structure-function relationship of the HET-s prion protein of Podospora anserina. EMBO J 22: 2071-2081.
50. Petkova AT, Leapman RD, Guo Z, Yau WM, Mattson MP, et al. (2005) Selfpropagating, molecular-level polymorphism in Alzheimer's beta-amyloid fibrils. Science 307: 262-265.
51. Nelson R, Eisenberg D (2006) Recent atomic models of amyloid fibril structure. Curr Opin Struct Biol 16: 260-265.
52. Lovell SC, Davis IW, Adrendall WB, de Bakker PIW, Word JM, et al. (2003) Structure validation by C-alpha geometry: phi,psi and C-beta deviation. Proteins 50: 437-450.
53. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
54. Samudrala R, Moult J (1998) An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 275: 895-916.
55. Tiana G, Colombo M, Provasi D, Broglia RA (2004) Deriving amino acid contact potentials from their frequencies of occurrence in proteins: A lattice model study. J Phys Condens Matter 16: 2551-2564.
56. Hubbard TJ (1994) Use of beta-strand interaction pseudo-potentials in protein structure prediction and modelling. In: Lathrop RH, editor. Proteins structure prediction minitrack of the 27th HICSS. New York: IEEE Computer Society Press. pp. 336-354.
57. Wouters MA, Curmi PM (1995) An analysis of side chain interactions and pair correlations within antiparallel β-sheets: The differences between backbone hydrogen-bonded and nonhydrogen-bonded residue pairs. Proteins 22: 119-131.
58. Zhu H, Braun W (1999) Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins. Protein Sci 8: 326-342.
59. Steward RE, Thornton JM (2002) Prediction of strand pairing in antiparallel and parallel β-sheets using information theory. Proteins 48: 178-191.