Role of elongation and secondary pathways in S6 amyloid fibril growth

Biophysical Journal

Volumn 102, Issue 9, 2012, Pages 2167-2175

  Lorenzen, Nikolai ^a,b   Cohen, Samuel I A ^c,d   Nielsen, Soren B ^a,b   Herling, Therese W ^c   Christiansen, Gunna ^a   Dobson, Christopher M ^c   Knowles, Tuomas P J ^c   Otzen, Daniel ^a,b  

^a AARHUS UNIVERSITY   (Denmark)

^b AARHUS UNIVERSITY   (Denmark)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; DIMERIZATION; KINETICS; PROTEIN CONFORMATION; ULTRASTRUCTURE;

AMYLOID; COMPUTER SIMULATION; DIMERIZATION; KINETICS; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION;

THERMUS THERMOPHILUS;

EID: 84860440128     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2012.03.047     Document Type: Article

References (44)

1. M.G. Spillantini, and M.L. Schmidt M. Goedert Alpha-synuclein in Lewy bodies Nature 388 1997 839 840
2. C.M. Dobson Protein folding and misfolding Nature 426 2003 884 890
3. C. Haass, and D.J. Selkoe Soluble protein oligomers in neurodegeneration: lessons from the Alzheimer's amyloid β-peptide Nat. Rev. Mol. Cell Biol. 8 2007 101 112
4. J. Hardy, and D.J. Selkoe The amyloid hypothesis of Alzheimer's disease: progress and problems on the road to therapeutics Science 297 2002 353 356
5. D.J. Selkoe Folding proteins in fatal ways Nature 426 2003 900 904
6. F. Chiti, and C.M. Dobson Protein misfolding, functional amyloid, and human disease Annu. Rev. Biochem. 75 2006 333 366
7. C.M. Dobson Protein misfolding, evolution and disease Trends Biochem. Sci. 24 1999 329 332
8. J.T. Jarrett, and P.T. Lansbury Jr. Seeding "one-dimensional crystallization" of amyloid: a pathogenic mechanism in Alzheimer's disease and scrapie? Cell 73 1993 1055 1058
9. M. Tanaka, and J.S. Weissman An efficient protein transformation protocol for introducing prions into yeast Methods Enzymol. 412 2006 185 200
10. S.R. Collins, and A. Douglass J.S. Weissman Mechanism of prion propagation: amyloid growth occurs by monomer addition PLoS Biol. 2 2004 e321
11. T.P. Knowles, and A.W. Fitzpatrick M.E. Welland Role of intermolecular forces in defining material properties of protein nanofibrils Science 318 2007 1900 1903
12. J. Kardos, and K. Yamamoto Y. Goto Direct measurement of the thermodynamic parameters of amyloid formation by isothermal titration calorimetry J. Biol. Chem. 279 2004 55308 55314
13. H.J. Kim, and E. Chatani S.R. Paik Seed-dependent accelerated fibrillation of α-synuclein induced by periodic ultrasonication treatment J. Microbiol. Biotechnol. 17 2007 2027 2032
14. A.M. Morris, M.A. Watzky, and R.G. Finke Protein aggregation kinetics, mechanism, and curve-fitting: a review of the literature Biochim. Biophys. Acta 1794 2009 375 397
15. F. Ferrone Analysis of protein aggregation kinetics Methods Enzymol. 309 1999 256 274
16. T.P.J. Knowles, and C.A. Waudby C.M. Dobson An analytical solution to the kinetics of breakable filament assembly Science 326 2009 1533 1537
17. S.I.A. Cohen, and M. Vendruscolo T.P. Knowles Nucleated polymerization with secondary pathways. I. Time evolution of the principal moments J. Chem. Phys. 135 2011 065105
18. F.A. Ferrone, J. Hofrichter, and W.A. Eaton Kinetics of sickle hemoglobin polymerization. II. A double nucleation mechanism J. Mol. Biol. 183 1985 611 631
19. C.B. Andersen, and D. Otzen C. Rischel Glucagon amyloid-like fibril morphology is selected via morphology-dependent growth inhibition Biochemistry 46 2007 7314 7324
20. J.S. Pedersen, G. Christensen, and D.E. Otzen Modulation of S6 fibrillation by unfolding rates and gatekeeper residues J. Mol. Biol. 341 2004 575 588
21. J.S. Pedersen, and D. Dikov D.E. Otzen The changing face of glucagon fibrillation: structural polymorphism and conformational imprinting J. Mol. Biol. 355 2006 501 523
22. D.E. Otzen, and O. Kristensen M. Oliveberg Structural changes in the transition state of protein folding: alternative interpretations of curved chevron plots Biochemistry 38 1999 6499 6511
23. D.E. Otzen, and M. Oliveberg Conformational plasticity in folding of the split β-α-β protein S6: evidence for burst-phase disruption of the native state J. Mol. Biol. 317 2002 613 627
24. D. Otzen Antagonism, non-native interactions and non-two-state folding in S6 revealed by double-mutant cycle analysis Protein Eng. Des. Sel. 18 2005 547 557
25. G. Zandomeneghi, and M.R.H. Krebs M. Fändrich FTIR reveals structural differences between native β-sheet proteins and amyloid fibrils Protein Sci. 13 2004 3314 3321
26. F. Oosawa, and S. Asakura Thermodynamics of the Polymerization of Protein 1975 Academic Press New York
27. A. Wegner Spontaneous fragmentation of actin filaments in physiological conditions Nature 296 1982 266 267
28. S.I.A. Cohen, and M. Vendruscolo T.P. Knowles Nucleated polymerization with secondary pathways. III. Equilibrium behavior and oligomer populations J. Chem. Phys. 135 2011 065107
29. M.F. Bishop, and F.A. Ferrone Kinetics of nucleation-controlled polymerization. A perturbation treatment for use with a secondary pathway Biophys. J. 46 1984 631 644
30. S. Chen, F.A. Ferrone, and R. Wetzel Huntington's disease age-of-onset linked to polyglutamine aggregation nucleation Proc. Natl. Acad. Sci. USA 99 2002 11884 11889
31. A. Vitalis, and R.V. Pappu Assessing the contribution of heterogeneous distributions of oligomers to aggregation mechanisms of polyglutamine peptides Biophys. Chem. 159 2011 14 23
32. F.A. Ferrone, and J. Hofrichter W.A. Eaton Kinetic studies on photolysis-induced gelation of sickle cell hemoglobin suggest a new mechanism Biophys. J. 32 1980 361 380
33. S.I.A. Cohen, and M. Vendruscolo T.P. Knowles Nucleated polymerization with secondary pathways. II. Determination of self-consistent solutions to growth processes described by non-linear master equations J. Chem. Phys. 135 2011 065106
34. J. Masel, V.A. Jansen, and M.A. Nowak Quantifying the kinetic parameters of prion replication Biophys. Chem. 77 1999 139 152
35. M. Tanaka, and S.R. Collins J.S. Weissman The physical basis of how prion conformations determine strain phenotypes Nature 442 2006 585 589
36. A.M. Ruschak, and A.D. Miranker Fiber-dependent amyloid formation as catalysis of an existing reaction pathway Proc. Natl. Acad. Sci. USA 104 2007 12341 12346
37. Y.-Q. Wang, and A.K. Buell S. Perrett Relationship between prion propensity and the rates of individual molecular steps of fibril assembly J. Biol. Chem. 286 2011 12101 12107
38. A.K. Buell, and G.G. Tartaglia T.P. Knowles Position-dependent electrostatic protection against protein aggregation ChemBioChem 10 2009 1309 1312
39. A.K. Buell, and J.R. Blundell T.P. Knowles Frequency factors in a landscape model of filamentous protein aggregation Phys. Rev. Lett. 104 2010 228101
40. T. Scheibel, J. Bloom, and S.L. Lindquist The elongation of yeast prion fibers involves separable steps of association and conversion Proc. Natl. Acad. Sci. USA 101 2004 2287 2292
41. A. Fersht Structure and Mechanism in Protein Science 1999 W.H. Freeman New York
42. J. Stöhr, and N. Weinmann D. Riesner Mechanisms of prion protein assembly into amyloid Proc. Natl. Acad. Sci. USA 105 2008 2409 2414
43. C.B. Andersen, and H. Yagi C. Rischel Branching in amyloid fibril growth Biophys. J. 96 2009 1529 1536
44. S.I.A. Cohen, and M. Vendruscolo T.P. Knowles Nucleated polymerization in the presence of pre-formed seed filaments Int. J. Mol. Sci. 12 2011 5844 5852