Different Propensity to Form Amyloid Fibrils by Two Homologous Proteins - Human Stefins A and B: Searching for an Explanation

Proteins: Structure, Function and Genetics

Volumn 55, Issue 2, 2004, Pages 417-425

  Jenko, Saša ^a   Škarabot, Miha ^a   Kenig, Manca ^a   Gunčar, Gregor ^a   Muševič, Igor ^a   Turk, Dušan ^a   Žerovnik, Eva ^a  

^a JO EF STEFAN INSTITUTE   (Slovenia)

Author keywords

AFM; Amyloid fibril; Conformational disease; Cystatin; Domain swapped dimer; Ionic interactions; Protein modeling; X ray diffraction

Indexed keywords

AMYLOID; CYSTATIN; DIMER; MONOMER; PROTEIN; STEFIN A; STEFIN B; THIOFLAVINE;

ALPHA HELIX; ARTICLE; ATOMIC FORCE MICROSCOPY; BETA SHEET; FLUORESCENCE; HUMAN; MAGNETIC FIELD; PH; PRIORITY JOURNAL; PROTEIN STRUCTURE; TRANSMISSION ELECTRON MICROSCOPY; X RAY DIFFRACTION;

AMYLOID; CRYSTALLOGRAPHY, X-RAY; CYSTATINS; FLUORESCENCE; HUMANS; KINETICS; MAGNETICS; MICROSCOPY, ATOMIC FORCE; MICROSCOPY, ELECTRON; MODELS, MOLECULAR; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY, AMINO ACID; SOLVENTS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 1842531945     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20041     Document Type: Article

References (50)

1. Cohen AS. General introduction and brief history of the amyloid fibril. In: Marrink J, Van Rijswijk MH, editors. Amyloidosis. Dordrecht: Nijhoff; 1986. p 3-19.
2. Sipe JD, Cohen AS. Review: history of the amyloid fibril. J Struct Biol 2000;130:88-98.
3. Goedert M, Spillantini MG, Davies SW. Filamentous nerve cell inclusions in neurodegenerative diseases. Curr Opin Neurobiol 1998;8:619-632.
4. Cohen FE. Prions, peptides and protein misfolding. Mol Med Today 2000;6:292-293.
5. Soto C. Protein misfolding and disease; protein refolding and therapy (review). FEBS Lett 2001;498:204-207.
6. Blake C, Serpell L. Synchrotron X-ray studies suggest that the core of the transthyretin amyloid fibril is a continuous β-sheet helix. Structure 1996;4:989-998.
7. Sunde M, Serpell LC, Bartlam M, Fraser PE, Pepys MB, Blake CCF. Common core structure of amyloid fibrils by;Synchrotron X-ray diffraction J Mol Biol 1997;273:729-739.
8. Kirschner D, Elliott-Brant R, Szumowski KE, Gonnerman WA, Kindy, MS, Sipe JD, Cathcart ES. In vitro amyloid fibril formation by synthetic peptides corresponding to the amino terminus of apoSAA isoforms from amyloid-susceptible and amyloid-resistant mice. J Struct Biol 1998;124:88-98.
9. Malinchik SB, Inouye H, Szumowski KE, Kirschner DA. Structural analysis of Alzheimer's β(1-40) amyloid: protofilament: assembly of tubular fibrils. Biophys J 1998;74:537-545.
10. Serpell LC, Fraser PE, Sunde M. X-ray fiber diffraction of amyloid fibrils. Methods Enzymol 1999;309:526-537.
11. Stine WB, Snyder SW, Ladror US, Wade WS, Miller MF, Perun TJ, Holzman TF, Krafft GA. The nanometer-scale structure of amyloid-beta visualized by atomic force microscopy. J Protein Chem 1996;15:193-203.
12. Ding TT, Harper JD. Analysis of amyloid-beta assemblies using tapping mode atomic force microscopy under ambient conditions. Methods Enzymol 1999;309:510-525.
13. Goldsbury CS, Cooper GJ, Goldie KN, Muller SA, Saafi EL, Gruijters WT, Misur MP, Engel A, Aebi U, Kistler J. Polymorphic fibrillar assembly of human amylin. J Struct Biol 1997;119:17-27.
14. Ionescu-Zanetti C, Khurana R, Gillespie JR, Petrick JS, Trabachino LC, Minert LJ, Carter SA, Fink AL. Monitoring the assembly of Ig light-chain amyloid fibrils by atomic force microscopy. Proc Natl Acad Sci USA 1999;96:13175-13179.
15. Goldsbury C, Kistler J, Aebi U, Arvine T, Cooper GS. Watching amyloid fibrils grow by time-lapse atomic force microscopy. J Mol Biol 1999;285:33-39.
16. Stubbs MT, Laber B, Bode W, Huber R, Jerala R, Lenarčič B, Turk V. The refined 2.4 Å X-ray structure of recombinant human stefin B in complex with the cysteine proteinase papain: a novel type of proteinase inhibitor interaction. EMBO J 1990;9:1939-1947.
17. Jenko S, Dolenc I, Gunčar G, Doberček A, Podobnik M, Turk D. Crystal structure of stefin A in complex with cathepsin H: N-terminal residues of inhibitors can adapt to the active sites of endo- and exopeptidases. J Mol Biol 2003;326:875-885.
18. Martin JR, Craven CJ, Jerala R, Kroon-Žitko L, Žerovnik E, Turk V, Waltho JP. The three-dimensional solution structure of human stefin A. J Mol Biol 1995;246:331-343.
19. Jerala R, Žerovnik E. Accessing the global minimum conformation of stefin A dimer by annealing under partially denaturing conditions. J Mol Biol 1999;291:1079-1089.
20. Staniforth RA, Giannini S, Higgins LD, Conroy MJ, Hounslow AM, Jerala R, Craven CJ, Waltho JP. Three-dimensional domain swapping in the folded and molten-globule states of cystatins, an amyloid-forming structural superfamily. EMBO J 2001;20:4774-81.
21. Janowski R, Kozak M, Jankowska E, Grzonka Z, Grubb A, Abrahamson M, Jaskolski M. Human cystatin C, an amyloidogenic protein, dimerizes through three-dimensional domain swapping. Nat Struct Biol 2001;8:316-320.
22. Žerovnik E, Virden R, Jerala R, Turk V, Waltho JP. On the mechanism of human stefin B folding. I. Comparison to homologous stefin A. Influence of pH and trifluoroethanol on the fast and slow folding phases. Proteins 1998;32:296-303.
23. Žerovnik E, Virden R, Jerala R, Kroon-Žitko L, Turk V, Waltho JP. Differences in the effects of TFE on the folding pathways of human stefins A and B. Proteins 1999;36:205-216.
24. Žerovnik E, Jerala R, Kroon-Žitko L, Pain RH, Turk V. Intermediates in denaturation of a small globular protein, recombinant human stefin B. J Biol Chem 1992a;267:9041-9046.
25. Žerovnik E, Jerala R, Kroon-Žitko L, Turk V, Lohner K. Characterization of the equilibrium intermediates in acid denaturation of human stefin B. Eur J Biochem 1997;245:364-372.
26. Žerovnik E, Lohner K, Jerala R, Laggner P, Turk V. Calorimetric measurements of thermal denaturation of stefins A and B; comparison to predicted thermodynamics of stefin B unfolding. Eur J Biochem 1992b;210:217-221.
27. Hamada D, Segawa S, Goto Y. Non-native alpha-helical intermediate in the refolding of beta-lactoglobulin, a predominantly beta-sheet protein. Nat Struct Biol 1996;3:868-873.
28. Žerovnik E, Pompe-Novak M, Škarabot M, Ravnikar M, Muševič I, Turk V. Human stefin B readily forms amyloid fibrils in vitro. Biochim Biophys Acta 2002a;1594:1-5.
29. Žerovnik E, Zavašnik-Bergant V, Kopitar-Jerala N, Pompe-Novak M, Škarabot M, Goldie K, Ravnikar M, Muševič I, Turk V. Amyloid fibril formation by human stefin B in vitro:;Immunogold labelling and comparison to stefin A. Biol Chem 2002b;383:859-863.
30. Žerovnik E, Turk V, Waltho JP. Amyloid fibril formation by human stefin B: influence of the initial pH-induced intermediate state. Biochem Soc Trans 2002c;30:543-547.
31. Žerovnik E. Amyloid-fibril formation: proposed mechanisms and relevance to conformational disease. Eur J Biochem 2002;69:3362-3371.
32. Dobson CM. Getting out of shape. Nature 2002;418:729-730.
33. Bucciantini M, Giannoni E, Chiti F, Baroni F, Formigli L, Zurdo J, Taddei N, Ramponi G, Dobson CM, Stefani M. Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases. Nature 2002;416:507-511.
34. Kenig M, Jerala R, Kroon-Žitko L, Žerovnik E, Turk V. Major differences in stability and dimerization properties of two chimeric mutants of human stefins. Proteins 2001;42:512-522.
35. Jerala R, Trstenjak M, Lenarčič B, Turk V. Cloning a synthetic gene for human stefin B and its expression in E. coli. FEBS Lett 1988;239:41-44.
36. Turk D. Weiterentwicklung eines Programms für Molekülgraphik und Elektrondichte-manipulation und seine Anwendung auf verschiedene Protein-strukturaufklärungen. PhD thesis, Technische Universität, München., 1992.
37. Levine H. Quantification of β-sheet amyloid fibril structures with thioflavin T. Methods Enzymol 1999;309:274-284.
38. Guijarro JI, Sunde M, Jones JA, Campbell ID, Dobson CM. Amyloid fibril formation by an SH3 domain. Proc Natl Acad Sci USA 1998;95:4224-4228.
39. Dobson CM. Protein misfolding, evolution and disease. Trends Biochem Sci 1999;24:329-332.
40. Chiti F, Webster P, Taddei N, Clark A, Stefani M, Ramponi G, Dobson CM. Designing conditions for in vitro formation of amyloid protofilaments and fibrils. Proc Natl Acad Sci USA 1999;96:3590-3594.
41. Buck M. Trifluoroethanol cosolvents come of age. Recent studies with peptides and proteins. Q Rev Biophys 1998;31:297-355.
42. Hamada D, Goto Y. The equilibrium intermediate of β-lactoglobulin with non-native α-helical structure. J Mol Biol 1997;269:479-487.
43. Konno T, Murata K, Nagayama K. Amyloid-like aggregates of a plant protein: a case of a sweet-tasting protein, monellin. FEBS Lett 1999;454:122-126.
44. Thirumalai D, Klimov DK, Dima RI. Emerging ideas on the molecular basis of protein and peptide aggregation. Curr Opin Struct Biol 2003;13:146-159.
45. Cuff JA, Clamp ME, Siddiqui AS, Finlay M, Barton GJ. Jpred: a consensus secondary structure prediction server. Bioinformatics 1998;14:892-893.
46. Combet C, Blanchet C, Geourjon C, Deleage G. NPS@: network protein sequence analysis. Trends Biochem Sci 2000;25:147-150.
47. Geourjon C, Deleage G. SOPMA: Significant improvement in protein secondary structure prediction by consensus prediction from multiple alignments. Cabios 1995;11:681-684.
48. Kirkitadze MD, Condron MM, Teplow DB. Identification and characterization of key kinetic intermediates in amyloid beta-protein fibrillogenesis. J Mol Biol 2001;312:1103-1119.
49. Kenig M. Stability and rate of folding of chimeric and some site-specific mutants of human stefins. PhD thesis, University of Ljubljana, Slovenia, 2002.
50. Merritt EA, Bacon DJ. Raster3D: photorealistic molecular graphics. Methods Enzymol 1997;277:505-524.