Systematic analysis of aggregates from 38 kinds of non disease-related proteins: Identifying the intrinsic propensity of polypeptides to form amyloid fibrils

Bioscience, Biotechnology and Biochemistry

Volumn 71, Issue 5, 2007, Pages 1313-1321

  Aso, Yoshikazu ^a   Shiraki, Kentaro ^b   Takagi, Masahiro ^a  

^a JAPAN ADVANCED INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^b UNIVERSITY OF TSUKUBA   (Japan)

Author keywords

Amyloid fibril formation; Atomic force microscopy; Circular dichroism

Indexed keywords

ATOMIC FORCE MICROSCOPY; DICHROISM; ETHANOL; HYDROGEN BONDS; POLYPEPTIDES; STABILIZATION;

AMYLOID FIBRIL FORMATION; DESTABILIZATION; FIBRILS; FRAGMENTATION; LACTOGLOBULIN;

ENZYMES;

BOVINAE;

ALCOHOL; AMYLOID; HEN EGG LYSOZYME; HISTONE; LACTOGLOBULIN; LYSOZYME; PROTEIN; TRYPSINOGEN; UNCLASSIFIED DRUG;

ANIMAL; ARTICLE; ATOMIC FORCE MICROSCOPY; CATTLE; CHEMISTRY; CHICKEN; CIRCULAR DICHROISM; COMPARATIVE STUDY; MASS SPECTROMETRY; PH; PROTEIN SECONDARY STRUCTURE; SPECTROFLUOROMETRY; SYNTHESIS; TEMPERATURE; ULTRASTRUCTURE;

AMYLOID; ANIMALS; CATTLE; CHICKENS; CIRCULAR DICHROISM; ETHANOL; HISTONES; HYDROGEN-ION CONCENTRATION; LACTOGLOBULINS; MICROSCOPY, ATOMIC FORCE; MURAMIDASE; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SPECTROMETRY, FLUORESCENCE; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TEMPERATURE; TRYPSINOGEN;

EID: 34347383011     PISSN: 09168451     EISSN: 13476947     Source Type: Journal    
DOI: 10.1271/bbb.60718     Document Type: Article

References (46)

1. Guijarro, J. I., Sunde, M., Jones, J. A., Campbell, I. D., and Dobson, C. M., Amyloid fibril formation by an SH3 domain. Proc. Natl. Acad. Sci. USA, 95, 4224-4228 (1998).
2. Litvinovich, S. V., Brew, S. A., Aota, S., Akiyama, S. K., Haudenschild, C., and Ingham, K. C., Formation of amyloid-like fibrils by self-association of a partially unfolded fibronectin type III module. J. Mol. Biol., 280, 245-258 (1998).
3. Fandrich, M., Fletcher, M. A., and Dobson, C. M., Amyloid fibrils from muscle myoglobin. Nature, 410, 165-166 (2001).
4. Fandrich, M., and Dobson, C. M., The behaviour of polyamino acids reveals an inverse side chain effect in amyloid structure formation. EMBO J., 21, 5682-5690 (2002).
5. Krebs, M. R., Wilkins, D. K., Chung, E. W., Pitkeathly, M. C., Chamberlain, A. K., Zurdo, J., Robinson, C. V., and Dobson, C. M., Formation and seeding of amyloid fibrils from wild-type hen lysozyme and a peptide fragment from the beta-domain. J. Mol. Biol., 300, 541-549 (2000).
6. Chiti, F., Bucciantini, M., Capanni, C., Taddei, N., Dobson, C. M., and Stefani, M., Solution conditions can promote formation of either amyloid protofilaments or mature fibrils from the HypF N-terminal domain. Protein Sci., 10, 2541-2547 (2001).
7. Yutani, K., Takayama, G., Goda, S., Yamagata, Y., Maki, S., Namba, K., Tsunasawa, S., and Ogasahara, K., The process of amyloid-like fibril formation by methionine aminopeptidase from a hyperthermophile, Pyrococcus furiosus. Biochemistry, 39, 2769-2777 (2000).
8. Hamada, D., and Dobson, C. M., A kinetic study of beta-lactoglobulin amyloid fibril formation promoted by urea. Protein Sci., 11, 2417-2426 (2002).
9. Uegaki1, K., Nakamura, T., Yamamoto, H., Kobayashi, A., Odahara, T., Harata, K., Hagihara, Y., Ueyama, N., Yamazaki, T., and Yumoto, N., Amyloid fibril formation by the CAD domain of caspase-activated DNase. Biopolymers, 79, 39-47 (2005).
10. Rochet, J. C., and Lansbury, P. T., Jr., Amyloid fibrillogenesis: themes and variations. Curr. Opin. Struct. Biol., 10, 60-68 (2000).
11. Sunde, M., Serpell, L. C., Bartlam, M., Fraser, P. E., Pepys, M. B., and Blake, C. C., Common core structure of amyloid fibrils by synchrotron X-ray diffraction. J. Mol. Biol., 273, 729-739 (1997).
12. Naiki, H., Higuchi, K., Hosokawa, M., and Takeda, T., Fluorometric determination of amyloid fibrils in vitro using the fluorescent dye, thioflavin T1. Anal. Biochem., 177, 244-249 (1989).
13. Klunk, W. E., Pettegrew, J. W., and Abraham, D. J., Quantitative evaluation of congo red binding to amyloidlike proteins with a beta-pleated sheet conformation. J. Histochem. Cytochem., 37, 1273-1281 (1989).
14. Kisiday, J., Jin, M., Kurz, B., Hung, H., Semino, C., Zhang, S., and Grodzinsky, A. J., Self-assembling peptide hydrogel fosters chondrocyte extracellular matrix production and cell division: implications for cartilage tissue repair. Proc. Natl. Acad. Sci. USA, 99, 9996-10001 (2002).
15. Kasai, S., Ohga, Y., Mochizuki, M., Nishi, N., Kadoya, Y., and Nomizu, M., Multifunctional peptide fibrils for biomedical materials. Biopolymers, 76, 27-33 (2004).
16. Chiti, F., Webster, P., Taddei, N., Clark, A., Stefani, M., Ramponi, G., and Dobson, C. M., Designing conditions for in vitro formation of amyloid protofilaments and fibrils. Proc. Natl. Acad. Sci. USA, 96, 3590-3594 (1999).
17. Srisailam, S., Wang, H. M., Kumar, T. K., Rajalingam, D., Sivaraja, V., Sheu, H. S., Chang, Y. C., and Yu, C., Amyloid-like fibril formation in an all beta-barrel protein involves the formation of partially structured intermediate(s). J. Biol. Chem., 277, 19027-19036 (2002).
18. Khurana, R., Uversky, V. N., Nielsen, L., and Fink, A. L., Is Congo red an amyloid-specific dye? J. Biol. Chem., 276, 22715-22721 (2001).
19. Konno, T., Murata, K., and Nagayama, K., Amyloid-like aggregates of a plant protein: a case of a sweet-tasting protein, monellin. FEBS Lett., 454, 122-126 (1999).
20. Jiao, Y., and Schaffer, T. E., Accurate height and volume measurements on soft samples with the atomic force microscope. Langmuir, 20, 10038-10045 (2004).
21. Serpell, L. C., Alzheimer's amyloid fibrils: structure and assembly. Biochim. Biophys. Acta, 1502, 16-30 (2000).
22. Serpell, L. C., Sunde, M., Benson, M. D., Tennent, G. A., Pepys, M. B., and Fraser, P. E., The protofilament substructure of amyloid fibrils. J. Mol. Biol., 300, 1033-1039 (2000).
23. Kad, N. M., Myers, S. L., Smith, D. P., Alastair Smith, D., Radford, S. E., and Thomson, N. H., Hierarchical assembly of beta(2)-microglobulin amyloid in vitro revealed by atomic force microscopy. J. Mol. Biol., 330, 785-797 (2003).
24. Katou, H., Kanno, T., Hoshino, M., Hagihara, Y., Tanaka, H., Kawai, T., Hasegawa, K., Naiki, H., and Goto, Y., The role of disulfide bond in the amyloidogenic state of beta(2)-microglobulin studied by heteronuclear NMR. Protein Sci., 11, 2218-2229 (2002).
25. Ohhashi, Y., Hagihara, Y., Kozhukh, G., Hoshino, M., Hasegawa, K., Yamaguchi, I., Naiki, H., and Goto, Y., The intrachain disulfide bond of beta(2)-microglobulin is not essential for the immunoglobulin fold at neutral pH, but is essential for amyloid fibril formation at acidic pH. J. Biochem. (Tokyo), 131, 45-52 (2002).
26. Song, Y., Schowen, R. L., Borchardt, R. T., and Topp, E. M., Effect of 'pH' on the rate of asparagine deamidation in polymeric formulations: 'pH'-rate profile. J. Pharm. Sci., 90, 141-156 (2001).
27. Li, A., Sowder, R. C., Henderson, L. E., Moore, S. P., Garfinkel, D. J., and Fisher, R. J., Chemical cleavage at aspartyl residues for protein identification. Anal. Chem., 73, 5395-5402 (2001).
28. Ahern, T. J., and Klibanov, A. M., The mechanisms of irreversible enzyme inactivation at 100 °C. Science, 228, 1280-1284 (1985).
29. Zale, S. E., and Klibanov, A. M., Why does ribonuclease irreversibly inactivate at high temperatures? Biochemistry, 25, 5432-5444 (1986).
30. Frare, E., Polverino De Laureto, P., Zurdo, J., Dobson, C. M., and Fontana, A., A highly amyloidogenic region of hen lysozyme. J. Mol. Biol., 340, 1153-1165 (2004).
31. Hirota Nakaoka, N., Hasegawa, K., Naiki, H., and Goto, Y., Dissolution of beta2-microglobulin amyloid fibrils by dimethylsulfoxide. J. Biochem. (Tokyo), 134, 159-164 (2003).
32. Kheterpal, I., Zhou, S., Cook, K. D., and Wetzel, R., Abeta amyloid fibrils possess a core structure highly resistant to hydrogen exchange. Proc. Natl. Acad. Sci. USA, 97, 13597-13601 (2000).
33. Fandrich, M., Forge, V., Buder, K., Kittler, M., Dobson, C. M., and Diekmann, S., Myoglobin forms amyloid fibrils by association of unfolded polypeptide segments. Proc. Natl. Acad. Sci. USA, 100, 15463-15468 (2003).
34. Zurdo, J., Guijarro, J. I., Jimenez, J. L., Saibil, H. R., and Dobson, C. M., Dependence on solution conditions of aggregation and amyloid formation by an SH3 domain. J. Mol. Biol., 311, 325-340 (2001).
35. Cardoso, I., Goldsbury, C. S., Muller, S. A., Olivieri, V., Wirtz, S., Damas, A. M., Aebi, U., and Saraiva, M. J., Transthyretin fibrillogenesis entails the assembly of monomers: a molecular model for in vitro assembled transthyretin amyloid-like fibrils. J. Mol. Biol., 317, 683-695 (2002).
36. Smith, D. P., Jones, S., Serpell, L. C., Sunde, M., and Radford, S. E., A systematic investigation into the effect of protein destabilisation on beta 2-microglobulin amyloid formation. J. Mol. Biol., 330, 943-954 (2003).
37. Martsev, S. P., Dubnovitsky, A. P., Vlasov, A. P., Hoshino, M., Hasegawa, K., Naiki, H., and Goto, Y., Amyloid fibril formation of the mouse V(L) domain at acidic pH. Biochemistry, 41, 3389-3395 (2002).
38. Konno, T., Multistep nucleus formation and a separate subunit contribution of the amyloidgenesis of heat-denatured monellin. Protein Sci., 10, 2093-2101 (2001).
39. Xie, M., and Schowen, R. L., Secondary structure and protein deamidation. J. Pharm. Sci., 88, 8-13 (1999).
40. Dobson, C. M., Protein folding and disease: a view from the first Horizon Symposium. Nat. Rev. Drug Discov., 2, 154-160 (2003).
41. Sacchettini, J. C., and Kelly, J. W., Therapeutic strategies for human amyloid diseases. Nat. Rev. Drug Discov., 1, 267-275 (2002).
42. Heegaard, N. H., Roepstorff, P., Melberg, S. G., and Nissen, M. H., Cleaved beta 2-microglobulin partially attains a conformation that has amyloidogenic features. J. Biol. Chem., 277, 11184-11189 (2002).
43. Heegaard, N. H., Jorgensen, T. J., Rozlosnik, N., Corlin, D. B., Pedersen, J. S., Tempesta, A. G., Roepstorff, P., Bauer, R., and Nissen, M. H., Unfolding, aggregation, and seeded amyloid formation of lysine-58-cleaved beta 2-microglobulin. Biochemistry, 44, 4397-4407 (2005).
44. Corlin, D. B., Sen, J. W., Ladefoged, S., Lund, G. B., Nissen, M. H., and Heegaard, N. H., Quantification of cleaved beta2-microglobulin in serum from patients undergoing chronic hemodialysis. Clin. Chem., 51, 1177-1184 (2005).
45. Esposito, G., Michelutti, R., Verdone, G., Viglino, P., Hernandez, H., Robinson, C. V., Amoresano, A., Dal Piaz, F., Monti, M., Pucci, P., Mangione, P., Stoppini, M., Merlini, G., Ferri, G., and Bellotti, V., Removal of the N-terminal hexapeptide from human beta2-microglobulin facilitates protein aggregation and fibril formation. Protein Sci., 9, 831-845 (2000).
46. Monti, M., Amoresano, A., Giorgetti, S., Bellotti, V., and Pucci, P., Limited proteolysis in the investigation of beta2-microglobulin amyloidogenic and fibrillar states. Biochim. Biophys. Acta, 1753, 44-50 (2005).