Searching for conditions to form stable protein oligomers with amyloid-like characteristics: The unexplored basic pH

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1804, Issue 1, 2010, Pages 223-234

  Ahmad, Basir ^a   Winkelmann, Julia ^a   Tiribilli, Bruno ^b   Chiti, Fabrizio ^a  

^a UNIVERSITY OF FLORENCE   (Italy)

^b ISTITUTO DEI SISTEMI COMPLESSI   (Italy)

Author keywords

Alkaline pH; Amyloid like oligomer; Congo red; HypF N; Premolten globule

Indexed keywords

AMYLOID; CONGO RED; ESCHERICHIA COLI PROTEIN; OLIGOMER;

ALKALINITY; ARTICLE; ATOMIC FORCE MICROSCOPY; BETA SHEET; CHEMICAL STRUCTURE; CIRCULAR DICHROISM; FLUORESCENCE; LIGHT SCATTERING; PH; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STABILITY; PROTEIN STRUCTURE; ULTRAVIOLET RADIATION;

AMYLOID; CARBOXYL AND CARBAMOYL TRANSFERASES; CIRCULAR DICHROISM; CONGO RED; ESCHERICHIA COLI PROTEINS; HYDROGEN-ION CONCENTRATION; MICROSCOPY, ATOMIC FORCE; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, QUATERNARY; SPECTROMETRY, FLUORESCENCE; THIAZOLES; TRIFLUOROETHANOL; TRYPTOPHAN;

ESCHERICHIA COLI;

EID: 71649100480     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2009.10.005     Document Type: Article

References (54)

1. Chiti F., and Dobson C.M. Protein misfolding, functional amyloid, and human disease. Annu. Rev. Biochem. 75 (2006) 333-366
2. Kayed R., Head E., Thompson J.L., McIntire T.M., Milton S.C., Cotman C.W., and Glabe C.G. Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis. Science 300 (2003) 486-489
3. Watson D., Castaño E., Kokjohn T.A., Kuo Y.M., Lyubchenko Y., Pinsky D., Connolly Jr. E.S., Esh C., Luehrs D.C., Stine W.B., Rowse L.M., Emmerling M.R., and Roher A.E. Physicochemical characteristics of soluble oligomeric Abeta and their pathologic role in Alzheimer's disease. Neurol. Res. 27 (2005) 869-881
4. Rosano C., Zuccotti S., Bucciantini M., Stefani M., Ramponi G., and Bolognesi M. Crystal structure and anion binding in the prokaryotic hydrogenase maturation factor HypF acylphosphatase-like domain. J. Mol. Biol. 321 (2002) 785-796
5. 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 (2001) 2541-2547
6. Marcon G., Plakoutsi G., Canale C., Relini A., Taddei N., Dobson C.M., et al. Amyloid formation from HypF-N under conditions in which the protein is initially in its native state. J. Mol. Biol. 347 (2005) 323-335
7. Calloni G., Lendel C., Campioni S., Giannini S., Gliozzi A., Relini A., Vendruscolo M., Dobson C.M., Salvatella X., and Chiti F. Structure and dynamics of a partially folded protein are decoupled from its mechanism of aggregation. J. Am. Chem. Soc. 130 (2008) 13040-13050
8. Campioni S., Mossuto M.F., Torrassa S., Calloni G., de Laureto P.P., Relini A., Fontana A., and Chiti F. Conformational properties of the aggregation precursor state of HypF-N. J. Mol. Biol. 379 (2008) 554-567
9. Bucciantini M., Giannoni E., Chiti F., Baroni F., Formigli L., Zurdo J., Taddei N., Ramponi G., Dobson C.M., and Stefani M. Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases. Nature 416 (2002) 507-511
10. Bucciantini M., Calloni G., Chiti F., Formigli L., Nosi D., Dobson C.M., and Stefani M. Prefibrillar amyloid protein aggregates share common features of cytotoxicity. J. Biol. Chem. 279 (2004) 31374-313782
11. Uversky V.N., and Ptitsyn O.B. Further evidence on the equilibrium "pre-molten globule state": four-state guanidinium chloride-induced unfolding of carbonic anhydrase B at low temperature. J. Mol. Biol. 255 (1996) 215-228
12. Uversky V.N., and Fink A.L. Conformational constraints for amyloid fibrillation: the importance of being unfolded. Biochim. Biophys. Acta 1698 (2004) 131-153
13. Morrow J.A., Segal M.L., Lund-Katz S., Philips M.C., Knapp M., Rupp B., and Weigraber K.H. Differences in stability among the human apolipoprotein E isoforms determined by the amino-terminal domain. Biochemistry 39 (2000) 11657-11666
14. Dockal M., Carter D.C., and Ruker F. Conformational transitions of the three recombinant domains of human serum albumin depending on pH. J. Biol. Chem. 275 (2000) 3042-3050
15. Rami B.R., and Udgaonkar J.B. pH-jump-induced folding and unfolding studies of barstar: evidence for multiple folding and unfolding pathways. Biochemistry 40 (2001) 15267-15279
16. Kuznetsova I.M., Turoverov K.K., and Uversky V.N. Use of the phase diagram method to analyze the protein unfolding-refolding reactions: fishing out the "invisible" intermediates. J. Proteome Res. 3 (2004) 485-494
17. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
18. Koradi R., Billeter M., and Wüthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14 (1996) 51-55
19. Woody R.W., and Dunker A.K. Aromatic and cystine side-chain circular-dichroism in proteins. In: Fasman G.D. (Ed). Circular Dichroism and the Conformational Analysis of Biomolecules (1996), Plenum Press, New York 109-157
20. Semisotnov G.V., Rodionova N.A., Razgulyaev O.I., Uversky V.N., Gripas A.F., and Gilmanshin R.I. Study of the "molten globule" intermediate state in protein folding by a hydrophobic fluorescent probe. Biopolymers 31 (1991) 119-128
21. Cardamone M., and Puri N.K. Spectrofluorimetric assessment of the surface hydrophobicity of proteins. Biochem. J. 282 (1992) 589-593
22. Kuwajima K. The molten globule state of α-lactalbumin. FASEB J. 10 (1996) 102-109
23. Voropai E.S., Samtsov M.P., Kaplevskii K.N., Maskevich A.A., Stepuro V.I., Povarova O.I., Kuznetsova I.M., Turoverov K.K., Fink A.L., and Uverskii V.N. Spectral properties of thioflavinT and its complexes with amyloid fibrils. J. Appl. Spectrosc. 70 (2003) 868-874
24. Dusa A., Kaylor J., Edridge S., Bodner N., Hong D.P., and Fink A.L. Characterization of oligomers during alpha-synuclein aggregation using intrinsic tryptophan fluorescence. Biochemistry 45 (2006) 2752-2760
25. Ferrão-Gonzales A.D., Robbs B.K., Moreau V.H., Ferreira A., Juliano L., Valente A.P., Almeida F.C., Silva J.L., and Foguel D. Controlling {beta}-amyloid oligomerization by the use of naphthalene sulfonates: trapping low molecular weight oligomeric species. J. Biol. Chem. 280 (2005) 34747-34754
26. Uversky V.N. Amyloidogenesis of natively unfolded proteins. Curr. Alzheimer Res. 5 (2008) 260-287
27. Mastrangelo I.A., Ahmed M., Sato T., Liu W., Wang C., Hough P., and Smith S.O. High-resolution atomic force microscopy of soluble Abeta42 oligomers. J. Mol. Biol. 358 (2006) 106-119
28. Greenfield N.J. Methods to estimate the conformation of proteins and polypeptides. Anal. Biochem. 235 (1996) 1-10
29. Brand L., and Gohlke J.R. Fluorescence probes for structure. Annu. Rev. Biochem. 41 (1972) 843-868
30. Chaffotte A.F., Guijarro J.I., Guillou Y., Delepierre M., and Goldberg M.E. The "pre-molten globule," a new intermediate in protein folding. J. Protein Chem. 16 (1997) 433-439
31. Ptitsyn O.B. Molten globule and protein folding. Adv. Protein Chem. 47 (1995) 83-229
32. Arai M., and Kuwajima K. Role of the molten globule state in protein folding. Adv. Protein Chem. 53 (2000) 209-282
33. Samaddar S., Mandal A.K., Mondal S.K., Sahu K., Bhattacharyya K., and Roy S. Solvation dynamics of a protein in the pre molten globule state. J. Phys. Chem. B 110 (2006) 21210-21215
34. Ahmad B., and Khan R.H. Studies on the acid unfolded and molten globule states of catalytically active stem bromelain: a comparison with catalytically inactive form. J. Biochem. 140 (2006) 501-508
35. Uversky V.N., and Ptitsyn O.B. Partly folded" state, a new equilibrium state of protein molecules: four-state guanidinium chloride-induced unfolding of beta-lactamase at low temperature. Biochemistry 33 (1994) 2782-2791
36. Yoon M.K., Shin J., Choi G., and Choi B.S. Intrinsically unstructured N-terminal domain of bZIP transcription factor HY5. Proteins 65 (2006) 856-866
37. Walsh D.M., Hartley D.M., Kusumoto Y., Fezoui Y., Condron M.M., Lomakin A., Benedek G.B., Selkoe D.J., and Teplow D.B. Amyloid beta-protein fibrillogenesis. Structure and biological activity of protofibrillar intermediates. J. Biol. Chem. 274 (1999) 25945-25952
38. Conway K.A., Harper J.D., and Lansbury Jr. P.T. Fibrils formed in vitro from alpha-synuclein and two mutant forms linked to Parkinson's disease are typical amyloid. Biochemistry 39 (2000) 2552-2563
39. Kayed R., Sokolov Y., Edmonds B., McIntire T.M., Milton S.C., Hall J.E., and Glabe C.G. Permeabilization of lipid bilayers is a common conformation-dependent activity of soluble amyloid oligomers in protein misfolding diseases. J. Biol. Chem 279 (2004) 46363-46366
40. Ionescu-Zanetti C., Khurana R., Gillespie J.R., Petrick J.S., Trabachino L.C., Minert L.J., Carter S.A., and Fink A.L. Monitoring the assembly of Ig light-chain amyloid fibrils by atomic force microscopy. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 13175-13179
41. Quintas A., Vaz D.C., Cardoso I., Saraiva M.J.M., and Brit R.M. Tetramer dissociation and monomer partial unfolding precedes protofibril formation in amyloidogenic transthyretin variants. J. Biol. Chem. 276 (2001) 27207-272013
42. Gosal W.S., Morten I.J., Hewitt E.W., Smith D.A., Thomson N.H., and Radford S.E. Competing pathways determine fibril morphology in the self-assembly of beta2-microglobulin into amyloid. J. Mol. Biol. 351 (2005) 850-864
43. Plakoutsi G., Taddei N., Stefani M., and Chiti F. Aggregation of the acylphosphatase from Sulfolobus solfataricus: the folded and partially unfolded states can both be precursors for amyloid formation. J. Biol. Chem. 279 (2004) 14111-14119
44. Malisauskas M., Ostman J., Darinskas A., Zamotin V., Liutkevicius E., Lundgren E., and Morozova-Roche L.A. Does the cytotoxic effect of transient amyloid oligomers from common equine lysozyme in vitro imply innate amyloid toxicity?. J. Biol. Chem. 280 (2005) 6269-6275
45. Soreghan B., Kosmoski J., and Glabe C. Surfactant properties of Alzheimer's A beta peptides and the mechanism of amyloid aggregation. J. Biol. Chem. 269 (1994) 28551-28554
46. Tjernberg L.O., Pramanik A., Björling S., Thyberg P., Thyberg J., Nordstedt C., Berndt K.D., Terenius L., and Rigler R. Amyloid beta-peptide polymerization studied using fluorescence correlation spectroscopy. Chem. Biol. 6 (1999) 53-62
47. LeVine III H. 4,4(′)-Dianilino-1,1(′)-binaphthyl-5,5(′)-disulfonate: report on non-beta-sheet conformers of Alzheimer's peptide beta(1-40). Arch. Biochem. Biophys. 404 (2002) 106-115
48. Kirkitadze M.D., Condron M.M., and Teplow D.B. Identification and characterization of key kinetic intermediates in amyloid beta-protein fibrillogenesis. J. Mol. Biol. 312 (2001) 1103-1119
49. Uversky V.N., Li J., and Fink A.L. Evidence for a partially folded intermediate in alpha-synuclein fibril formation. J. Biol. Chem. 276 (2001) 10737-10744
50. Goldsbury C., Goldie K., Pellaud J., Seelig J., Frey P., Müller S.A., Kistler J., Cooper G.J., and Aebi U. Amyloid fibril formation from full-length and fragments of amylin. J. Struct. Biol. 130 (2000) 352-362
51. Uversky V.N., Gillespie J.R., Millett I.S., Khodyakova A.V., Vasiliev A.M., Chernovskaya T.V., Vasilenko R.N., Kozlovskaya G.D., Dolgikh D.A., Fink A.L., Doniach S., and Abramov V.M. Natively unfolded human prothymosin alpha adopts partially folded collapsed conformation at acidic pH. Biochemistry 38 (1999) 15009-15016
52. Goto Y., and Fink A.L. Conformational states of β-lactamase: molten globule states at acidic and alkaline pH with high salt. Biochemistry 28 (1989) 945-952
53. Kumar R., Prabhu N.P., Rao D.K., and Bhuyan A.K. The alkali molten globule state of horse ferricytochrome c: observation of cold denaturation. J. Mol. Biol. 364 (2006) 483-495
54. Walsh D.M., and Selkoe D.J. A beta oligomers-a decade of discovery. J. Neurochem. 101 (2007) 1172-1184