Aggregation properties of a short peptide that mediates amyloid fibril formation in model proteins unrelated to disease

Journal of Biosciences

Volumn 36, Issue 4, 2011, Pages 679-689

  Chaudhary, Nitin ^a   Singh, Shashi ^a   Nagaraj, Ramakrishnan ^a  

^a CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY   (India)

Author keywords

Amyloid fibrils; atomic force microscopy; non fibrillar structures; peptide self association; SH3 domain

Indexed keywords

AMYLOID; AMYLOID PROTEIN; ASPARTYLISOLEUCYLASPARTYLLEUCYLHISDITYLLEUCINE CARBOXYLAMIDE; ASPARTYLISOLEUCYLASPARTYLLEUCYLHISDITYLLEUCINE CARBOXYLIC ACID; MICA; PEPTIDE; SODIUM CHLORIDE; UNCLASSIFIED DRUG;

AGGREGATE; AGGREGATION; ATOMIC FORCE MICROSCOPY; BRAIN; HOMOLOGY; MICA; PEPTIDE; PH; PROTEIN; SALT;

ARTICLE; CIRCULAR DICHROISM; COMPLEX FORMATION; CONCENTRATION RESPONSE; CONTROLLED STUDY; PEPTIDE ANALYSIS; PEPTIDE SYNTHESIS; PH MEASUREMENT; PROCESS MODEL; PROTEIN AGGREGATION; PROTEIN ASSEMBLY; PROTEIN CONFORMATION; PROTEIN PROCESSING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

1-PHOSPHATIDYLINOSITOL 4-KINASE; AMINO ACID SEQUENCE; AMYLOID; ANIMALS; BRAIN CHEMISTRY; CATTLE; CHICKENS; CIRCULAR DICHROISM; HYDROGEN-ION CONCENTRATION; MICROSCOPY, ATOMIC FORCE; MOLECULAR MIMICRY; MOLECULAR SEQUENCE DATA; OLIGOPEPTIDES; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SOLUTIONS; SPECTRIN; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; SRC HOMOLOGY DOMAINS;

BOVINAE;

EID: 80054979271     PISSN: 02505991     EISSN: 09737138     Source Type: Journal    
DOI: 10.1007/s12038-011-9104-3     Document Type: Article

References (54)

1. M Anderson OV Bocharova N Makarava L Breydo VV Salnikov IV Baskakov 2006 Polymorphism and ultrastructural organization of prion protein amyloid fibrils: an insight from high resolution atomic force microscopy J. Mol. Biol. 358 580 596 16519898 10.1016/j.jmb.2006.02.007 1:CAS:528:DC%2BD28XjvVamtb0%3D
2. Atherton E 1989 Solid phase synthesis: A practical approach (Oxford: IRL Press)
3. HH Bauer U Aebi M Haner R Hermann M Muller HP Merkle 1995 Architecture and polymorphism of fibrillar supramolecular assemblies produced by in vitro aggregation of human calcitonin J Struct Biol 115 1 15 7577226 10.1006/jsbi.1995.1024 1:CAS:528:DyaK2MXpt1ykurs%3D
4. HK Blackley GH Sanders MC Davies CJ Roberts SJ Tendler MJ Wilkinson 2000 In-situ atomic force microscopy study of beta-amyloid fibrillization J. Mol. Biol. 298 833 840 10801352 10.1006/jmbi.2000.3711 1:CAS:528:DC%2BD3cXivFGjtL0%3D
5. D Burdick B Soreghan M Kwon J Kosmoski M Knauer A Henschen J Yates C Cotman, et al. 1992 Assembly and aggregation properties of synthetic Alzheimer's A4/beta amyloid peptide analogs J. Biol. Chem. 267 546 554 1730616 1:CAS:528:DyaK38XjvFSmtA%3D%3D
6. N Chaudhary S Singh R Nagaraj 2008 Organic solvent mediated self-association of an amyloid forming peptide from beta2-microglobulin: an atomic force microscopy study Biopolymers 90 783 791 18798577 10.1002/bip.21087 1:CAS:528:DC%2BD1cXhsV2qtL3P
7. N Chaudhary S Singh R Nagaraj 2009 Morphology of self-assembled structures formed by short peptides from the amyloidogenic protein tau depends on the solvent in which the peptides are dissolved J. Pept. Sci. 15 675 684 19714684 10.1002/psc.1172 1:CAS:528:DC%2BD1MXhtFSnsbbE
8. T Chiba Y Hagihara T Higurashi K Hasegawa H Naiki Y Goto 2003 Amyloid fibril formation in the context of full-length protein: effects of proline mutations on the amyloid fibril formation of beta2-microglobulin J. Biol. Chem. 278 47016 47024 12958308 10.1074/jbc.M304473200 1:CAS:528:DC%2BD3sXovFKktrc%3D (Pubitemid 37452285)
9. M Fandrich MA Fletcher CM Dobson 2001 Amyloid fibrils from muscle myoglobin Nature (London) 410 165 166 10.1038/35065514 1:CAS:528: DC%2BD3MXitVyktb4%3D (Pubitemid 32216577)
10. Fandrich M, Forge V, Buder K, Kittler M, Dobson CM and Diekmann S 2003 Myoglobin forms amyloid fibrils by association of unfolded polypeptide segments. Proc. Natl. Acad. Sci. USA 100 15463-15468 (Pubitemid 38021012)
11. Y Fezoui DM Hartley DM Walsh DJ Selkoe JJ Osterhout DB Teplow 2000 A de novo designed helix-turn-helix peptide forms nontoxic amyloid fibrils Nat. Struct. Biol. 7 1095 1099 11101888 10.1038/81937 1:CAS:528:DC%2BD3cXovVahsLo%3D
12. BI Giasson IV Murray JQ Trojanowski VM Lee 2001 A hydrophobic stretch of 12 amino acid residues in the middle of alpha-synuclein is essential for filament assembly J. Biol. Chem. 276 2380 2386 11060312 10.1074/jbc.M008919200 1:CAS:528:DC%2BD3MXhtVGjsrw%3D
13. S Gnanakaran R Nussinov AE Garcia 2006 Atomic-level description of amyloid beta-dimer formation J. Am. Chem. Soc. 128 2158 2159 16478138 10.1021/ja0548337 1:CAS:528:DC%2BD28XoslGrug%3D%3D
14. C Goldsbury P Frey V Olivieri U Aebi SA Muller 2005 Multiple assembly pathways underlie amyloid-beta fibril polymorphisms J. Mol. Biol. 352 282 298 16095615 10.1016/j.jmb.2005.07.029 1:CAS:528:DC%2BD2MXpslyltrk%3D (Pubitemid 41213315)
15. Gorbitz CH 2001 Nanotube formation by hydrophobic dipeptides. Chemistry - Eur. J. 7 5153-5159
16. WJ Goux L Kopplin AD Nguyen K Leak M Rutkofsky VD Shanmuganandam D Sharma H Inouye, et al. 2004 The formation of straight and twisted filaments from short tau peptides J. Biol. Chem. 279 26868 26875 15100221 10.1074/jbc. M402379200 1:CAS:528:DC%2BD2cXkvFGgu70%3D (Pubitemid 38812520)
17. Guijarro JI, Sunde M, Jones JA, Campbell ID and Dobson CM 1998 Amyloid fibril formation by an SH3 domain. Proc. Natl. Acad. Sci. USA 95 4224-4228 (Pubitemid 28207893)
18. PI Haris D Chapman 1995 The conformational analysis of peptides using Fourier transform IR spectroscopy Biopolymers 37 251 263 7540054 10.1002/bip.360370404 1:CAS:528:DyaK2MXlvFarurg%3D
19. JD Harper SS Wong CM Lieber PT Lansbury Jr 1999 Assembly of A beta amyloid protofibrils: an in vitro model for a possible early event in Alzheimer's disease Biochemistry 38 8972 8980 10413470 10.1021/bi9904149 1:CAS:528:DyaK1MXjsl2jtLo%3D (Pubitemid 29334658)
20. Iconomidou VA, Chryssikos GD, Gionis V, Vriend G, Hoenger A and Hamodrakas SJ 2001 Amyloid-like fibrils from an 18-residue peptide analogue of a part of the central domain of the B-family of silkmoth chorion proteins. FEBS Lett. 499 268-273 (Pubitemid 32553877)
21. Iconomidou VA, Vriend G and Hamodrakas SJ 2000 Amyloids protect the silkmoth oocyte and embryo. FEBS Lett. 479 141-145 (Pubitemid 30616422)
22. Ivanova MI, Sawaya MR, Gingery M, Attinger A and Eisenberg D 2004 An amyloid-forming segment of beta2-microglobulin suggests a molecular model for the fibril. Proc. Natl. Acad. Sci. USA 101 10584-10589 (Pubitemid 38955785)
23. Ivanova MI, Thompson MJ and Eisenberg D 2006 A systematic screen of beta(2)-microglobulin and insulin for amyloid-like segments. Proc. Natl. Acad. Sci. USA 103 4079-4082
24. M Jackson HH Mantsch 1995 The use and misuse of FTIR spectroscopy in the determination of protein structure Crit. Rev. Biochem. Mol. Biol. 30 95 120 7656562 10.3109/10409239509085140 1:CAS:528:DyaK2MXlvFGnsrw%3D
25. R Jansen W Dzwolak R Winter 2005 Amyloidogenic self-assembly of insulin aggregates probed by high resolution atomic force microscopy Biophys. J. 88 1344 1353 15574704 10.1529/biophysj.104.048843 1:CAS:528:DC%2BD2MXhtlyjtL0%3D (Pubitemid 40975961)
26. JA Jarvis DJ Craik MC Wilce 1993 X-ray diffraction studies of fibrils formed from peptide fragments of transthyretin Biochem. Biophys. Res. Commun. 192 991 998 8507211 10.1006/bbrc.1993.1514 1:CAS:528:DyaK3sXkvV2gsbo%3D (Pubitemid 23218512)
27. S Jones J Manning NM Kad SE Radford 2003 Amyloid-forming peptides from beta2-microglobulin-Insights into the mechanism of fibril formation in vitro J. Mol. Biol. 325 249 257 12488093 10.1016/S0022-2836(02)01227-5 1:CAS:528:DC%2BD38XpsFyitLY%3D (Pubitemid 36062686)
28. NM Kad NH Thomson DP Smith DA Smith SE Radford 2001 Beta(2)-microglobulin and its deamidated variant, N17D form amyloid fibrils with a range of morphologies in vitro J. Mol. Biol. 313 559 571 11676539 10.1006/jmbi.2001.5071 1:CAS:528:DC%2BD3MXnslCrtrw%3D (Pubitemid 33052287)
29. Kardos J, Okuno D, Kawai T, Hagihara Y, Yumoto N, Kitagawa T, Zavodszky P, Naiki H, et al. 2005 Structural studies reveal that the diverse morphology of beta(2)-microglobulin aggregates is a reflection of different molecular architectures. Biochim. Biophys. Acta 1753 108-120 (Pubitemid 41597437)
30. King DS, Fields CG and Fields GB 1990 A cleavage method which minimizes side reactions following Fmoc solid phase peptide synthesis. Int. J. Pept. Protein Res. 36 255-266 (Pubitemid 20293378)
31. T Kortemme MJ Kelly LE Kay J Forman-Kay L Serrano 2000 Similarities between the spectrin SH3 domain denatured state and its folding transition state J. Mol. Biol. 297 1217 1229 10764585 10.1006/jmbi.2000.3618 1:CAS:528:DC%2BD3cXitl2rtb0%3D
32. GV Kozhukh Y Hagihara T Kawakami K Hasegawa H Naiki Y Goto 2002 Investigation of a peptide responsible for amyloid fibril formation of beta 2-microglobulin by achromobacter protease I J. Biol. Chem. 277 1310 1315 11687582 10.1074/jbc.M108753200 1:CAS:528:DC%2BD38XnvFOrsw%3D%3D (Pubitemid 34968884)
33. Lopez De La Paz M, Goldie K, Zurdo J, Lacroix E, Dobson CM, Hoenger A and Serrano L 2002 De novo designed peptide-based amyloid fibrils. Proc. Natl. Acad. Sci. USA 99 16052-16057 (Pubitemid 35462747)
34. D Losic LL Martin MI Aguilar DH Small 2006 Beta-amyloid fibril formation is promoted by step edges of highly oriented pyrolytic graphite Biopolymers 84 519 526 16752395 10.1002/bip.20549 1:CAS:528:DC%2BD28XhtVChur%2FN (Pubitemid 44519211)
35. B Morel S Casares F Conejero-Lara 2006 A single mutation induces amyloid aggregation in the alpha-spectrin SH3 domain: analysis of the early stages of fibril formation J. Mol. Biol. 356 453 468 16375922 10.1016/j.jmb.2005.11.062 1:CAS:528:DC%2BD28XmsFWrtw%3D%3D (Pubitemid 43099983)
36. AK Paravastu AT Petkova R Tycko 2006 Polymorphic fibril formation by residues 10-40 of the Alzheimer's beta-amyloid peptide Biophys. J. 90 4618 4629 16565054 10.1529/biophysj.105.076927 1:CAS:528:DC%2BD28XlvVaksb8%3D (Pubitemid 43830905)
37. AT Petkova RD Leapman Z Guo WM Yau MP Mattson R Tycko 2005 Self-propagating, molecular-level polymorphism in Alzheimer's beta-amyloid fibrils Science 307 262 265 15653506 10.1126/science.1105850 1:CAS:528:DC%2BD2MXisVKksA%3D%3D (Pubitemid 40116242)
38. M Reches E Gazit 2003 Casting metal nanowires within discrete self-assembled peptide nanotubes Science 300 625 627 12714741 10.1126/science.1082387 1:CAS:528:DC%2BD3sXjtVymurk%3D (Pubitemid 36520583)
39. M Reches E Gazit 2006 Designed aromatic homo-dipeptides: formation of ordered nanostructures and potential nanotechnological applications Phys. Biol. 3 S10 19 16582461 10.1088/1478-3975/3/1/S02 1:CAS:528:DC%2BD28XjvVChtLY%3D
40. M Reches Y Porat E Gazit 2002 Amyloid fibril formation by pentapeptide and tetrapeptide fragments of human calcitonin J. Biol. Chem. 277 35475 35480 12095997 10.1074/jbc.M206039200 1:CAS:528:DC%2BD38Xnt1WmtL0%3D
41. WK Surewicz HH Mantsch D Chapman 1993 Determination of protein secondary structure by Fourier transform infrared spectroscopy: a critical assessment Biochemistry 32 389 394 8422346 10.1021/bi00053a001 1:CAS:528: DyaK3sXjsFahtQ%3D%3D (Pubitemid 23034873)
42. K Tenidis M Waldner J Bernhagen W Fischle M Bergmann M Weber ML Merkle W Voelter, et al. 2000 Identification of a penta- and hexapeptide of islet amyloid polypeptide (IAPP) with amyloidogenic and cytotoxic properties J. Mol. Biol. 295 1055 1071 10656810 10.1006/jmbi.1999.3422 1:CAS:528:DC%2BD3cXotlSjtA%3D%3D
43. A Thompson AR White C McLean CL Masters R Cappai CJ Barrow 2000 Amyloidogenicity and neurotoxicity of peptides corresponding to the helical regions of PrP(C) J. Neurosci. Res. 62 293 301 11020222 10.1002/1097- 4547(20001015)62:2<293::AID-JNR14>3.0.CO;2-Y 1:CAS:528: DC%2BD3cXns1aqur8%3D
44. Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D and Eisenberg D 2006 The 3D profile method for identifying fibril-forming segments of proteins. Proc. Natl. Acad. Sci. USA 103 4074-4078
45. L Tjernberg W Hosia N Bark J Thyberg J Johansson 2002 Charge attraction and beta propensity are necessary for amyloid fibril formation from tetrapeptides J. Biol. Chem. 277 43243 43246 12215440 10.1074/jbc.M205570200 1:CAS:528:DC%2BD38Xos1ems7g%3D (Pubitemid 35285710)
46. SM Tracz A Abedini M Driscoll DP Raleigh 2004 Role of aromatic interactions in amyloid formation by peptides derived from human Amylin Biochemistry 43 15901 15908 15595845 10.1021/bi048812l 1:CAS:528: DC%2BD2cXpvVGhu7c%3D (Pubitemid 39665089)
47. Ventura S, Zurdo J, Narayanan S, Parreno M, Mangues R, Reif B, Chiti F, Giannoni E, et al. 2004 Short amino acid stretches can mediate amyloid formation in globular proteins: the Src homology 3 (SH3) case. Proc. Natl. Acad. Sci. USA 101 7258-7263 (Pubitemid 38638020)
48. von Bergen M, Barghorn S, Biernat J, Mandelkow EM and Mandelkow E 2005 Tau aggregation is driven by a transition from random coil to beta sheet structure. Biochim. Biophys. Acta 1739 158-166 (Pubitemid 40018535)
49. M von Bergen S Barghorn L Li A Marx J Biernat EM Mandelkow E Mandelkow 2001 Mutations of tau protein in frontotemporal dementia promote aggregation of paired helical filaments by enhancing local beta-structure J. Biol. Chem. 276 48165 48174
50. von Bergen M, Friedhoff P, Biernat J, Heberle J, Mandelkow EM and Mandelkow E 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. USA 97 5129-5134 (Pubitemid 30313683)
51. WJ Waddell 1956 A simple ultraviolet spectrophotometric method for the determination of protein J. Lab. Clin. Med. 48 311 314 13346201 1:CAS:528:DyaG2sXitlSq
52. Wolf P 1983 A critical reappraisal of Waddell's technique for ultraviolet spectrophotometric protein estimation. Anal Biochem. 129 145-155
53. K Yamaguchi S Takahashi T Kawai H Naiki Y Goto 2005 Seeding-dependent propagation and maturation of amyloid fibril conformation J. Mol. Biol. 352 952 960 16126222 10.1016/j.jmb.2005.07.061 1:CAS:528:DC%2BD2MXhtVWit7nL (Pubitemid 41267080)
54. M Zhu PO Souillac C Ionescu-Zanetti SA Carter AL Fink 2002 Surface-catalyzed amyloid fibril formation J. Biol. Chem. 277 50914 50922 12356747 10.1074/jbc.M207225200 1:CAS:528:DC%2BD38Xps12nuro%3D (Pubitemid 36042259)