β-Helix is a likely core structure of yeast prion Sup35 amyloid fibers

Kishimoto, Aiko; Hasegawa, Kazuya; Suzuki, Hirofumi; Taguchi, Hideki; Namba, Keiichi; Yoshida, Masasuke

doi:10.1016/j.bbrc.2004.01.117

Cited by 120 publications

(117 citation statements)

References 40 publications

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“…Amyloid fibrils can be formed by both normal and variant proteins of different origins and with no primary sequence homology (6, 7). They are highly ordered molecular assemblies with similar biophysical and ultrastructural characteristics, including a typical x-ray diffraction pattern and a predominant ␤-sheet conformation (5,(8)(9)(10)(11)(12)(13). The similarity among the different amyloid deposits and their ubiquity suggests that such structures might represent a generic form of the noncovalent packing of polypeptide chains (6,7,14).…”

Section: Charge Transport and Intrinsic Fluorescence In Amyloid-like mentioning

confidence: 99%

Charge transport and intrinsic fluorescence in amyloid-like fibrils

Mercato

Pompa²,

Maruccio³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

199

203

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Section: Charge Transport and Intrinsic Fluorescence In Amyloid-like mentioning

confidence: 99%

Charge transport and intrinsic fluorescence in amyloid-like fibrils

Mercato

Pompa²,

Maruccio³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

199

203

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“…X-ray fiber diffraction data for Sup35 fibrils have been presented as support for this proposal (69). Fig.…”

Section: Effects Of Hydration On Solid State Nmr Spectra Argue Againsmentioning

confidence: 93%

Parallel β-Sheets and Polar Zippers in Amyloid Fibrils Formed by Residues 10−39 of the Yeast Prion Protein Ure2p

et al. 2005

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We report the results of solid state nuclear magnetic resonance (NMR) and atomic force microscopy measurements on amyloid fibrils formed by residues 10-39 of the yeast prion protein Ure2p (Ure2p ). Measurements of intermolecular 13 C-13 C nuclear magnetic dipole-dipole couplings indicate that Ure2p 10-39 fibrils contain in-register parallel β-sheets. Measurements of intermolecular 15 N-13 C dipole-dipole couplings, using a new solid state NMR technique called DSQ-REDOR, are consistent with hydrogen bonds between sidechain amide groups of Gln18 residues. Such sidechain hydrogen bonding interactions have been called "polar zippers" by M.F. Perutz and have been proposed to stabilize amyloid fibrils formed by peptides with glutamine-and asparaginerich sequences, such as Ure2p . We propose that polar zipper interactions account for the inregister parallel β-sheet structure in Ure2p 10-39 fibrils and that similar peptides will also exhibit parallel β-sheet structures in amyloid fibrils. We present molecular models for Ure2p fibrils that are consistent with available experimental data. Finally, we show that solid state 13 C NMR chemical shifts for 13 C-labeled Ure2p 10-39 fibrils are insensitive to hydration level, indicating that the fibril structure is not affected by the presence or absence of bulk water. AbbreviationsNMR, nuclear magnetic resonance; Aβ, β-amyloid peptide; Ure2p 10-39 , residues 10-39 of the Ure2p yeast prion protein; EM, electron microscopy; FMOC, 9-fluorenylmethoxycarbonyl; TFA, trifluoroacetic acid; AFM, atomic force microscopy; MAS, magic-angle spinning; fpRFDR-CT, constant-time finite-pulse radiofrequency-driven recoupling; REDOR, rotational echo double resonance; DSQ, double single-quantum; TPPM, two-pulse phase modulation; CSA, chemical shift anisotropy; MD, molecular dynamics One goal of current efforts to elucidate the molecular structures of amyloid fibrils (1-35) is to identify the intermolecular interactions that determine the details of these structures and make amyloid fibrils a stable structural state for many peptides and proteins despite their diversity of amino acid sequences (36)(37)(38)(39)(40)(41). Recent studies by solid state nuclear magnetic resonance (NMR) of fibrils formed by the β-amyloid (Aβ) peptide associated with Alzheimer's disease (5,13,16,18,24,30,31), by various Aβ fragments (1,3,4,(6)(7)(8)12,21,25), and by other amyloidforming peptides (22) indicate that the β-sheets in amyloid fibrils have structures that tend to maximize contacts among hydrophobic residues when the component peptides contain continuous hydrophobic segments. Electrostatic interactions appear to play a secondary role, dictating the choice between parallel and antiparallel β-sheet structures when either type of structure could maximize hydrophobic contacts (6,21,23) and dictating the precise registry of *corresponding author: Dr. Robert Tycko, National Institutes of Health, Building 5, Room 112, Bethesda, MD 20892-0520. phone 301-402-8272, fax 301-496-0825, e-mailrobertty@mail.nih -sh...

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“…〈 Sup35p fragment with sequence GNNQQNY has been shown to form in-register parallel ␤-sheets in a crystalline state (25), but it has not been established that this crystal structure is directly relevant to the structure of Sup35NM fibrils. Fluorescence spectroscopy of pyrene-labeled Sup35NM fibrils has been used to argue against an in-register parallel ␤-sheet structure and to support a ␤-helical structure (26), as proposed earlier based on fiber diffraction (27). Electron paramagnetic resonance spectroscopy of spin-labeled Sup35NM fibrils has been used to probe intermolecular contacts and strain-dependent variations in rigidity that may be associated with the ␤-sheet structure (28).…”

Section: T He Nonchromosomal Gene [Psi ϩ ] Of Saccharomyces Cerevisiaementioning

confidence: 96%

Amyloid of the prion domain of Sup35p has an in-register parallel β-sheet structure

Shewmaker¹,

Wickner²,

Tycko

2006

Proc. Natl. Acad. Sci. U.S.A.

272

302

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The [PSI ؉ ] prion of Saccharomyces cerevisiae is a self-propagating amyloid form of Sup35p, a subunit of the translation termination factor. Using solid-state NMR we have examined the structure of amyloid fibrils formed in vitro from purified recombinant Sup35 1-253 , consisting of the glutamine-and asparagine-rich Nterminal 123-residue prion domain (N) and the adjacent 130-residue highly charged M domain. Measurements of magnetic dipole-dipole couplings among 13 C nuclei in a series of Sup35NM fibril samples, 13 C-labeled at backbone carbonyl sites of Tyr, Leu, or Phe residues or at side-chain methyl sites of Ala residues, indicate intermolecular 13 C-13 C distances of Ϸ0.5 nm for nearly all sites in the N domain. Certain sites in the M domain also exhibit intermolecular distances of Ϸ0.5 nm. These results indicate that an in-register parallel ␤-sheet structure underlies the [PSI ؉ ] prion phenomenon. The Sup35p prion domain (Sup35N, residues 1-123) is asparagine-and glutamine-rich, is poor in charged residues, and has five imperfect nine-residue repeats with consensus YQQYN-PQGG. Sequence shuffling shows that the repeats are not necessary for prion generation or propagation and that amino acid content of the prion domain (not the sequence) determines whether a protein can form a prion (13). Certain point mutations in the prion domain can block propagation of [PSI ϩ ] introduced with the wild sequence (14, 15), although the mutant sequence may itself form a prion (16). Thus, propagation of an existing prion is very sequence-specific, as in the species barriers of mammalian prion diseases (reviewed in ref. 17).Amyloid fibrils are filamentous protein aggregates exhibiting ''cross-␤'' x-ray fiber diffraction patterns, indicating the presence of ␤-sheets formed by ␤-strands that are oriented approximately perpendicular to the fiber axis, with interstrand hydrogen bonds approximately parallel to the fiber axis (reviewed in ref. 18). The fact that the prion domains of Ure2p (another yeast prion protein with an N-terminal prion domain rich in asparagine and glutamine) and Sup35p can be shuffled and yet still form prions and amyloid (13,19) suggests that the amyloid on which these prions are based has an in-register parallel ␤-sheet structure (20, 21). A prion amyloid structure based on antiparallel ␤-sheets or ␤-helices would necessarily be stabilized by interactions among specific sets of unlike residues. These interactions would likely be destroyed by shuffling the sequence. In contrast, an in-register parallel ␤-sheet structure can be stabilized by intermolecular hydrophobic interactions (22,23) or polar side chain interactions [e.g., the ''polar zipper'' interactions suggested by Perutz et al. (24)] among like residues. Shuffling the sequence would still allow like residues to align and interact in such a structure. Thus, shuffleability of a prion domain suggests an in-register parallel ␤-sheet structure.The molecular structures of amyloid fibrils, particularly those formed by bona fide proteins, are difficult t...

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β-Helix is a likely core structure of yeast prion Sup35 amyloid fibers

Cited by 120 publications

References 40 publications

Charge transport and intrinsic fluorescence in amyloid-like fibrils

Charge transport and intrinsic fluorescence in amyloid-like fibrils

Parallel β-Sheets and Polar Zippers in Amyloid Fibrils Formed by Residues 10−39 of the Yeast Prion Protein Ure2p

Amyloid of the prion domain of Sup35p has an in-register parallel β-sheet structure

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