Probing the Structure of the Infectious Amyloid Form of the Prion-forming Domain of HET-s Using High Resolution Hydrogen/Deuterium Exchange Monitored by Mass Spectrometry

Nazabal, Alexis; Maddelein, Marie‐Lise; Bonneu, Marc; Saupe, Sven J.; Schmitter, Jean‐Marie

doi:10.1074/jbc.m413185200

Cited by 31 publications

(27 citation statements)

References 45 publications

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“…Recently this methodology has been adapted with great success to probe the conformation of fibrillar aggregates that are notoriously difficult to study by most conventional methods (27,(31)(32)(33). The H/D exchange approach exploits the fact that backbone amide hydrogens located within the unstructured regions of proteins exchange very rapidly, whereas those in- volved in systematically H-bonded structures, such as ␤-sheets and ␣-helices, usually exchange far more slowly (34).…”

Section: Discussionmentioning

confidence: 99%

β-Sheet core of human prion protein amyloid fibrils as determined by hydrogen/deuterium exchange

Wintrode²,

Surewicz

2007

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

212

261

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Propagation of transmissible spongiform encephalopathies is associated with the conversion of normal prion protein, PrP C , into a misfolded, oligomeric form, PrP Sc . Although the high-resolution structure of the PrP C is well characterized, the structural properties of PrP Sc remain elusive. Here we used MS analysis of H/D backbone amide exchange to examine the structure of amyloid fibrils formed by the recombinant human PrP corresponding to residues 90 -231 (PrP90 -231), a misfolded form recently reported to be infectious in transgenic mice overexpressing PrP C . Analysis of H/D exchange data allowed us to map the systematically H-bonded ␤-sheet core of PrP amyloid to the C-terminal region (staring at residue Ϸ169) that in the native structure of PrP monomer corresponds to ␣-helix 2, a major part of ␣-helix 3, and the loop between these two helices. No extensive hydrogen bonding (as indicated by the lack of significant protection of amide hydrogens) was detected in the N-terminal part of PrP90 -231 fibrils, arguing against the involvement of residues within this region in stable ␤-structure. These data provide long-sought experimentally derived constraints for high-resolution structural models of PrP amyloid fibrils.prion diseases ͉ transmissible spongiform encephalopathy ͉ amyloid structure ͉ mass spectrometry

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Section: Discussionmentioning

confidence: 99%

β-Sheet core of human prion protein amyloid fibrils as determined by hydrogen/deuterium exchange

Wintrode²,

Surewicz

2007

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

212

261

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“…This property is shared by the yeast prion proteins Ure2p (8) and Sup35p (9,10), whose prion domains are larger, enriched in Asn and Gln residues, and located at their N termini. In the absence of the remainder of HET-s, its prion domain has the propensity to fibrillize and to infect (5,6,11). These are also properties that HET-s holds in common with Ure2p and Sup35p (12)(13)(14).…”

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confidence: 99%

“…Recently, a ␤-solenoid model has been proposed for HET-s-(218 -289) fibrils, based on mutational analysis, hydrogen/deuterium exchange, and solid-state NMR spectroscopy (11,16). Generically, solenoid proteins are axially coiled structures with each coil containing a set of secondary structure elements (17,18).…”

mentioning

confidence: 99%

Mass Analysis by Scanning Transmission Electron Microscopy and Electron Diffraction Validate Predictions of Stacked β-Solenoid Model of HET-s Prion Fibrils

Sen

Baxa

Simon

et al. 2007

Journal of Biological Chemistry

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“…Previous studies of amyloid structure have used HX in various modes (26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36). We used conditions (low pH and temperature) where the exchange of even unprotected amide hydrogens can be measured so that unstructured as well as structured regions can be directly determined.…”

mentioning

confidence: 99%

Structure and properties of α-synuclein and other amyloids determined at the amino acid level

Mar

Greenbaum

Mayne

et al. 2005

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

199

190

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The structure of ␣-synuclein (␣-syn) amyloid was studied by hydrogen-deuterium exchange by using a fragment separation-MS analysis. The conditions used made it possible to distinguish the exchange of unprotected and protected amide hydrogens and to define the order͞disorder boundaries at close to amino acid resolution. The soluble ␣-syn monomer exchanges its amide hydrogens with water hydrogens at random coil rates, consistent with its natively unstructured condition. In assembled amyloid, long N-terminal and C-terminal segments remain unprotected (residues 1-Ϸ38 and 102-140), although the N-terminal segment shows some heterogeneity. A continuous middle segment (residues Ϸ39 -101) is strongly protected by systematically H-bonded cross-␤ structure. This segment is much too long to fit the amyloid ribbon width, but non-H-bonded amides expected for directionchanging loops are not apparent. These results and other known constraints specify that ␣-syn amyloid adopts a chain fold like that suggested before for amyloid-␤ [Petkova et al. M any proteins and polypeptides are able to adopt the generic massively aggregated structure known as amyloid (1). The macroscopic fibrillar character of amyloid is obvious by direct electron microscopic observation, but its detailed structure and the structural basis of its unusual behavior remains a challenging problem (2-9).Methods based on the hydrogen exchange (HX) behavior of polypeptides can provide useful information. The backbone amide hydrogens of proteins engage in continual exchange with the hydrogens of solvent water. These hydrogens, uniformly distributed at every amino acid (except proline) in every protein molecule, provide built-in, structure-sensitive, nonperturbing probes that can be used to study soluble or insoluble proteins under any desired conditions. Hydrogens that are freely exposed to solvent exchange at known rates that depend on pH, temperature, neighboring residues, and the hydrogen isotopes used (10,11). Hydrogens that are protected by structure, almost always in H bonds, exchange far more slowly. Their exchange is modulated by dynamic structural events that reversibly separate protecting H bonds and transiently expose them to the normal chemical exchange process. Accordingly, HX measurements can distinguish the presence and absence of protecting structure, determine the thermodynamic stability and dynamic properties of local and surrounding structure, and probe the effects of mutations, manipulations, and conditions, in principle, at amino acid resolution (12).The development of multidimensional solution NMR methods (13-15) has made high-resolution analysis of HX behavior routine for small soluble proteins (16). A fragment separation method that does not depend on solution NMR measurement extends HX studies to large proteins and insoluble protein systems (17)(18)(19). In this method, hydrogen isotope exchange can be performed under conditions that are most pertinent for the protein system being studied. Timed samples are then placed into slow HX condition...

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Probing the Structure of the Infectious Amyloid Form of the Prion-forming Domain of HET-s Using High Resolution Hydrogen/Deuterium Exchange Monitored by Mass Spectrometry

Cited by 31 publications

References 45 publications

β-Sheet core of human prion protein amyloid fibrils as determined by hydrogen/deuterium exchange

β-Sheet core of human prion protein amyloid fibrils as determined by hydrogen/deuterium exchange

Mass Analysis by Scanning Transmission Electron Microscopy and Electron Diffraction Validate Predictions of Stacked β-Solenoid Model of HET-s Prion Fibrils

Structure and properties of α-synuclein and other amyloids determined at the amino acid level

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