Conformational Polymorphism of the Amyloidogenic Peptide Homologous to Residues 113–127 of the Prion Protein

Abstract

Conformational transitions are thought to be the prime mechanism of amyloid formation in prion diseases. The prion proteins are known to exhibit polymorphic behavior that explains their ability of "conformation switching" facilitated by structured "seeds" consisting of transformed proteins. Oligopeptides containing prion sequences showing the polymorphism are not known even though amyloid formation is observed in these fragments. In this work, we have observed polymorphism in a 15-residue peptide PrP (113-127) that is known to form amyloid fibrils on aging. To see the polymorphic behavior of this peptide in different solvent environments, circular dichroism (CD) spectroscopic studies on an aqueous solution of PrP (113-127) in different trifluoroethanol (TFE) concentrations were carried out. The results show that PrP (113-127) have sheet preference in lower TFE concentration whereas it has more helical conformation in higher TFE content (>40%). The structural transitions involved in TFE solvent were studied using interval-scan CD and FT-IR studies. It is interesting to note that the alpha-helical structure persists throughout the structural transition process involved in amyloid fibril formation implicating the involvement of both N- and C-terminal sequences. To unravel the role of the N-terminal region in the polymorphism of the PrP (113-127), CD studies on another synthetic peptide, PrP (113-120) were carried out. PrP(113-120) exhibits random coil conformation in 100% water and helical conformation in 100% TFE, indicating the importance of full-length sequence for beta-sheet formation. Besides, the influence of different chemico-physical conditions such as concentration, pH, ionic strength, and membrane like environment on the secondary structure of the peptide PrP (113-127) has been investigated. At higher concentration, PrP (113-127) shows features of sheet conformation even in 100% TFE suggesting aggregation. In the presence of 5% solution of sodium dodecyl sulfate, PrP (113-127) takes high alpha-helical propensity. The environment-dependent conformational polymorphism of PrP (113-127) and its marked tendency to form stable beta-sheet structure at acidic pH could account for its conformation switching behavior from alpha-helix to beta-sheet. This work emphasizes the coordinative involvement of N-terminal and C-terminal sequences in the self-assembly of PrP (113-127).

β-Lactoglobulin Assembles into Amyloid through Sequential Aggregated Intermediates

“…33 The amide I infrared absorption or Raman band has been observed to lose intensity associated with the native state and to gain intensity associated with cross-β. 25,32,34,35 Circular dichroism of the peptide backbone absorption band is also sensitive to secondary structure and has given similar results. 36,37 Fluorescence spectroscopy has been used to detect conformational changes either by noncovalent labeling with dyes such as 1-anilino-8-naphthalenesulfonate (ANS) that are specific for exposed hydrophobic patches [38][39][40][41] or by covalent attachment of fluorescent dyes.…”

“…18 Many amyloidogenic peptides and proteins exhibit conformational polymorphism; they can exist in multiple stable conformations. 32 Conformational changes are typically observed during amyloid assembly. In their native state, the precursor proteins may not, in general, contain the secondary structural elements present in the final amyloid assembly.…”

From conversion to aggregation: Protofibril formation of the prion protein

“…Residues 109-122 encompass the E1 region in our model, which supports our finding that the hydrophobic N-terminal residues increase the extended structure of PrP by backbone hydrogen bonding to the preexisting ␤-sheet. Experimentally, this region prefers extended conformations to helical conformations under certain conditions (30,31), and it can take on more than one type of extended form (29). In addition, a peptide from this portion of the sequence (residues 106-126) is neurotoxic (19,49).…”

“…By using a structure from this ensemble, we modeled a prion aggregate that agrees with electron microscopy (EM) data from in vitro infectious Syrian hamster and mouse PrP two-dimensional protofibril crystals (24). Other experimental results such as changes in PrP C antibody binding sites (25,26), PrP Sc selective epitopes (27), differential proteinase K digestion (13,28), fiber diffraction (29), solid-state NMR (30)(31)(32), and peptide binding studies of PrP Sc (33)(34)(35) are consistent with our model.…”

Molecular Dynamics Simulations and Free Energy Analyses on the Dimer Formation of an Amyloidogenic Heptapeptide from Human β2-Microglobulin: Implication for the Protofibril Structure

“…One of the stabilization forces of the fibril structure is likely to be the main-chain hydrogen bonds. Apart from structural characterization of amyloid-related proteins, considerable effort has been devoted to smaller amyloid-forming peptides, mostly fragments from prion protein [10][11][12] and amyloid b protein. 13,14 A recent breakthrough was the high resolution structure of an amyloid-like fibril of the peptide GNNQQNY originated from yeast prion by X-ray crystallography.…”