Prion fibrils structural studies

IV. Recent Advances in Structural Studies of Amyloid and Prion Fibrils. 10... 

The contributions to this volume demonstrate that structural studies of fibrous /1-proteins, as well as prion and amyloid fibrils, have advanced rapidly thanks in large part to improved experimental techniques and better theoretical analysis of the ever-increasing structural data. It is also possible to learn from studies of naturally occurring silks (Dicko et al., this volume) howvariations in the conditions of production of silk threads from the same protein can produce a variety of /1-structures with very distinct... 

Govaerts et al. (2004) proposed a parallel /1-helix model for prion rods that is consistent in overall dimensions with their low-resolution EM studies of two-dimensional PrP 27-30 crystals (Wille et al, 2002). In this model, residues 89-174 form 4 coils, or complete helical turns (Jenkins and Pickersgill, 2001), of a left-handed, parallel /Hielix (Fig. 5B). The coils of one monomer are proposed to stack on the coils of another to form an extended triangular -structure. Three of these triangular units pack together to form the fibril (Fig. 5G and D). The G-terminal a-helices (a2 and a3) of monomeric PrP are proposed to retain their native structure in the fibril and pack around the outside of the trimer (Fig. 5G and D). The presence of these helices in the prion rods is consistent with antibody binding studies (Peretz et al, 1997), the presence of a disulfide bond (Turk et al, 1988), and FTIR measurements (Wille et al, 1996). 

What is the nature of the insoluble forms of the prion protein They are hard to study because of the extreme insolubility, but the conversion of a helix to (3 sheet seems to be fundamental to the process and has been confirmed for the yeast prion by X-ray diffraction.11 It has been known since the 1950s that many soluble a-helix-rich proteins can be transformed easily into a fibrillar form in which the polypeptide chains are thought to form a P sheet. The chains are probably folded into hairpin loops that form an antiparallel P sheet (see Fig. 2-ll).ii-11 For example, by heating at pH 2 insulin can be converted to fibrils, whose polarized infrared spectrum (Fig. 23-3A) indicates a cross-P structure with strands lying perpendicular to the fibril axis >mm Many other proteins are also able to undergo similar transformation. Most biophysical evidence is consistent with the cross-P structure for the fibrils, which typically have diameters of 7-12 rnn."-11 These may be formed by association of thinner 2 to 5 nm fibrils.00 However, P-helical structures have been proposed for some amyloid fibrils 3 and polyproline II helices for others. 1 11... 

Several studies since then have supported this suggestion, and now it is widely accepted that conformational change/structural perturbation is a prerequisite for amyloid formation. Structural perturbation involves destabilization of the native state, thus forming nonnative states or partially unfolded intermediates (kinetic or thermodynamic intermediates), which are prone to aggregation. Mild to harsh conditions such as low pH, exposure to elevated temperatures, exposure to hydrophobic surfaces and partial denaturation using urea and guanidinium chloride are used to achieve nonnative states. Stabilizers of intermediate states such as trimethylamine N-oxide (TMAO) are also used for amyloidogenesis. However, natively unfolded proteins, such as a-synuclein, tau protein and yeast prion, require some structural stabilization for the formation of partially folded intermediates that are competent for fibril formation. Conditions for partial structural consolidation include low pH, presence of sodium dodecyl sulfate (SDS), temperature or chemical chaperones. 

Sun Y, Breydo L, Makarava N, Yang Q, Bocharova OV, Baskakov IV (2007) Site-specific conformational studies of prion protein (PrP) amyloid fibrils revealed two cooperative folding domains within amyloid structure. J Biol Chem 282 9090-9097... 

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