There are several (P102L, P105L, A117V, M129V, G131V, Y145Stop, R148H, Q160Stop, D178N, V180I, T183A, H187R, T188R, E196K, F198S, E200K, D202N, V203I, R208H, V210I, E211Q, Q212P, and Q217R). The pathogenic conversion process from PrPC to PrPSc could be related to the thermal stability of PrPC [6], since the mutations related to familial forms of the prion diseases are rather concentrated in helices 2 and 3, and the thermodynamical stability profile shows that diverse residues in helices 2 and 3 are less stable [7]. Moreover, the conversion might also be related with the global conformational fluctuation of PrPC, as a Carr–Purcell–Meiboom–Gill relaxation–dispersion study revealed that slow fluctuation on a time scale of microseconds to milliseconds occurs, again, in helices 2 and 3[8],[9].

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PrPC has an intrinsically disordered N-terminal region, and a predominantly α-helical C-terminal region from residues ~120-230, containing three α-helices and two short . A connects the middle of helices 2 and 3. The presence of the N-terminal region has little impact on the structure of the C-terminal domain [1]. The structure of PrPC is highly conserved amongst mammals, and only differs slightly in birds, reptiles and amphibians[2]. The vast majority of structures have been determined by NMR spectroscopy, but two structures have been reported by X-ray crystallography. In sheep PrP, the X-ray structure is similar to those determined by NMR spectroscopy, however in human PrP, the X-ray structure is a dimer in which helix 3 is swapped between monomers, and the disulphide bond is rearranged to be intermolecular between the dimer subunits.

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In sporadic prion disease, the spontaneous refolding or misfolding of PrPC into PrPSc initiates the cascade. In genetic prion diseases, point mutations in PrP make this structural transition more likely to occur than in the wild type protein. Infectious etiology is explained by introduction of exogenous PrPSc which then initiates refolding of endogenous PrPC.

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The phenomenon of prion strains (disease subtypes with specific clinical, biochemical and neuropathological features, replicating with high fidelity) was initially difficult to equate with the "protein only" hypothesis of prion diseases. However, there is now evidence from a range if studies suggesting that strains are enciphered in the structure of PrPSc. One potential mechanism for this is alternate threading of the β-helix.

The naturally ocuring prion diseases include Creutzfeldt-Jakob disease (CJD) in people, bovine spongiform encephalopathy (BSE) commonly known as "mad cow" disease, scrapie in sheep and goats, and chronic wasting disease in deer. In all cases post mortem analysis of brain tissue is characterized by aggregates of PrPSc. The sporadic, genetic and infectious etiologies of prion diseases can be explained by a simple protein-based model in which PrPC is converted into PrPSc that in turn initiates an autocatalytic refolding cascade of PrPC in a template-dependent manner.

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The prion protein (PrP) is a cell surface glycoprotein, which can exist in two alternatively folded conformations: a cellular isoform denoted (PrPC) and a disease associated isoform termed PrPSc.

Fourier transform infrared (FTIR) spectroscopy, and circular dichroism (CD) studies first demonstrated that PrPSc had very different proportions of α-helices and β-sheet to PrPC[3]. There are a number of technical obstacles in determining the atomic resolution structure of PrPSc, and the most detailed information to date has been obtained by electron microscopy of 2D crystals[4]. Analysis of 2D crystals binding specific heavy metal ions, and of redacted constructs of PrP, provide a basis for structural modeling. A model the N-terminal region and part of the C-terminal domain, up to the disulphide bond, refolds into a β-helical structure[5]. Support for this β-helical model comes from the structure of the fungal prion Het-s (2rnm).

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