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Prion Protein Mutation Database

Architecture of PrP

In humans, a single exon encodes the 253 amino acid (aa) prepro-PrPC 1 (see PrP Gene Structure) of 32-35 kDa mass; differential splicing does not occur. A 22 aa signal peptide is cleaved from the N-terminus during synthesis in the endoplasmic reticulum and the 23 residue attachment signal sequence on the C-terminus is cleaved upon addition of a glycosyl phosphoinositol (GPI) anchor at serine 2302, through which PrPC tethers to the extracellular leaflet of the plasma membrane. Mature PrPC (residues 23-230) is composed of an independent and flexible, random coil N-terminal region (residues 23-124) and a rigid globular C-terminal domain (residues 125-230) – Figure 1. PrPC is correctly folded before being transported to the Golgi complex, where is it differentially glycosylated to either un-, mono- or di-glycosylated species of PrPC 3-4. The sequence and structure of PrPC is highly conserved across mammalian species. Insertions and deletions are the most common pathogenic mutations leading to prion disease in the N-terminal coil, whereas, in the globular domain, missense mutations predominate5 (see Schematic of Pathogenecity).

Figure 1: Architecture of PrP. Upper panel: the PRNP primary translation product, preproPrPC, formed of 253 amino acids (aa) with cleavable N- and C-termini signal peptide (22 aa) and GPI anchor (23 aa) sequences, respectively. This yields a 208 aa mature protein. Middle panel: mature PrPC domain annotation is shown. The charged clusters, CC1 and CC2, are shown in grey. The octapeptide repeat region, where binding of Cu2+ or Zn2+ occurs is shown in navy blue. The hydrophobic region is in powder blue, and the palindrome and conserved glycines are highlighted. Secondary structural elements are shown in sky blue for β-sheets and purple for the α-helices. The single disulphide bond in PrPC, between Cys179 and Cys214 is shown, as are the two variably occupied asparagine glycosylation sites at N181 and N179. Lower panel: the gross arrangement of PrPC is shown, with the N-terminal flexible coil and the globular C-terminal domain.

The unstructured N-terminal region of PrPC contains several important functional elements (Figure 1). The first region of importance spans residues 51-91; it contains a nonapeptide, PQGGGGWGQ, followed by an octapeptide repeat region [PHGGGWGQ]4  (aa 60-91)6 that coordinates copper and zinc with high affinity7-12. There are also two polybasic charged clusters, CC(KKRPK at residues 23-27) and CC2 (KPSKPKTNMK at residues 101-110), as well as an hydrophobic region (residues 112-134) containing an alanine-rich palindrome of residues AGAAAAGA (residues 113-120). It is of note that the octapeptide repeat domain is among the most highly conserved regions of the prion protein13. In contrast, the globular domain contains all the acidic residues of the chain14. The complementary polybasic stretches, (CC1 and CC2) in the N-terminus and electronegative surfaces from the globular C-terminus, provide the mechanism for molecular compaction that is stabilised by Cu2+ and Zn2+ binding14.

The PrPC N-terminus binds both copper and zinc in vivo and participates in metal ion homeostasis (see PrP Function). Cu2+ and Zn2+ ions coordinate to the N-terminal differently – Cu2+ interacts with the octapeptide repeat domain11-12, and also with residues His96 and His1119-10, whereas, all four histidine residues in the octapeptide repeat domain coordinate a single Zn2+ ion with a dissociation constant of approximately 200 mM9,15-16. Residues HGGGW in each octapeptide repeat constitutes the fundamental Cu2+-binding unit10. Most of the copper ions bind in a domain composed of tandem PHGGGWGQ repeats. At low Cu2+ occupancy, coordination is provided by three or four His imidazoles; at high occupancy, coordination is from the His imidazole and deprotonated amide-nitrogen atoms of the two Gly residues that immediately follow His (Figure 2). The high occupancy coordination mode stabilises Cu2+ over Cu+ and thus suppresses copper-redox activity. The affinity for Cu2+ varies significantly, with Kd values of 0.12 nM at low occupancy and Kd 7-12 mM, at high occupancy. Such affinities are well matched to the known Cu2+ concentrations in the synapse where PrP is localised and is highly suggestive of a role in neuronal metal ion homeostasis10,15.

Figure 2: Chemistry of the Cu2+-octapeptide repeat interaction. Panel A shows the Cu2+-HGGGW complex at high occupancy, involving coordination through deprotonated amide nitrogens and exhibits weaker affinity characterised by a Kd in the range of 7.0 – 12.0 mM. Panel B shows binding at low occupancy, which favours multiple His coordination and binds the octapeptide repeat domain with a lower dissociation constant (Kd 0.12 nM), and thus, higher affinity10.

Beyond localised coordination, both Cu2+ and Zn2+, promote long-range quaternary structure interactions in PrPC 17-18; octapeptide repeat metal binding results in a cis interaction between the flexible N-terminal domain and the globular C-terminus, an association that is stabilised by electrostatic charge complementarity between the polybasic N-terminus clusters, CC1 and CC2, and a negatively charged patch on the C-terminal globular domain14,19. There is emerging evidence to suggest that this interaction serves as a critical regulatory element in PrP physiology and in suppression of neurotoxicity15-16,19. Evans et al19 have shown that Cu2+-bound octapeptide repeat region interacts with a specific region of the globular C-terminal domain defined by the exposed surface of α-helices 2 and 3, as well as the N-terminal portion of α-helix 1 (mouse PrP numbering: α-helix 1, I138, F140-W144, Y149-R150; α-helix 2, N172, V175-H176, V179-N180, T187; α-helix 3, E199, E206-R207, E210-Q211). The N-terminus interacts with the same globular domain surface (mouse PrP numbering: α-helix 1, M137, I138, F140-D143, D146, Y149-R150, N152-M153; α-helix 2, Q171, N172-N173, H176-D177, V179, I181, T187-V188, T190, G194, α-helix 3, D201, E206, V209, Q211) when studied using Cd2+ as a proxy for Zn2+ 16. Notably, the globular domain docking surface is formed of a highly conserved, electronegative pocket15,19 and these residues overlap with the epitopes of PrP antibodies known to cause severe acute neurotoxicity15,20-21.

The majority of PRNP gene mutations that give rise to human prion disease are point mutations located in helices α2 and α3, and often involve amino acid substitutions that attenuate the overall negative charge of this domain5,22-23. Furthermore, with Zn2+ coordinated, several point mutations corresponding to human PrPC mutations E200K and D178N, were shown to decrease the apparent strength of this cis interaction17. Patients with octapeptide repeat insertion mutations, have an earlier onset of prion disease5,22, and this may, in part, be due to alteration of the cis interaction with the globular C-terminal domain. Deletion of one octapeptide repeat occurs as an uncommon polymorphism in the European population22, however, deletion of two repeats is pathogenic5,24. This again may relate to disruption of the N-terminus-C-terminus structural dynamics, as at least three octapeptide segments are required to bind Cu2+ and mediate the interaction9,19. It is therefore, plausible that a disruption of metal-mediated cis interaction, and hence of the quaternary PrP fold, may be a causative factor in prion-mediated toxicity and certain inherited prion diseases. In support of this notion, is the finding that both Cu2+ and Zn2+ arrest in vitro PrPSc amplification17,25. It is then interesting to note that deletion of the entire N-terminal domain is found to be benign in transgenic mice26 and this protein retains its conversion potential to PrPSc 27. However, internal N-terminal deletions that retain the CC1 cluster are neurotoxic26 and deletions that leave greater portions of the N-terminus intact are progressively more neurologically damaging15,28.

The N-terminal hydrophobic region (residues 112-134, Figure 1) has a predicted high propensity for β-sheet secondary structure, thought to undergo significant structural transition following prion infection – as antibodies directed toward mouse PrP residues 90-120 detect PrPC but not PrPSc 29 – and is proposed to be involved in PrPc-PrPSc interaction, as a misfolding initiation site that effects prion propagation30-32. Indeed, cells transfected with a PrP transgene that expresses mutant PrP with a deletion of the AGAAAAGA palindrome (residues 113-120) cannot be infected with PrPSc 33, indicating the necessity of the palindrome for PrPC to PrPSc conversion. Furthermore, peptides that include the AGAAAAGA region inhibit in vitro conversion of PrPCto PrPSc in a cell-free conversion model, again underlining the importance of these amino acids in the PrPC-PrPSc interaction and subsequent prion propagation34-35.

In addition to the palindrome, the hydrophobic core is glycine rich, and arranged in GXXXG motifs; a frequent motif in transmembrane a-helices that is reported to stabilise helix-helix associations and permit close packing of transmembrane domains36. The glycine residues in this region show perfect conservation across all mammalian species identified to date13,37-38 . Relatively conservative amino acid substitutions of the glycine residues in this region have been shown to diminish prion propagation and infectivity – reinforcing the importance of the hydrophobic region in conversion of PrPC to PrPSc 37-38. Furthermore, the most neurotoxic deletion mutant in mice, as determined by the relative amount of wild-type expression required to rescue the phenotype, involves deletion of the hydrophobic region, however, these PrPC mutants do not form PrPSc 15,28,39.

Conforming with the above findings, a Gly127Val polymorphism (in the hydrophobic domain, see Figure 3) localised to the region in Papua New Guinea affected by the Kuru epidemic, was found to confer resistance to Kuru5,40.  The protection provided by this variant was replicated in transgenic mice expressing human PrP41, whereby, heterozygous Gly127Val mice exhibited profoundly reduced susceptibility to infection with kuru and classical CJD prions, and Val127 homozygosity conferred complete resistance to all inoculated prion strains41. The structural mechanism underlying this intrinsic resistance to prion propagation has recently been elucidated42. It has been shown that the Val127 polymorphism alters the regional backbone geometry, and consequently facilitates greater stability of dimeric Val127 PrPC assembly through increased inter-molecular hydrogen bonding and extension of the dimer interface. This in turn, is thought to affect the conversion potential of Gly127Val to PrPSc and account for the powerful effect of this polymorphism on prion disease42. This proposed mechanism is supported by two lines of evidence: first, the PrPC dimerisation surface has been mapped to the hydrophobic region43; and second, PrPC dimerisation inhibits PrPSc and prion replication44-45. These findings contrast with the influential PrPC codon 129 polymorphism that also modulates prion disease susceptibility. Methionine is the ancestral amino acid at position 129 (Figure 3); 37% of the UK population are Met homozygotes, 12% are Val homozygotes, and 51% are Met/Val heterozygous at this site. At position 129, it is homozygosity for either methionine or valine that predisposes to iatrogenic and sporadic CJD, whereas the heterozygous state confers significant protection against these prion diseases. Unlike the mechanism revealed for the Gly127Val variant, this is thought to occur through inhibition of homotypic PrP interactions46-49. Of note, the Glu219Lys polymorphism, found in the Japanese population, is also associated with resistance to sporadic CJD50. It is similarly thought that variant Glu219Lys sequesters PrPC from PrPSc conversion by preventing homologous dimerisation, but this is suggested to occur through alteration of the surface charge distribution51.

The globular C terminus contains three α-helices (residues: α1, 144-154; α2, 173-194; and α3, 200-228) and a short anti-parallel β-sheet (residues: β1, 128-131 and β2, 161-164). These elements are assembled in two parts, β1-α1-β2 and α2-α3, in the hydrophobic core52-53. A single disulphide bond stabilises the globular domain and two variably occupied asparagine-linked glycosylation sites (N181 and N197) lie within a loop formed by the Cys179-Cys214 bridge53-56. It has been proposed that reduction of this disulphide bond, as could occur in intra-cellular compartments, may act as a structural trigger that initiates prion propagation57. The tertiary structure of mouse PrP globular domain was solved by NMR in 199658. Since that time, high resolution PrP structures have been determined for an array of mammalian species53,59-65; they have collectively revealed a highly conserved fold (Figure 3). Furthermore, comparison of PrPC purified from bovine brain, and recombinantly produced bovine PrP in Escherichia coli, displayed a similar structure, indicating that glycosylation and the GPI anchor do not affect the overall PrP fold66.

Figure 3: Sequence and structure conservation PrP across mammalian species. Annotated alignment of eleven selected mammalian species, for which a high-resolution PrP structure has been determined. Important functional regions in the N-terminus are highlighted as follows:  charged clusters CC1 and CC2 in grey, the octapeptide repeat region in navy blue and the hydrophobic region in powder blue. Secondary structural elements are highlighted in sky blue for β-sheets and purple for α-helices. The disulphide bond between Cys179 and Cys214 is shown, and the two variably occupied asparagine glycosylation sites at N181 and N179 are underlined. The following structures deposited in the Protein Data Bank were used: human 1QLX, bovine 1DX0, sheep 1XYU, elk 1XYW, mouse 1AG2, Syrian hamster 1B10, pig 1XYQ, cat 1XYJ, dog 1XYK, bank vole 2K56 and wallaby 2KFL.

Despite important scientific advances, the relationship between pathogenic PRNP mutations, PrP structure and prion disease phenotype remains incompletely understood. Mutations in the globular domain are predominantly concentrated in the region of the β2-α2 loop and in the α2-α3 inter-helical interface (Figure 4). See individual mutation pages for detailed discussion of each pathogenic missense variant – these can accessed through the PrP Mutation Map

Figure 4: Location of pathogenic mutations on PrPCA model structure of the prion protein, that includes the proposed metal-ion binding region is shown. The octapeptide repeat region is shown in navy blue, with a single Cu2+ ion coordinating His61, His69, His77 and His85 (as depicted schematically in Figure 2). The hydrophobic region is shown in powder blue. Secondary structural elements are sky blue for β-sheets and purple for α-helices. Black Cα spheres indicate the locations of possible, probable and definite pathogenic missense mutations in the prion protein (see Schematic of Pathogenicity). Glycans at Asn181 and Asn197and the glycosylphosphatidylinositol anchor are shown in light grey.


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