Read with caution!
This post was written during early stages of trying to understand a complex scientific problem, and we didn't get everything right. The original author no longer endorses the content of this post. It is being left online for historical reasons, but read at your own risk.
Notes from March 2, 2012 – Day 2 of the prion workshop at Koch Institute
First, a clarification point: despite the confusing terminology sometimes used by researchers, none of the following three factors are perfectly correlated with one another. That is to say, each has been observed in the absence of each of the others:
1. Proteinase K resistance
2. Transmissibility (i.e. a “prion” state)
3. Toxicity (i.e. it kills you)
We discussed PrP structure and what’s known about its lifecycle. From the nucleus it passes through the ER and Golgi on its way to the cell membrane, where it spends most of its time hanging on the outside of the cell, though in some diseases (including FFI?) it is found on the inside of the cell. In murine PrP, codons 1-23 (at the N-terminus) and 231-254 (at the C-terminus) are cleaved off before translation. The final protein product contains a GPI anchor at the C-terminus which localizes PrP to the cell membrane, followed by a “core” region which appears to be relatively rigid (it doesn’t breathe much), then the octapeptide repeat region (PHGGGWGQ, x5 in mice and humans, x6 in cows), then a basic region rich in K and R at the N-terminus. (See also: this diagram of PrP and the location of different mutations). The octapeptide repeats are believed to be important for disease/infectivity based on the observation that the insertion of murine PrP repeats into yeast proteins promote the formation of prions. The octapeptide repeats also bind copper and manganese  provide multiple frames for potential overlap, and thus might be involved in seeding aggregation as well. The GPI anchor appears to play an important role in keeping PrP in its place on the membrane and possibly in preserving its correct conformation: lack of a GPI anchor causes cerebral amyloid angiopathy, a phenotype similar to Alzheimer’s  . Again, the issue of late onset was discussed: is it due to higher synthesis of PrP or reduced cleanup of PrP? Calpains can degrade PrP but it’s not known if increased calpain action would be good or bad– there is some evidence that the calpains may promote disease by cleaving PrP into toxic bits.
The debate over where PrP is expressed was also discussed. Some studies have shown it in neurons but not astrocytes, and some have shown the opposite, with very high expression in astrocytes. Some of this discrepancy may have to do with measurements taken at different stages– for instance RNAseq might detect high transcription levels, but translation could still be suppressed. Alternately PrP might be synthesized in astrocytes but transported elsewhere.
Finally we discussed several pathways related to PrP. Clusterin (CLU) is 100% coregulated with PrP; Pi4k2a is also strongly co-expressed with PrP. STI1 and Laminin both interact with PrP (as receptors?), GPX3 may have some relationship, and five genes share with PRNP the distinction of being associated with thalamic disease and being necessary in astrocytes: VAC14, ATRN, SMO, MT3 and HTT (Huntingtin). Clusterin may be of particular interest, as there is one SNP in Clusterin that is the second-highest Alzheimer’s risk factor after ApoE4. Any proteins that control sulfydril states inside and outside the cell would be of interest since the disulfide bond in PrP appears to be important in disease and it may be the case that D178N causes disease wholly or in part because it is proximate to C179 which needs to form a disulfide bond with C214 — perhaps the change in interactions around 178 makes this disulfide bond less stable or more difficult to form in the first place, leading to wider conformational changes.