Molecular Simulation Studies on the Prion Protein Variants: Insights into the Intriguing Effects of Mutations

Prion diseases, or transmissible spongiform encephalopathies (TSE), are a group of rare fatal neurodegenerative maladies that affect humans and animals. The fundamental breakthrough in TSE research was the discovery of the "prion"⎯proteinaceous infectious particle⎯ and the verification of the “protein-only” hypothesis, which states that prions could self-propagate by converting the cellular prion protein (PrPC) into the scrapie form, PrPSc (or prions), and lead to neurodegeneration without using any nucleic acids. The concept of prions may unify neurodegenerative diseases under a common pathogenic mechanism. Indeed, growing evidence shows that TSE may share similar pathogenesis with common neurodegenerative syndromes such as Alzheimer’s disease and Parkinson’s disease, for which there are currently no cure. Today, PrP is one of the most studied models for protein misfolding mechanism and TSE serve as an excellent model for studying many other neurodegenerative diseases. Understanding the molecular mechanism of the PrP misfolding process may profoundly influence the development of diagnostics and effective therapies for neurodegenerative diseases in general. Investigating human (Hu) PrP TSE-linked mutations (more than 50 currently identified mutations, linked to ~15% of the cases) may be very instrumental in this respect, as it can provide hints on the molecular basis of the PrPC→PrPSc conversion. These mutations cause spontaneous TSE, which are likely due to modifications in the native structure of PrPC. They are located all over the structure. Polymorphisms (i.e. non-pathogenic, naturally occurring mutations) in the PrP gene have been found to influence the etiology and neuropathology of the disease in both humans and sheep. In transgenic (Tg) mice, artificial mutations can determine the susceptibility to the infection of different prion strains. Intriguingly, mouse (Mo) PrP containing artificial mutations (denoted MoPrP chimera, hereinafter) have very different effects in vitro: some MoPrP chimera were found to resist PrPSc infection, whereas some others did not; some of the resistant MoPrP chimeras even exhibited a protective effect (known as the dominant-negative effect) over the co-expressed endogenous wild-type (WT) MoPrPC. Most mutations are located in the folded globular domain (GD) while fewer are located in the intrinsically disordered N-terminal domain (N-term). The N-term of PrPC has been suggested to serve multiple functions in vivo, which likely relies on the structural flexibility of this domain. Therefore, characterizing the structural features of the N-term is central for investigating not only the mutations in this domain, but also the physiological role of the N-term. Based on previous studies in our lab, in this thesis we first applied molecular dynamics simulations to studying the impact of all the known Hu TSE-linked mutations in HuPrPC GD. We next applied the same approach to study the GD structure of MoPrP chimeras which contain one or two residues from Hu or sheep PrP sequence. By studying these PrP variants, we aim to identify the structural determinants of the mutants that may play a role in the PrPC→PrPSc conversion. Our calculations discovered that these mutants exhibit different structural features from those of the WT PrP GD mainly in two common regions that are likely the “hot spots” in the protein misfolding process. These features can be classified into different types that are correlated to the types of mutants (i.e. pathogenic, resistant or dominant-negative), thus hinting to the molecular mechanisms of PrPSc formation and propagation. We have then predicted the structure of the entire PrP N-term and the impact of the Hu TSE-linked mutations in this domain using a novel Monte Carlo-based simulation approach, PROFASI. PROFASI has already shown to provide structural predictions in a disordered protein such as α-synuclein. Our results are consistent with available experimental data and therefore firmly allow us to provide the first overview on the structural determinants of all Hu TSE-linked mutations in PrP.