Molecular Dynamics Simulations On The Folding And Aggregation Of Prion Protein

Prion diseases, also known as transmissible spongiform encephalopathy, are a series of fatal neurodegenerative disorders, which include Kuru, Fatal Familial Insomnia, Gerstmann-Straussler-Scheinker Syndrome in humans and Scrapie, Bovine Spongiform Encephalopathy in animals. The onset of prion disease is closely related to the abnormal folding and progressive aggregation of prion proteins (PrP). However, the mechanism underlying the transition from cellular prion protein (PrPc) to its pathologic form (PrPSc) has not been fully elucidated.The deeper comprehension of PrPC-PrPSc conversion is very critical to answer the central questions of prion disease, thus, it is necessary to gain insights into the structure of PrPSc.Due to the noncrystalline and oligomeric nature of PrPSc, it is very difficult to resolve its structure by regular experimental techniques. MD simulations can obtain unique high-resolution structural information to study the folding and disease-related misfolding of proteins. In this paper, we employed MD and its sampling enhanced algorithm REMD to simulate the folding and aggregation of prion protein and its critical sequences, which is important to the research of prion diseases and the rational drug design.In Chapter 1, we briefly described amyloid diseases, the structure and biophysical properties of prion and its critical sequences. A·general introduction of conventional MD and REMD simulations was also given. Furthermore, we summarized the researches of prion protein based on MD simulations and the methods applied in this field. In the other four chapters of the dissertation, we tried to elucidate the folding and aggregation of prion at different level.First, we explored the impacts exerted by the Cysl79-Cys214 disulfide bond on the structure of prion protein.Native prion protein contains a disulfide bond and the SS-bond plays a significant role in PrPC-PrPSc conversion. In Chapter 2,the dynamics of the wild type, reduced and C179A/C214A mutated prion were simulated for 100 ns respectively. Rupture of the disulfide bond leads to obvious structural changes. The HI helix shifts downward and outward and the elongation of P-sheet has also been observed. Furthermore, the hydrophobic core in prion has been perturbed. The structural alterations caused by breakage of the disulfide bond are similar to those resulted from acid environment, denaturing conditions or pathogenic mutations, which implies that the rupture of the disulfide bond alter the structure of PrP and may induce its misfolding.Then, we probed the conformational space and aggregation propensity of PrP106-126, which is a prion protein fragment corresponding to residues 106-126. The peptide exhibits similar properties to full-length prion and plays a critical role in the conformational transitions between cellular prion and its pathogenic pattern. Soluble oligomers of PrP106-126 are considered to be responsible for neurotoxicity. Thus, PrP106-126 can serve as the model of full-length prion. The conformational property of PrP106-126 and its aggregation behaviors are not clear. In Chapter 3, we studied the folding and dimerization of the peptide based on REMD simulations. The monomer of PrP106-126 displays significant structural flexibility and no stable structures have been sampled. The dimeric PrP106-126 still exhibits considerable structural diversities and the dimers are mainly stabilized by hydrophobic interactions. To further investigate the assembly of PrP106-126, the processes of trimer and tetramer formation were simulated by performing longtime (1 μs) conventional MD simulations. The spontaneous formation of oligomers has taken place. Stable oligomers which contain high contents of β-sheet have been sampled. Furthermore, the oligomers share similar structural element which is the β-hairpin structures formed in hydrophobic C-teminal with residue 118-120 in turn. The β-hairpin structures may maintain the oligomers of PrP106-126. The study provided the structural information of PrP106-126 in detail and gave further insights into the mechanism underlying the initial oligomerization of PrP106-126.Furthermore, we studied the conformational properties of PrP106-126 and its mutants more deeply. Experiments have shown that the A117V mutation enhances the aggregation of PrP106-126, while the H111S mutation abolishes the assembly. However, the mechanism of the changes in the aggregation behaviors of PrP106-126 upon the two mutations is not fully understood. In this study, REMD simulations were performed to investigate the conformational ensemble of the WT PrP106-126 and its two mutants A117V and H111S. The obtained results indicate that the three species are all intrinsically disordered but they have distinct morphological differences. The A117V mutant has a higher propensity to form P-hairpin structures than the WT, while the H111S mutant has a higher population of helical structures. Furthermore, the A117V mutation increases the hydrophobic solvent accessible surface areas of PrP106-126 and the H111S mutation reduces theexposure of hydrophobic residues. It can be concluded that the difference in populations of β-hairpin structures and the change of hydrophobic solvent accessible areas may induce the different aggregation behaviors ofthe A117V and the H111S mutated PrP106-126. Understanding why the two mutations have contrary effects on the aggregation of PrP106-126 is very meaningful for further elucidation of the mechanism underlying aggregation and the inhibitor design against aggregation process.Finally, we have investigated the folding and aggregation of the palindrome sequence, which is located in PrP106-126. The palindrome sequences AGAAAAGA (PrP113-120) of prion protein display strong propensity to form amyloid and are critical in the structural conversion. The mutation related with Gerstmann-Straussler-Scheinker Syndrome also occurs in this conservative region. However, the effects of the mutation on the structures and aggregation tendency of the peptide are still obscure. In Chapter 5, the 1-,2-,4-peptide systems of the palindrome sequence and its A117V mutant have been studied by performing REMD simulations. The simulations of monomers suggest that the mainstream structures of WT and A117V are both random coil and they also obtain helical structures. Differently, the intrinsic disorder of PrP106-126 has been enhanced by the A117V mutation. REMD simulations of 2-and 4-peptide systems indicate that the β-sheet contents as well as the populations of oligomers have been increased by the introduction of A117V mutation. This phenomenon may be caused by the enhancement of interchain interactions such as backbone hydrogen bonding and hydrophobic contacts induced by the A117V mutation. The work probed the effects of the A117V mutation on the structural properties and aggregation propensity of the palindrome sequences in atomic level, which is useful to the comprehension of prion disease and shed light on the origin of Gerstmann-Straussler-Scheinker syndrome.