Farklı prıon proteini varyantlarının yanlış katlanma mekanizmalarının moleküler dinamik simülasyonları ile araştırılması

Transmissible Spongiform Encephalopathies(TSE) are fatal neurodegenerative diseases. Examples are: bovine spongiform encephalopathy (BSE) in cow, scrapie in sheep and Creutzfeldt Jakob disease (CJD) in humans. A misfolded version of a protein named prion causes these diseases. Properly folded protein(PrPC) is rich of α-helix. The misfolded protein (PrPSc) contains less α-helix and is mostly comprised of β-sheets. Encounter of PrPC and PrPSc catalyzes the misfolding and disease propagation. The disease is transferred between individuals via transfer of these proteins. PrPSc can create oligomers or fibrils. The N-terminus of this protein is disordered and it is believed that it binds Cu2+. The ordered part at the C-terminus is comprised of 3 α-helices and 2 β-strands in the correctly folded state. In the literature, the part of the protein which causes the disease is controversial. Also, the misfolded shape and misfoling pathways are unknown. The predominantly accepted idea is that helices 2 and 3 (H2 and H3) at the C-terminus create a β-sheet by misfolding. Existance of more than one misfolded shape and pathway is also possible. However, the 3-dimensional PrPSc shape is still unknown and there is a need for researches on this subject. This study will contribute to enlighting of these misfolding pathways by using molecular dynamic simulations. One of the most common form of TSE is scrapie. For scrapie development, the 136th, 154th and 171st residues are important. This study focuses on 3 variants. First of these variants is weakly resistant wild type (ARQ: A136, R154, Q171), the second one is the most susceptible mutant (VRQ: V136, R154, Q171) and the other one is the most resistant mutant (ARR: A136, R154, R171). Simulations have been made with generalized Born continuum solvation method and Amber ff10 force field at 310 and 330 Kelvin. Simulation durations are 400-700ns. Fluctuated regions (except termini) of the proteins in all 3 simulations at 310K are: 1) H1 and the loop between H1 and β-strand 1(residues 135-149); 2) the loop between β-strand 2 and H2 (residues 168-177); 3) C-terminus of H2 and the loop between H2 and H3 (residues 186-204). Movement of the region between 168-177 is similiar in all 3 variants. In the other two regions, the magnitude and direction of the movements are found to be different in all 3 variants. ARR which is the most resistant variant has the lowest mobility. VRQ, the most susceptible variant, is the most mobile variant in the simulations. Therefore, it is seen that there is a relation between susceptibility and mobility. Especially, in VRQ, H1 is relocated with respect to H3. Position of H1 in the other two variants (ARR, ARQ) is not too far from crystal structures. Hence it is seen that valine as the 136th residue has an effect regarding the reposition of H1. The other two variants have alanine instead of valine as the 136th residue. In order to accelerate the conformational changes, simulations have been performed at 330 K and H1 has changed its position in all these simulations, including ARR and ARQ. In addition, VRQ has deformed its β-sheet in the 330 K simulations. These results are compatible with the 'banana peeling model' which suggests that relocation of H1 is necessary for the conversion of H2 and H3 to β-sheet.