Insights into Structural Properties of Denatured Human Prion 121-230 at Melting Temperature Studied by Replica Exchange Molecular Dynamics

Investigation of the conformation of human prion protein in ethanol solution using molecular dynamics simulations

When the conformation of protein is changed from its natural state to a misfolded state, some diseases will happen like prion disease. Prion diseases are a set of deadly neurodegenerative diseases caused by prion protein misfolding and aggregation. Monohydric alcohols have a strong influence on the structure of protein. However, whether monohydric alcohols inhibit amyloid fibrosis remains uncertain. Here, to elucidate the effect of ethanol on the structural stability of human prion protein, molecular dynamics simulations were employed to analyze the conformational changes and dynamics characteristics of human prion proteins at different temperatures. The results show that the extension of β-sheet occurs more easily and the α-helix is more easily disrupted at high temperatures. We found that ethanol can destroy the hydrophobic interactions and make the hydrogen bonds stable, which protects the secondary structure of the protein, especially at 500 K.Communicated by Ramaswamy H. Sarma.

Characterizing the denatured state ensemble of ubiquitin under native conditions using replica exchange molecular dynamics

The representative structures of the denatured state ensemble of ubiquitin under a native condition and heat-denatured ubiquitin simulated from a fully extended conformation.

Liberation of GPI-anchored prion from phospholipids accelerates amyloidogenic conversion

Prion diseases or transmissible spongiform encephalopathies are a rare group of fatal neurodegenerative illnesses in humans and animals caused by misfolding of prion protein (PrP). Prion protein is a cell-surface glycosylphosphatidylinositol (GPI)-anchored glycoprotein expressed mostly in the central and peripheral nervous system, and this membrane-bound protein can be cleaved from the cell membranes by phosphoinositide phospholipase C. Numerous studies have investigated GPI-free recombinant PrP, but the role of GPI on misfolding of PrP is not well known. In this study, we synthesized a GPI analog that was covalently linking to a PrP S230C mutant, resulting in S230C-GPI. The structural changes in S230C-GPI upon binding to lipid vesicles composed of mixtures of the zwitterionic lipid (POPC) and the anionic lipid (POPG) were analyzed by circular dichroism spectroscopy, and the amyloid aggregation of S230C-GPI in the liberation from phospholipid vesicles was monitored by proteinase K-digestion assay. Our results indicate that S230C-GPI in the liberation of lipid vesicles has high tendency to misfold into amyloid fibrils, while the membrane-bound S230C-GPI proteins are highly stable and rarely convert into amyloid forms. In addition, the role of cholesterol in S230C-GPI was studied. The effect of GPI, cholesterol and phospholipid vesicles on misfolding of PrP is further discussed.

Molecular dynamics simulations of amyloid fibrils: an in silico approach

Amyloid fibrils play causal roles in the pathogenesis of amyloid-related degenerative diseases such as Alzheimer's disease, type II diabetes mellitus, and the prion-related transmissible spongiform encephalopathies. The mechanism of fibril formation and protein aggregation is still hotly debated and remains an important open question in order to develop therapeutic method of these diseases. However, traditional molecular biological and crystallographic experiments could hardly observe atomic details and aggregation process. Molecular dynamics (MD) simulations could provide explanations for experimental results and detailed pathway of protein aggregation. In this review, we focus on the applications of MD simulations on several amyloidogenic protein systems. Furthermore, MD simulations could help us to understand the mechanism of amyloid aggregation and how to design the inhibitors.