Prion protein dynamics before aggregation

Abstract

Prion diseases, like Alzheimer's disease and Parkinson disease, are rapidly progressive neurodegenerative disorders caused by misfolding followed by aggregation and accumulation of protein deposits in neuronal cells. Here we measure intramolecular polypeptide backbone reconfiguration as a way to understand the molecular basis of prion aggregation. Our hypothesis is that when reconfiguration is either much faster or much slower than bimolecular diffusion, biomolecular association is not stable, but as the reconfiguration rate becomes similar to the rate of biomolecular diffusion, the association is more stable and subsequent aggregation is faster. Using the technique of Trp-Cys contact quenching, we investigate the effects of various conditions on reconfiguration dynamics of the Syrian hamster and rabbit prion proteins. This protein exhibits behavior in all three reconfiguration regimes. We conclude that the hamster prion is prone to aggregation at pH 4.4 because its reconfiguration rate is slow enough to expose hydrophobic residues on the same time scale that bimolecular association occurs, whereas the rabbit sequence avoids aggregation by reconfiguring 10 times faster than the hamster sequence.protein folding | protein aggregation | intramolecular diffusion | prion disease | astemizole P rion disease, also known as transmissible spongiform encephalopathy (TSE) is attributed to misfolding followed by ordered aggregation and accumulation of protein deposits in neuronal cells (1-3). According to the "protein-only" hypothesis, the central event in prion (PrP) pathogenesis is the conformational conversion of the cellular α-helical rich isoform, PrP C , into misfolded β-sheet rich isoform, PrP Sc (3-6). The infectious form PrP Sc is believed to catalyze the conversion of PrP C , thereby permitting transmission between individuals and species (3, 7-10). However, there is very little known about PrP C before ordered aggregation. No putative aggregation precursor structure has been definitively identified; the protein may even be completely unstructured. It is believed that PrP C repeatedly cycles between the cell surface (∼pH 7.0) and endocytic compartment that has a pH as low as 4. 4 (11, 12). Aggregated prion has been isolated from this compartment so it has been suggested that aggregation initiates in late endosomes (13,14). Also, the reduction of the disulfide bridge has been reported to augment misfolding in vitro and may play a significant role in prion pathogenesis (15)(16)(17)(18)(19)(20). However, the physical basis for aggregation of prion, particularly under certain solvent conditions, is still poorly understood.Protein folding is a diffusive search of the unfolded polypeptide chain over the energy landscape in conformational space for a minimum energy state (21). Intramolecular diffusion (diffusion of one part of the chain relative to another) plays a critical role by determining the rate at which an unfolded polypeptide chain finds its native state (22-25). It has been measured for various peptides and pro...

Microsecond sub-domain motions and the folding and misfolding of the mouse prion protein

“…Earlier studies have indicated that the dynamics in the U state of prion protein play a role in initiating misfolding and oligomerisation (Yu et al, 2012; Srivastava and Lapidus, 2017). In the current study it was shown that the fluctuations within the N state of the protein are responsible for the misfolding of the moPrP.…”

“…More importantly, unlike the protein used in the current study, the protein used for the force spectroscopy measurements had a disrupted disulphide bond, and it is known that disruption of the disulphide bond in the prion protein leads to its unfolding to a molten globule form (Maiti and Surewicz, 2001; Honda, 2018). Fluctuations in SHaPrP (90-231), which could be important in aggregation, had also been identified using Trp-Cys contact quenching experiments carried out at pH 4.4 (Srivastava and Lapidus, 2017). In that study, the data appeared to suggest that the fluctuations might arise from the U state, but that could not have been the case because several other studies have shown that SHaPrP (90-231) is natively structured at acidic pH (Bjorndahl et al, 2011; Donne et al, 1997), including at pH 4 (Khan et al, 2010).…”

Hijacking Endocytosis and Autophagy in Extracellular Vesicle Communication: Where the Inside Meets the Outside

“…A high load of energy is required for the activity of the proton pump to maintain the acidic conditions required for the activity of lysosomal enzymes (Mindell, 2012). A low pH could serve as a spark triggering protein aggregation as it was shown for prion conversion (DeMarco and Daggett, 2007;Srivastava and Lapidus, 2017). Indeed, a protonation-based model approach demonstrated that the partial unfolding and dissociation of one alpha-helices of PrP C result in the loss of critical longrange salt bridges, which favor the conversion to a PrP Sc -like structure (DeMarco and Daggett, 2007).…”

The role of water mobility in protein misfolding

“…These data indicate that the presence of these ions could have a great effect on both the water mobility in the solvation shell and protein mobility in vitro. The rate of dimerisation is directly linked to the rate of protein reconfiguration, where slow reconfiguration allows for dimerisation to occur, while fast reconfiguration reduces the likelihood of sustainable contacts that result in successful dimerisation 17 . The mobility of water increases in bulk and in the solvation shell in the presence of CsI compared to…”