In a recently published study bioRxiv* Preprint servers, researchers demonstrated the effects of an amyloidogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protein fragment called SFYVYSRVK (SK9) on the monomers and fibrils of α-synuclein (aS), a potential risk factor for Parkinson’s Illness .
Learn: Effect of a SARS-COV-2 amyloidogenic protein fragment on α-synuclein monomers and fibrils. Photo credit: NIAID
Although most people infected with coronavirus disease 2019 (COVID-19) fully recover from the disease, there is not much data on the long-lasting or delayed neurological consequences of SARS-CoV-2 infection. Loss of smell and other neurological deficits have been reported during acute SARS-CoV-2 infection. In addition, several reports have suggested the potential risk of Parkinson’s disease and other neurodegenerative diseases associated with SARS-CoV-2.
A likely mechanism of Parkinson’s disease post-COVID-19 is SARS-CoV-2-mediated amyloid formation as aggregates of aS. In vitro reports suggest that SARS-CoV-2 enhances aS-amyloid formation by interacting with amyloidogenic regions on the nucleocapsid (N), envelope protein (E), and spike (S) proteins.
A mechanism similar to Alzheimer’s disease, involving the formation of amyloid fibrils as an immune response to infection, leading to entrapment and neutralization of the pathogen has been hypothesized for the increased amyloid formation leading to Parkinson’s disease in COVID-19. However, in-depth information on exposure to SARS-CoV-2, the occurrence of fibrils and the resulting symptoms of the disease is not available.
About the study
In the present study, researchers investigated how the interaction of the SARS-CoV-2 residual fragment termed SK9, located at the C-terminus of the E protein, affected the conformational ensemble of aS monomers and the stability of two resolved ones Fibril polymorphs called Rod and affects the Twister structures.
A helix-rich model of the aS-monomer structure was resolved in the micellar environment using nuclear magnetic resonance (NMR) solution and stored in the Protein Data Bank (PDB) under the identification code: 1XQ8. The team assessed the binding of SK9 to aS and whether it changes the conformational ensemble of aS using a complementary set of molecular dynamics simulations. To evaluate the stability of the aS-fibril-rod and twister polymorphs, five-layer, two-protofilament decamers were generated using cryogenic electron microscopy (cryo-EM) structures.
Initial conformation of the α-synuclein monomer (a) as resolved by solution NMR (PDB ID: 1XQ8) and (b) after heating to 500 K to obtain a randomized extended conformation. The initial conformation for the fibril as deduced by cryo-EM structures is in (c) for the rod (PDB ID: 6CU7) and in (d) for the twister (PDB ID: 6CU8) polymorph shown. In (e) and (f) the corresponding structures are shown for the fibrils where the individual chains are extended to residues 38-120. Acidic residues are colored red and basic blue, while the SK9 segments are shown in yellow. The N and C termini are represented by green and orange spheres, respectively.
The results show that although the rod and twister polymorphs share a bent β-arc architecture, they have different inter-protofilament interfaces. While the interface in the twister polymorph was formed by the hydrophobic aggregation-initiating non-amyloid β-component (NAC) region from residues G68–A78, the preNAC region from residues E46–A56 encompasses the interface in the rod polymorph.
The C-terminal residues of the rod polymorph were more organized than those of the twister polymorph, implying a higher stability of the rod polymorph than the twister. Nonetheless, six common mutations of aS: A53V, A53T, A53E, G51D, H50Q, and E46K destabilized the preNAC site of the rod structure but did not disrupt the twister polymorph, likely resulting in a population shift from rod to twister.
Visual examinations show that the aS monomers were more stranded and extended in the presence of SK9. Furthermore, in the presence of SK9, the ensemble of the aS shifted to more solvent-exposed, loosely packed, and larger conformations. This conclusion implies that binding of SK9 exposes more hydrophobic residues in aS and likely alters aS amyloid monomer production by changing the ensemble towards more aggregation-prone conformations.
The interaction of SK9 further increases the selectivity of the aS ensemble in the rod-fibril seeding conformations by inducing higher flexibility, residue exposure, and reduced helix tilt, particularly in the E46-A56 segment, which changes during rod-fibril seeding. Polymorphs forms the interface between the protofilaments. In addition, the interaction between SK9 and the rod fibril significantly increased the frequency and lifetime of two contacts, E46-K80 and V52-A76.
Nevertheless, SK9 has little effect on the stability of newly formed or existing rod and twister fibrils. Although binding of SK9 stabilized twister fibril geometry, this did not lead to significant changes in twister fibril amounts.
Representative final configurations were extracted from (a) the experimentally determined twister-like α-synuclein fibril model (PDB ID: 6CU8) and (c) the extended model from simulations. Corresponding final snapshots extracted from simulations in the presence of the SK9 segment are shown in (b) and (d). N- and C-terminus are represented by blue and red spheres, respectively. For the extended model configurations in (c) and (d), only residues 43-83 are shown. The temporal evolution of the RMSD in the simulation of these systems is shown in (e) and the remaining RMSF in (f). We again calculate RMSD and RMSF only for the experimentally resolved region 43–83, ie neglecting the disordered and unresolved parts of the fibril models, considering all backbone atoms. Only some typical error bars are shown to make the numbers easier to read.
The study results suggest that since the mutations present in aS that affected rod fibril stability were associated with Parkinson’s disease, shifting the frequency within rod and twister fibrils increases the likelihood of developing Parkinson’s disease will change. This conclusion is particularly significant during COVID-19 as SARS-CoV-2 SK9 increases the likelihood of rod polymorph formation.
The study shows that the presence of SK9 changes the ensemble from aS to more aggregation-prone conformations. Interestingly, although the twister fibril was thought to be more cytotoxic, the interaction of SK9 resulted in a preference for aS monomer conformations that likely form the rod-shaped fibrils associated with risk for Parkinson’s disease.
However, additional simulations using other amyloidogenic segments of SARS-CoV-2 proteins, particularly in the S, are needed to understand whether this effect is selective for SK9. Furthermore, the study shows that binding of SK9 to the rod and twister fibril polymorphs had only a minor impact on the stability of these fibrils.
bioRxiv publishes preliminary scientific reports that are not peer-reviewed and therefore should not be relied upon as conclusive, guide clinical practice/health behavior, or be treated as established information.