Amyloid aggregation prediction algorithms identified two short peptides from ORF6 and ORF10 that are likely to form amyloids
Figure 1 shows selected output from bioinformatics tools applied to predict the amyloidogenicity of peptide sequences within larger polypeptides. Application of the ZIPPER tool to ORF-6 provides more than 10 choices of six-residue windows of the sequence predicted to be highly amyloidogenic (Figure 1a), while ORF10 shows only 3 such highly amyloidogenic sequence windows (Figure 1b). To narrow down our search for candidate peptides we also used the TANGO algorithm, for ORF6 there are two regions that are predicted to be highly aggregation prone, I14LLIIMR and D30YIINLIIKNL. The region I14-R20 overlaps almost perfectly with the hexapeptide I14LLIIM identified by ZIPPER. The region 30-40 also contains multiple hits in ZIPPER, but as this study was limited to two candidate peptides we chose ILLIIM as our first candidate as it closely resembles the sequence ILQINS from Hen Egg White Lysozyme which has previously been seen to be highly amyloidogenic (the mutation TFQINS in human lysozyme is disease-linked).43–45 Looking now at the TANGO plots for ORF-10 the main aggregation prone sequence is residues F11TIYSLLLC, although there are no high stability hexapeptides in this sequence predicted by ZIPPER. The octapeptide R24NYIAQVD was chosen due to its zwitterionic residue pair R-D which physically should strongly enhance interpeptide association, despite being too far apart in the sequence to trigger the highly local bioinformatics algorithms. Encouragingly ZIPPER also predicts the hexapeptide NYIAQV contained within RNYIAQVD to be highly amyloidogenic. Based on the outputs from ZIPPER and TANGO and also on experience of making and studying amyloid we selected RNYIAQVD and ILLIIM to be synthesised and their amyloid forming capability investigated.
Nanoscale imaging reveals both peptide sequences self-assemble into fibrillar structures
AFM imaging of the two peptide assemblies revealed that both peptides assembled in as little as 2 hours at 1 mg mL−1 (figures S1 and S2) into needle-like crystalline assemblies. AFM and TEM imaging of assemblies formed at either 1 or 5 mg mL−1 for 24 h revealed that assemblies from both peptides tend to stack on top of each other forming multilaminar nanofibrillar structures (Figure 2a-d and S3-5). Evidence of lateral assembly of the needles was also observed but this appears to happen more frequently in the ILLIIM assemblies (figure 2g) compared to RNYIAQVD. ILLIIM tends to form very large (2-3 microns in width) multi laminar crystalline assemblies (Figure 2g). AFM was used to investigate the height of the individual assemblies of both ILLIIM and RNYIAQVD. Figure 2 a,b shows a line section through a multilaminar RNYIAQVD assembly and a step height of 5.5 nm. Similarly for ILLIIM (Figure S3) we see mulitlaminar stacking with heights that vary between 4-9 nm, in figure 2 c the step height analysis of a single ILLIIM assembly (no evidence of stacking) is over 12 nm tall. RNYIAQVD assemblies are seen to have single step heights varying from 5-20 nm (figure S4) suggesting a heterogeneous distribution of assembly widths.
Statistical analysis of the fibril widths and contour lengths was performed using the freely available software tool FiberApp.34 The analysis of fibril width distribution was taken from the z-axis (height) of the AFM images, both peptide assemblies show a heterogenous distribution of fibril widths due to the previously observed tendency of both assemblies (figure 2 f and h) to form multilaminar stacks. Analysis of the distribution of the contour length of the two assemblies showed a biphasic distribution of lengths for both fibrils with two broad sub-populations centred around 1 and 3 µm (figure 2j and 2l). The sub-population at 3 µm was seen to be much larger for the RNYIAQVD peptide (figure 2j) compared to the ILLIIM (figure 2l). This population of longer fibrils correlates with the observation from figure 2 that for RNYIAQVD longer, thinner assemblies are favoured (self-assembly via fibril extension) over the wider shorter assemblies more commonly seen for ILLIIM (assembly via lateral association of protofilaments). Analysis of the persistence length of the fibrils (figure S6) showed that whilst both peptides formed very straight linear fibrils, the stiffness of RNYIAQVD (λ = 41.92 µm) is greater than that of ILLIIM (λ = 31.96 µm).
X-ray scattering, spectroscopic characterisation and molecular modelling confirm the amyloid nature of the assemblies
Figure 3 shows the radially averaged 1D SAXS plots for ILLIIM and RNYIAQVD at the lower concentration studied (at the higher concentration, sedimentation made recording X-ray scattering spectra impossible). In the central part of the scattering curve the ILLIIM assemblies produced a slope with a q−2 dependence which is consistent with the form factor of an infinite 2D surface.43 Together with the AFM and TEM data this implies a wide flat ribbon architecture similar to that seen in related amyloidogenic short peptides.43,46 RNYIAQVD however, displays a q−4 dependence in the (later) central part of the scattering curve, appearing more towards the high-q limit. Porod’s law indicates that q−4 scaling (at high q but still less than 0.1Å−1) is consistent with any aggregates having sharp and well-defined flat (2D) surfaces but does not otherwise specify shape.47
Figure 3b shows the CD spectra of mature assemblies, of both peptides. Assemblies of ILLIIM display a quite simple spectrum indicating dominance of β-sheets, with a minimum between 225-230 nm and a strong maximum at 205 nm.43 The CD spectra of RNYIAQVD are less obvious and seem to resemble the typical spectra of a random polypeptide coil, except in that there is a well-defined minimum at 203 nm (a typical random coil is < 200 nm) and additional shoulder appears at around 215 nm.
To further investigate the predicted secondary structure of both peptide assemblies we employed the secondary structure analysis software BeStSel (figure S7).35,48 As expected from the classic shape of the spectra the predicted secondary structure of ILLIIM is exclusively made up of β-sheets (49 %) and β-turns (51 %). Interestingly, the BeStSel analysis predicts a mixture of right twisted and left twisted β-sheets, with a slight preference of left twist (30 % of the total structure) compared to right twist (19 %). RNYIAQVD however, appears to be composed of a more complex mixture of secondary structures, that are still dominated by β-sheets and β-turns (totalling 42 %). The remainder was composed of helical signal (23 %) and further backbone conformation which could not be assigned (35 %). Interestingly almost all of the β-sheets in RNYIAQVD are predicted to be right-handed, with only 0.9 % displaying a left-handed twist. Part-helical CD spectra do not necessarily imply helical structure, especially considering that a single octapeptide cannot literally be 23% helix (two residues). Backbone conformation as reported by CD correlates through sheet structure to assembled tertiary structure but no single level of organisation exclusively dictates any other, this is especially true in the case of coupling the twist of a peptide strand to the overall twist of the aggregate, which can relax to meet surface and shape-driven constraints through intersheet and interchain as well as intrachain degrees of freedom.43
The amyloid nature of the two assemblies is further confirmed by the WAXS spectra (figure 3d) of the peptide assemblies which possessed a number of strongly diffracting Bragg peaks. Both peptides have a clear peak at 1.38 Å−1 corresponding to a d-spacing of 4.6 Å which is indicative of an amyloid assembly composed of extended β sheets.49 ILLIIM also has a very strong Bragg reflection at 0.58 Å−1 (11 Å) corresponding to a typical intersheet spacing given moderately bulky hydrophobic sidechains forming a steric zipper. RNYIAQVD has a number of well-defined Bragg peaks in between 0.3-0.8 Å−1 which are consistent with a mixture of first and second order reflections corresponding to an amyloid-like 3D symmetry. Discovery of sub-Å resolution structures from solution WAXS is highly challenging, however given the simple nature of the scattering from the ILLIIM system it was possible to produce an atomistic model matching the observed peaks. The sheet-like shape factor and the presence of peaks at roughly 2π/4.6 Å−1 and 2π/11 Å−1 indicate assembly dominated by the hydrogen bonding axis (with the typical parallel β sheet period of ≈ 4.8 Å) and by a sidechain-sidechain hydrophobic zipper interface. A candidate structure of size 6×50×1 peptides was constructed following this geometry and found to reproduce the observed WAXS and to fully exclude water at the steric zipper (figure 4).
Assembly Kinetics and cytotoxicity
The thioflavin T stain (ThT), which becomes highly fluorescent upon binding to β-sheets present in amyloid fibrils was used to assess the assembly kinetic of both ILLIIM and RNYIAQVD (figure 3c). Both peptides show rapid assembly kinetics reaching a plateau after 30-60 minutes. Longer amyloidogenic polypeptides typically show a distinct lag phase in their assembly kinetics, however this was not observed in these sequences. This apparent lack of a lag phase in the assembly kinetics behaviour is typical of amyloidogenic short peptides, which have been previously seen to assemble very rapidly.43,50 This is highly likely to be due to a lack of additional non-amyloidogenic amino acid sequences acting as a kinetic barrier to amyloid formation. The ThT signal for ILLIIM at 5 mg mL−1 plateaus at about 300 a.u., this is slightly stronger than the maximum signal generated from mature fibrils of the somewhat homologous peptide ILQINS, which was around 250 a.u.41,43–45 suggesting that the amyloidogenicity of the two peptides is comparable. RNYIAQVD, whilst showing similar ThT values at low concentrations (1 mg mL−1), generated a ThT signal nearly 3 times as large at 5 mg mL−1 suggesting that the assembly of this peptide is highly concentration dependent. For reasons yet unknown, it seems that RNYIAQVD appears to reach a maximum ThT value and then begin to drop, this can be seen at both concentrations but is most obvious at the higher concentration. This could be due to a reversible self-assembly as seen in other functional amyloids,46,49–51 or to self-quenching of the amyloid bound aromatic ThT molecules, or simply to a reduction of exposed ThT-binding sites as larger aggregates with a lower surface area to volume ratio come to dominate the solution.
Cytotoxicity of both studied peptides also began to drop slightly (without statistical significance) at the highest concentrations tested (vide infra, figure 5), together with the drop in ThT response this supports the existence of a kinetically or thermodynamically available aggregate structure with reduced ‘amyloid activity’. This is reminiscent of strongly amyloid correlated diseases such as AD, where the toxicity of amyloid can vary dramatically, with the relation between the amount of amyloid deposited to the progress of the disease being idiosyncratic and highly non-linear.52
ILLIIM and RNYIAQVD peptide assemblies are both highly toxic towards the neuroblastoma cell line SH-SY5Y
Given the physical evidence, and the discussions referred to in the introduction of various means by which SARS-CoV-2 and other viral infections could enhance their fitness (to the detriment of the host) by production of amyloidogenic peptides, we hypothesised that the SARS-CoV-2 viral transcript fragments ILLIIM and RNYIAQVD are toxic to human neurons. This is in particular supported by the previously reported neuroinvasive capabilities of SARS-CoV-2,7,8 the noted similarities of the symptoms to a (hopefully transient form of) Alzheimer’s disease5 and the previous detection of amyloid assemblies driven by other viruses.21 To investigate this further we performed cytotoxicity assays of the two peptide sequences against a human derived neuroblastoma cell line (SH-SY5Y) often used as a model cell line for studying Parkinson’s and other neurodegenerative diseases.53 We found that both assemblies were highly toxic after 48 h incubation with the peptide assemblies. Concentrations as low as 0.05 and < 0.04 mM (for RNYIAQVD and ILLIIM respectively) were seen to reduce the viability of cultured cells after 48 h to > 50% (IC50) of the cell lines (Figure 5a,b). This toxicity in relation to concentration is similar to that reported for Aβ4254 although expression levels and time-scales (sudden for COVID versus chronic for AD) are likely to be very different.
To gain further insight into the mechanism of cell death occurring in the peptide exposed cells, we performed a detailed flow cytometry analysis using the apoptotic stain Annexin V and the viability dye 7-AAD. Figure 5c shows representative flow cytometry plots; cells can be identified as viable (bottom left quadrant), viable but undergoing early apoptosis (bottom right), necrotic (top left) or non-viable due to late-stage apoptosis (top right). The percentages of cells in these quadrants is roughly equal for all conditions tested except in the case of late stage apoptosis where we see a large increase in the cells exposed to the peptide assemblies (a 6.25 fold increase for RNYIAQVD at 2.5 mg mL−1). Quantification over a range of concentrations showed that on average cells exposed to both ILLIIM and RNYIAQVD had a 3-5 fold increase in late stage apoptosis compared to SH-SY5Y cells cultured in the absence of peptide assemblies (Figure 5d-e). No evidence of increasing necrosis was seen in any of the samples, suggesting that the amyloid assemblies are triggering programmed cell death via an apoptotic pathway. The mechanisms of cell death in neurodegenerative diseases are complex, and can vary between different diseases,55 and here we provide evidence that induction of apoptosis maybe an important mechanism of neuronal death in COVID-19. Intriguingly, the conserved protein ORF-6 from SARS-CoV (not SARS-CoV-2) has previously been shown to induce apoptosis.56 The toxic nature of these amyloid assemblies warrants further investigations into the potential presence of amyloid aggregates from SARS-CoV-2 in the CNS of COVID-19 patients, and the potential role of amyloids in the neurological symptoms observed.