Chemicals and reagents

The peptides (Mel and PP) were purchased from BACHEM (Switzerland) with the highest purity available. Wild-type α-synuclein plasmid construct (AS-pRK172) was gifted by Prof. Roland Riek, ETH Zurich, Switzerland. All chemicals and reagents, unless otherwise specified, were purchased from Sigma, USA.

Peptide oligomerization

To study the peptide oligomerization, Mel and PP were dissolved in 0.5 ml of 5% D-mannitol, 0.01% sodium azide, and pH 5.5 at a concentration of 2 mg/ml in 1.5 ml eppendorf tubes. The eppendorf tubes containing peptide solutions were placed into an EchoTherm model RT11 rotating mixture (Torrey Pines Scientific, USA) and rotated at 50 rpm inside a 37°C incubator. Similarly, to study the peptide oligomerization in the presence of heparin, PP and Mel were dissolved in 0.5 ml of 5% D-mannitol, 0.01% sodium azide, pH 5.5 at a concentration of 2 mg/ml in presence of 400 μM low molecular weight (LMW) heparin (MW 5 kDa, CalBioChem) in 1.5 ml eppendorf tubes and were incubated as described above. For SDS induced aggregation study, 25 μM of Mel in Gly-NaOH buffer (pH 9.2) was incubated with and without 2.5 mM SDS at 37°C.

The α-synuclein (AS) protein was expressed in E. coli (BL21) cells and purified as previously described by Volles and Lansbury [33] with slight modification [34,35]. To isolate the preformed AS oligomers, lyophilized protein (10 mg/ml) was solubilized in PBS (pH 7.4) as described before [34]. The protein solution was then centrifuged (18,000 x g, 4°C, 30 min), to remove any aggregated fibrillar species and the clear supernatant was injected in size exclusion chromatography (SEC) column (Superdex 200 10/300 GL). The elution was performed in the same buffer at 4°C with AKTA purifier (GE Healthcare) at a flow rate of 0.4 ml/min. The fraction close to the void volume (8.0 ml) contains oligomeric species [34], which were collected and used for further biophysical characterization and toxicity measurement. Monomeric fraction (close to 15 ml of elution) was also collected and used as control.

For isolating pure oligomers of Mel and PP, we used 10 KDa molecular weight cut-off (MWCO) Amicon Ultra (0.5 ml) centrifugal filters (Merck Millipore, Germany). These centrifugal filters were used as per manufacturer’s instructions. Two weeks incubated Mel and PP (in the presence of heparin) samples were used for isolating the pure oligomers by centrifugation method. Since monomeric Mel (2846.50 Da) and PP (4181.77 Da) have molecular weights below 10 KDa, during centrifugation, the upper fraction of filter retained mostly oligomeric species (retentate) and the flow-through fractions were mostly comprised of monomeric entities. The isolated retentates of Mel and PP were further used for biophysical characterization.

Circular dichroism (CD) spectroscopy

For the secondary structural analysis, CD spectroscopy was performed. For this study, 15 μl of each peptide solution (2 mg/ml) was diluted to 200 μl in 5% D-mannitol, 0.01% sodium azide, pH 5.5. The sample was then placed into a 0.1 cm path-length quartz cell (Hellma, Forest Hills, NY) and CD spectra were acquired at 25°C using JASCO J-810 CD spectropolarimeter. Spectra were recorded in the range of 198–260 nm. AS (monomers and oligomers) isolated from SEC were also used for CD spectroscopy. Three independent experiments were performed with each sample. CD spectra of Mel (25 μM) in the presence of SDS (2.5 mM) and liposomes were also recorded similarly. Smoothing of raw data and subtraction of buffer spectra were done as per manufacturer’s instructions.

Fourier transform infrared spectroscopy (FTIR)

Secondary structural analysis of two weeks incubated peptide samples (in the presence and absence of heparin) were carried out using FTIR spectroscopy. For this study, the samples were prepared as described before [34]. FTIR spectra were acquired in the spectral range of 1800–1500 cm^-1 with Bruker Vertex-80 instrument equipped with DTGS detector [34]. For each spectrum, 32 scans at the resolution of 4 cm^-1 were recorded and the resultant absorption spectra were deconvoluted and curve fitted in the amide-I region (1700–1600 cm^-1) as per manufacturer’s instructions.

Atomic force microscopy (AFM)

To evaluate the morphology of oligomers, AFM analysis was performed. For this study, the samples were diluted to a final concentration of 10 μM (in double distilled water) and spotted on a freshly cleaved mica sheet for 1 min at room temperature (RT). The mica sheets were then washed with double distilled water and dried in a vacuum desiccator. The imaging was done using Veeco Nanoscope IV Multimode AFM in tapping mode with etched silicon cantilever. Minimum five different areas of three independent samples were scanned with a scan rate of 1.5 Hz.

Electron microscopy (EM)

To study the morphology of oligomers under an electron microscope, samples were diluted with double distilled water to reach the peptide concentration of 50 μM. The diluted solutions were spotted on a glow-discharged, carbon-coated formvar grid (Electron Microscopy Sciences, Fort Washington, PA), incubated for 5 min on the grid and washed with double distilled water two times, and finally stained with 1% (w/v) aqueous uranyl formate solution. The air-dried EM grids were used for the imaging. EM analysis was performed using the electron microscope (FEI Tecnai G2 12) at 120 kV with nominal magnifications in the range of 26,000 to 60,000. Images were recorded digitally using SIS Megaview III imaging system. At least two independent experiments were carried out for each sample.

Dynamic light scattering (DLS) experiment

DLS experiment was performed using DynaPro-MS800 instrument (Protein Solutions Inc.). It monitors the scattered light at 90° relative to the excitation. A 50 μl of 2 mg/ml solutions of two weeks incubated peptides (in the presence and absence of heparin) was used for size analysis using DLS. Water, buffer alone and buffer with heparin were used as controls. The preformed AS oligomers (isolated from SEC) were also used for size analysis. For each sample, at least 30 measurements each with 5-s duration were performed. Two sets of experiments were performed independently and raw data were processed with the software provided by the manufacturer.

Thioflavin T (ThT) binding assay

To analyze the amyloidogenic nature (tinctorial properties) of peptide oligomers, ThT binding assay was performed. For this study, a 5 l aliquot of each sample was diluted to 200 μl in 5% D-mannitol and 2 μl of 1 mM ThT was added to it. The samples were then excited at 450 nm and emission spectra were recorded in the range of 460–500 nm using Horiba-JY (Fluoromax 4) spectrofluorometer. Three independent experiments were performed for each sample and the emission intensity values at 480 nm were plotted. The slit widths of 5 nm were used for both excitation and emission. For measuring the ThT binding of Mel (incubated with SDS), 4 μl ThT was added to 200 μl solution containing 25 μM of Mel. ThT binding was performed immediately after addition of SDS (d0) and also after 5 days of incubation (d5).

Congo red (CR) binding assay

To evaluate the amyloidogenic properties of Mel and PP oligomers, CR binding assay was performed [36]. For this study, 20 μl aliquot of incubated sample was mixed with 150 μl of PBS buffer (containing 10% ethanol). Then 30 μl of 100 μM CR solution (prepared in PBS containing 10% ethanol) was added to the samples and incubated for 10 min in dark at RT. After this, the CR absorbance was measured in the range of 300 to 700 nm using JASCO V-650 spectrophotometer. Similarly, CR absorbance of AS monomers, AS oligomers, and CR alone were recorded as controls. Three independent experiments were performed for each sample and the absorbance values at 510 nm were plotted.

Prediction of oligomerization propensity

The intrinsic oligomerization ability of Mel and PP was calculated (at pH 5.5) using Zyggregator software [37] with default parameters.

Dot blot assay

Dot blot assays were performed with oligomer specific A11 [5] and fibril specific OC antibody [38]. For this study, two weeks incubated peptide samples (in presence and absence of heparin) and AS oligomers isolated from SEC were used. AS monomers (isolated from SEC) and preformed AS fibrils were also used as controls. For this, 5 μl of each sample was spotted on the nitrocellulose membrane (Immobilon-NC, Millipore) and then air-dried for 10 min at RT. After the air-drying, two subsequent washes (2 x 8 min) were performed with PBST (137 mM NaCl, 2.7 mM KCl, 10 mM Na₂HPO₄, 2mM KH₂PO₄, and 0.1% tween 20). The blots were then blocked with 5% non-fat milk powder (Himedia, India) in PBST for 1 h at RT and then incubated with oligomer specific A11 antibody (dilution-1: 500, AHB0052, Invitrogen). Another blot was used for fibrils specific OC antibody (dilution-1: 600, AB2286, Millipore). The incubations were performed at 4°C. After overnight incubation, blots were washed twice (2x8 min) with PBST and again incubated with horseradish peroxidase (HRP) conjugated secondary antibody (dilution-1: 1000, Cat. 401253, Calbiochem). Finally, three subsequent washes were performed with TBST (50 mM Tris, 150 mM NaCl, and 0.1% tween 20) and the blots were developed with chemiluminescent substrate (West Pico, Pierce Thermo Scientific, USA).

Cell morphology analysis

To evaluate the cellular toxicity of oligomers, morphology analysis of oligomers treated and untreated SH-SY5Y cells were performed. In brief, cells were seeded onto sterile coverslips at a density of 10,000 cells per well in 24 well cell culture dish and incubated for 24 h. After incubation, media were discarded. Fresh media with peptide samples were added to the cells such that the final peptide concentration was 10 μM. As a control, a similar volume of D-mannitol was also diluted in media and added to cells. The cells were further incubated in a 5% CO₂ humidified environment at 37°C. After 30 h of incubation, cell morphology was directly visualized under phase contrast microscope (Olympus IX-51).

Lactate dehydrogenase release (LDH) assay

To quantify the cellular toxicity of oligomers, lactate dehydrogenase (LDH) release assay [39] was performed using SH-SY5Y neuronal cell line. SH-SY5Y cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) (Himedia, India) supplemented with 10% FBS (Invitrogen, USA), 100 units/ml penicillin and 100 μg/ml streptomycin in a 5% CO₂ humidified environment at 37°C. For LDH assay, cells were seeded in 96-well plates in 100 μl medium at a cell density of ~10,000 per well and incubated for 24 h. After incubation, cell culture medium was replaced with fresh medium containing different concentrations of oligomers (2.5 μM, 5.0 μM and 10 μM) and cells were incubated for 30 h. AS monomers and freshly dissolved Mel were also used in this experiment. After incubation, LDH assay was performed using LDH toxicological kit (TOX-7, Sigma, USA), according to the manufacturer’s instructions. For positive control (100% cell death), 0.5% TritonX-100 was used and only 5% D-mannitol alone in cell culture media was used as a negative control. The percentage of cell death was calculated by considering 100% cell death, when cells were treated with 0.5% TritonX-100.

Liposome preparation

Liposomes were prepared using 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dipalmitoyl-sn-glycero-3-phospho- (1'-rac-glycerol) (sodium salt) (Lipoid GmbH, Germany) (DPPG). Chloroform-containing lipid solutions were dried in a rotary vacuum evaporator in order to obtain a thin film. Residual chloroform was removed under vacuum. For cryo-SEM studies, the lipid film was hydrated in phosphate buffer saline (PBS), pH 7.4 for 30 min at 45°C and then used. For the calcein release assay, the dried lipid film resulting from evaporation was resuspended in 25 mM aqueous calcein dye (Sigma, USA), which was prepared in 2N NaOH and the pH was adjusted to 7.4 in PBS (pH 7.4). The resuspended solution, at a final lipid concentration of 4 mg/ml, was incubated for 30 min at 45°C with 100 rpm rotation to allow the vesicle formation. After 30 min, the lipid suspensions were sonicated at 40 KHz, 40% amplitude for 3 min to form small unilamellar vesicles (100–200 nm diameters). To remove the excess calcein, the solution was centrifuged at 4°C for 30 min with a speed of 18,000 x g and the supernatant was discarded. The pellet was suspended gently in PBS (pH 7.4) and the centrifugation was repeated thrice. The calcein-loaded liposome was diluted to 100 fold in PBS and the calcein fluorescence was measured before and after adding 0.5% Triton X-100. After treatment with Triton X-100, high increase in calcein fluorescence (excitation at 490 nm, emission in the range of 500–600 nm) was obtained, however, very minimal calcein fluorescence (~10%, background fluorescence) was observed in the absence of Triton X-100. The liposomes were used immediately for the study.

Liposome damage study

To visualize the oligomer mediated liposome damage; freshly prepared liposomes (~400–700 nm diameters) were used in the study. The liposomes were diluted to 100 fold in PBS (pH 7.4) and incubated with 10 μM oligomers (Mel and PP) in a reaction volume of 50 μl at RT for 30 min. After incubation, morphology of treated and untreated liposomes was visualized using cryo-FEG SEM (JSM-7800F-thermal field emission scanning electron microscope, JEOL).

Nile Red (NR) binding assay

NR is a hydrophobic dye that is frequently used to measure the extent of hydrophobic surface exposure of proteins/peptides [35,40]. Preformed AS oligomers and two weeks incubated Mel/PP samples were diluted in 200 l of 5% D-mannitol such that the final concentration became 10 μM in which 0.2 l of 1 mM NR (prepared in DMSO) was added to the solution. The mixture was incubated for 5 min in dark at RT. The NR fluorescence was recorded using Horiba-JY (Fluoromax 4) with excitation at 550 nm and emission from 565–750 nm. The excitation and emission slit widths were 2 nm and 5 nm, respectively. For controls, fluorescence spectra of NR alone and NR in presence of AS monomers (isolated from SEC) were also recorded under similar conditions.

Planar bilayer recordings

Artificial bilayer lipid membrane (BLM) was constructed from 1, 2-diphytamoyl-sn-glycero-3-phosphocholine (DPhPC; Avanti Polar Lipids, Alabaster. AL). DPhPC, dissolved in n-decane (20 mg/ml) was painted in a small aperture (150 mM diameter), partitioning two aqueous chambers in a Delrin cuvette (Warner Instrument, USA). The cis and trans chambers were filled with symmetrical solution of 1 M KCl, 5 M MgCl₂ and 10 mM HEPES (pH 7.4). The cis chamber was held at virtual ground and the trans chamber was connected to the head-stage of amplifier (Axopatch 200B, Molecular Probes, USA). Mel and PP (incubated with and without heparin for two weeks) were added (1μM) to the cis and stirred for 5–10 min. AS oligomers and monomers (isolated from SEC), were also included in the study. Channel activity was monitored at different voltages. Data was filtered at 1 kHz (low pass) and digitized at 5 kHz using amplifier Axopatch 200B (Molecular Devices, USA). The pClamp software (version 9, Molecular Devices) was used for data acquisition and analysis. Additional analysis was done using Sigma Plot 11. Single channel conductance was calculated from all point histogram.

Calcein release assay

To study the dye leakage ability of oligomers, calcein release assay was performed using calcein-loaded liposomes. The freshly prepared calcein-loaded liposomes were 100 fold diluted in PBS (pH 7.4) before starting the experiment. The oligomers were added to these diluted liposomes at a final concentration of 10 μM and in a reaction volume of 150 μl. Peptide samples incubated in the absence of heparin and AS monomers isolated from SEC were also used as controls. To achieve 100% calcein release, 0.5% Triton X-100 was used as a positive control. The reaction was started in a clear bottom 96 well fluorescence plate (Sigma, USA) and the time-dependent fluorescence intensity (at 520 nm) was recorded (excitation at 495 nm) at 25°C using spectraMax M2e microplate reader (Molecular Devices, USA).

Mel and PP form helix-rich globular oligomers

Both, Mel and PP possess helical propensity as shown in Fig. 1A. For studying the oligomerization, Mel and PP were dissolved in 5% D-mannitol at a concentration of 2 mg/ml (with and without 400 μM heparin) and incubated at 37°C with slight rotation. To evaluate the secondary structure of Mel and PP (in presence and absence of heparin), CD spectroscopy was performed before and after two weeks of incubation. Immediately after dissolution, Mel showed the mostly unstructured conformation as evident from single negative minima near 198 nm in far-UV CD spectroscopy (Fig. 1B). However, Far-UV CD spectrum of PP showed two negative minima; one at ~ 222 nm and another at ~208 nm, respectively, characteristics of helix-rich conformation. Interestingly, PP did not change its helical conformation even after addition of the heparin, suggesting that heparin might not be able to induce further structural transition in PP (Fig. 1B). However, when heparin was added to Mel peptide, it immediately transformed into helical conformation, as evident by two negative minima near 222 nm and 208 nm, respectively in its far-UV CD spectrum (Fig. 1B).

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Fig 1. Structural characterization of Mel and PP.

(A) Structural model of Mel (red, PDB ID: 2MLT) and PP (blue, bovine PDB ID: 1BBA). (B) CD spectra of Mel and PP at day 0 (d0) and after 15 days (d15) in presence and absence of heparin. After the addition of heparin and subsequent incubation for two weeks, the secondary structure of PP remained mostly unchanged (helical). (C) FTIR spectra of two weeks incubated PP and Mel (in the absence and presence of heparin). Y-axis represents the absorbance (AU) and X-axis represents the wavenumber (cm^-1). Wavenumbers corresponding to the maximum absorbance are represented with arrow marks. Consistent with CD data, FTIR study also showed that in the presence of heparin, unstructured Mel transformed into helical conformation, whereas PP remained mostly helical both in presence and absence of heparin after incubation.

https://doi.org/10.1371/journal.pone.0120346.g001

The CD data suggest that unlike PP, heparin interaction to Mel peptide induced a drastic structural rearrangement. Further structural analysis of these samples after two weeks showed that Mel and PP (in the presence of heparin) retained their helicity during the course of incubation (Fig. 1B). The CD data thus suggest that helical conformations of Mel and PP were fairly stable and resisted any subsequent structural transition. PP (incubated in the absence of heparin) also showed helical conformation, however, Mel peptide, which was incubated in the absence of heparin, remained mostly unstructured (Fig. 1B). Consistent with CD data, the FTIR spectroscopy also revealed that PP samples incubated in absence and presence of heparin were of mainly helical conformation as characterized by the absorbance maxima at 1655 cm^-1 and 1656 cm^-1, respectively (Fig. 1C). However, Mel showed large conformational transition from RC (1648 cm^-1) to helix (1658 cm^-1) due to the addition of heparin (Fig. 1C). The CD and FTIR data of Mel, thus suggest that even though Mel has helical propensity, it alone cannot undergo structural transition and requires either helix-favoring condition or any additive like heparin.

Further, we analyzed the morphology of PP and Mel incubated both in presence and absence of heparin. AFM analysis of Mel sample (in the presence of heparin) showed globular oligomers (S2 Fig.), however, these oligomeric species were mostly absent in Mel alone sample (S2 Fig.). This data suggests that structural transition in Mel (in the presence of heparin) might have initiated oligomerization. We also examined the morphology of PP (in presence and absence of heparin) and we found that heparin also induced instant oligomerization in PP (S2 Fig.). Further morphology analysis of two weeks incubated samples by EM and AFM showed that the size of oligomers increased during incubation; however, they remained mostly globular in morphology (Fig. 2). Interestingly, the microscopy data revealed that Mel formed large oligomers, whereas PP showed relatively small oligomers, in the presence of heparin (Fig. 2). PP incubated in the absence of heparin did not show any globular oligomeric species, however, it showed some amorphous like structure in EM (S3 Fig.), suggesting that heparin is required for these oligomeric assemblies. However, Mel sample, which was incubated in the absence of heparin also showed oligomeric species in EM and AFM but smaller than Mel oligomers formed in the presence of heparin (S3 Fig.). This data suggests that Mel has propensity to self-assemble, however, this process can be accelerated in the presence of heparin. It is interesting to note that, both Mel and PP possess stretches of basic amino acids (I²⁰-K²¹-R²²-K²³-R²⁴-Q²⁵ for Mel and R³³-P³⁴-R³⁵ for PP) (S1 Fig.), which might be responsible for interaction with anionic polymer, heparin [41,42].

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Fig 2. Morphological characterization of Mel and PP oligomers.

EM and AFM analysis were performed to visualize the morphology of two weeks incubated Mel and PP (in the presence of heparin). EM (left panel) and AFM (middle panel) images showing oligomer formation in the presence of heparin. The right panel shows 3D AFM height images of oligomer. Scale bars for EM images are 500 nm. Height scales for AFM images are also shown.

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To further characterize the oligomers size in solution, DLS experiment was performed. The two weeks incubated peptide samples (in the presence and absence of heparin) were used for DLS experiment and their hydrodynamic radii were measured (Fig. 3). The DLS analysis revealed that the Mel peptide, which was incubated in the absence of heparin has average hydrodynamic radius (Rh) of 35.5±0.6 nm. However, Mel peptide, which was incubated in the presence of heparin, has average Rh of 58.4±1.6 nm. Furthermore, PP sample, which was incubated in the presence of heparin, has average Rh of 6.5±0.2 nm. However, the Rh value of PP sample incubated in the absence of heparin was 0.55±0.01 nm (Fig. 3), suggesting that the addition of heparin caused oligomerization of PP. The DLS data thus correlate well with AFM and EM results and collectively suggest that heparin accelerated the oligomerization of Mel and promoted its assembly into bigger oligomers. However, PP oligomerized in the presence of heparin only and showed lesser Rh compared to Mel oligomers.

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Fig 3. Hydrodynamic radius of oligomers.

Dynamic light scattering (DLS) was performed to obtain the hydrodynamic radius (Rh) of peptide samples incubated for two weeks in presence and absence of heparin. The Rh values of peptides incubated in the presence of heparin increased considerably.

https://doi.org/10.1371/journal.pone.0120346.g003

Tinctorial properties of Mel and PP oligomers formed in the presence of heparin

Although both peptides (Mel and PP) are not involved in amyloid diseases, we checked whether Mel and PP oligomers, which were formed in presence of heparin, bind to any amyloid specific dye such as ThT and CR. In this context, it has been recently shown that many peptides/proteins, which are not associated with any neurological disorder, also form cytotoxic oligomers, which show tinctorial properties of amyloids [13,14]. When bound to amyloids or amyloidogenic oligomers, ThT gives a significantly high fluorescence emission signal at 480 nm when excited at 450 nm [43]. Similarly the molar absorptivity of CR (at ~540 nm) increases after binding with amyloid oligomers/fibrils [36,44,45]. We found that Mel and PP oligomers, which were formed in the presence of heparin, moderately bound to ThT (Fig. 4A) and CR dye (Fig. 4B), suggesting their amyloidogenic nature. PP and Mel, which were incubated in the absence of heparin, did not show significant ThT and CR binding, suggesting that heparin has induced amyloidogenic oligomer formation.

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Fig 4. Tinctorial properties of Mel and PP oligomers.

(A) ThT binding assay and (B) CR binding assay of two weeks incubated Mel and PP (in the presence and absence of heparin). ThT and CR binding showing that both Mel and PP oligomers, which were formed in the presence of heparin, bind moderately with these dyes.

https://doi.org/10.1371/journal.pone.0120346.g004

We also isolated the pure oligomers of Mel and PP (using 10 KDa MWCO centrifugal filters) for their further structural and biophysical characterization. Consistent with data obtained prior to isolation, the isolated pure oligomers of Mel and PP also showed helix-rich conformation (Fig. 5A), and moderately bind to ThT (Fig. 5B) and CR dye (Fig. 5C). Furthermore, these isolated pure oligomers showed globular morphology (Fig. 5D).

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Fig 5. Biophysical characterization of isolated Mel and PP oligomers.

(A) CD spectroscopy of isolated oligomers of Mel and PP in the presence of heparin. Both oligomers showed helical conformation in CD. (B) ThT fluorescence of the isolated Mel and PP oligomers showing moderate ThT binding. (C) CR binding of the isolated Mel and PP oligomers. (D) EM images showing large globular oligomeric morphology of the isolated Mel and PP oligomers formed in the presence of heparin. Scale bar is 500 nm.

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As Mel and PP oligomers (formed in the presence of heparin) showed tinctorial properties similar to amyloid, we, therefore, checked the intrinsic amyloidogenic propensity of these peptides using Zyggregator algorithm [37]. The Zyggregator prediction clearly showed that both Mel and PP possess intrinsic tendency to form amyloidogenic oligomers, however, this propensity is comparatively higher for Mel (Fig. 6). Although both PP and Mel formed oligomers in presence of heparin, which bind moderately to ThT and CR, at this point, it is not clear how helical oligomers, which lacked β-sheet structure bind to ThT and CR dye. It is possible that a fraction of both PP and Mel form amyloid fibrils (which may not detectable in CD and FTIR studies (Fig. 1), which may bind moderately to ThT and CR. For this, we examined the immunoreactivity of these oligomers with amyloid oligomer specific (A11) and amyloid fibril specific (OC) antibodies [5,38] using dot blot assay. Two weeks incubated peptide samples (in the presence and absence of heparin) were used for this study. The β-sheet rich AS oligomers and unstructured AS monomers (both isolated using SEC) were used as positive and negative controls, respectively. The A11 antibody showed immunoreactivity only with β-sheet rich AS oligomers (S4 Fig.). However, Mel and PP oligomers did not show any immunoreactivity with A11 antibody.

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Fig 6. Oligomerization prediction of Mel and PP.

The intrinsic oligomerization ability of Mel and PP peptide was calculated (at pH 5.5) using Zyggregator software. The positive values (in red) represent aggregation propensity of corresponding amino acid.

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The data suggest that helical oligomers of PP and Mel might lack the epitopes for A11 antibody (S4 Fig.). When we examined the immunoreactivity of these samples with amyloid fibril specific OC-antibody [38] (S4 Fig.), which binds to β-sheet rich amyloid fibrils, the peptide oligomers were also found to be non-immunoreactive with OC antibody, suggesting the absence of β-sheet rich fibrillar aggregates in these samples. Unstructured AS monomers and preformed β-sheet rich AS fibrils were used as OC-negative and OC-positive controls, respectively. The peptides incubated in the absence of heparin were found negative for both A11 and OC immunoreactivity (S4 Fig.). The data suggest that irrespective of the absence of fibrils, these helix-rich oligomers may provide the structural milieu for binding with ThT and CR similar to amyloid fibrils. Previously, protein/peptide aggregates with helix-rich structure also showed both ThT and CR binding [46,47].

The oligomers are cytotoxic to SH-SY5Y neuronal cells

Mel and PP oligomers (formed in the presence of heparin) showed tinctorial properties similar to PD associated AS oligomers. Therefore, the cytotoxicity of these oligomers was evaluated using SH-SY5Y cells. For cytotoxicity measurements, we performed morphological analysis of SH-SY5Y cells and LDH release assay in absence and presence of 10 μM oligomers. Our morphological analysis data revealed that after 30 h of treatment with PP oligomers, the number of cells was decreased compared to buffer control (Fig. 7A). Further analysis of cells showed significant loss of neuritic extensions as evident from the measurements of neuritic lengths in the presence of oligomers (measured using ImageJ software, NIH) (Fig. 7B). However, cells in the presence of Mel oligomers showed complete death and only cell debris were observed (Fig. 7A) and therefore we were unable to calculate neurite length of Mel treated cells. Further, concentration-dependent LDH assay was performed to quantify the cell death (Fig. 7C and S5 Fig.) induced by these oligomers. LDH is a soluble cytosolic enzyme that is released into the culture medium following the loss of membrane integrity and cell death [39]. This method is widely used to assay the toxicity of chemicals or environmental toxic factors on cells [39]. PP oligomers (10 μM), which were formed in the presence of heparin after two weeks of incubation showed ~ 35% cell death in LDH release assay (Fig. 7C). However, in similar conditions, PP incubated for two weeks in the absence of heparin did not show significant LDH release/cell death (Fig. 7C), suggesting that the toxicity of PP is a consequence of its oligomerization in presence of heparin.

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Fig 7. Cytotoxicity of Mel and PP oligomers.

(A) Phase contrast images of SH-SY5Y cells showing damaged morphology of cells by PP and Mel oligomers. Scale bars are 100 μm. (B) Neurite length of SH-SY5Y cells treated with Mel and PP oligomers that were quantified using ImageJ software (NIH). The cells treated with oligomers showing reduced neurite length when compared to control. Due to complete death of cells in Mel oligomer treated samples, the calculation was only conducted for control samples (buffer) and PP oligomers treated samples. (C) LDH assay depicting % cell death in SH-SY5Y cells treated with oligomers. Both PP and Mel oligomers (formed in the presence of heparin) showed cytotoxicity. PP incubated in the absence of heparin did not show any toxicity; however, Mel incubated alone showed cytotoxicity.

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Interestingly, our study revealed that 10 μM Mel oligomers (both formed in the presence and absence of heparin) after two weeks of incubation showed ~100% cytotoxicity in LDH assay, consistent with our cell morphology analysis. Previously, it has been shown that Mel has hemolytic activity and suggested that this activity is related to its oligomerization [48]. The morphological analysis and LDH data collectively suggest that the helical oligomers of Mel and PP are cytotoxic to SH-SY5Y cells. However, it is not clear at this point why the extent of toxicity by Mel oligomers formed in presence and absence of heparin is similar irrespective of their different oligomers sizes. The data suggest that the toxicity of Mel oligomers might not be correlated with their size prior to the addition into cell culture. We also compared the toxicity of freshly dissolved Mel (10 μM) (S6 Fig.) and unstructured Mel oligomers formed after two weeks of incubation in the absence of heparin (Fig. 7C). The LDH data showed that both preparations of Mel (freshly dissolved and two weeks incubated) were highly toxic (~100%) to SH-SY5Y similar to large oligomers formed in the presence of heparin. It is reported that cell surface glycosaminoglycans can induce structural transition of unstructured Mel into helix-rich conformation [25]. We believe that this toxicity may arise due to in situ helix-rich oligomer formation by Mel on the cell surface.

To study further that the cell membrane might have a role in structural change and oligomerization of Mel, we studied the Mel oligomerization in the presence of membrane-mimicking condition (SDS) and membrane vesicles (Fig. 8). Our data suggest that both of these conditions instantly promoted helix formation of Mel (Fig. 8A and 8B, respectively). To further analyze the oligomerization of Mel (25 μM) in the presence of SDS (2.5 mM), we performed morphological analysis of Mel after 5 days incubation in SDS. The AFM analysis showed the presence of fibrillar species along with the globular oligomers (Fig. 8C). Moreover, this aggregated Mel sample in the presence of SDS also showed tinctorial property like ThT fluorescence (Fig. 8D), suggesting that these aggregates are amyloidogenic in nature. It is interesting to note that ThT fluorescence was also observed on day 0 sample (S7 Fig.), suggesting that the addition of SDS may immediately induce the oligomerization of Mel. The data collectively suggests that like other amyloidogenic proteins, membrane-mimicking environment may also promote the self-assembly of Mel into oligomers.

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Fig 8. Biophysical characterization of Mel in presence of SDS and liposome.

(A) CD spectroscopy showing the helical conformation of Mel after immediate addition of SDS (2.5 mM) in Gly-NaOH buffer (20 mM, pH 9.2). (B) Mel showing immediate conversion to helical conformation after addition of liposomes. (C) AFM images of Mel (incubated in the presence of SDS at 37°C) showing large globular oligomers and some fibrillar species (shown in the inset). (D) ThT binding of Mel after 5 days of incubation in the presence of SDS.

https://doi.org/10.1371/journal.pone.0120346.g008

Hydrophobic surface exposure of oligomers

It has been suggested that the extent of hydrophobic surface exposure may play a crucial role in cellular toxicity of protein aggregates [49,50]. We hypothesize that along with structural and morphological changes, oligomerization may induce hydrophobic surface exposure of the peptides that in turn promote their insertion in the cell membrane and thereby cytotoxicity. To test this, Nile Red (NR), which is a neutral dye and sensitive for detecting exposed hydrophobic surface of the protein/peptide [51,52] was used. The NR binding data showed a significantly high NR fluorescence intensity after binding to peptide oligomers formed in the presence of heparin compared to peptides incubated in the absence of heparin (Fig. 9). The present data thus suggest that due to oligomerization, the hydrophobic surface exposure of the protein/peptide increases, which then interacts and damages the cell membrane and eventually kills the cells.

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Fig 9. Hydrophobic surface exposure of oligomers.

Hydrophobic surface exposure in terms of NR binding by Mel and PP samples, incubated for two weeks in presence and absence of heparin. The data suggesting increased hydrophobic surface exposure during heparin-induced peptide oligomerization.

https://doi.org/10.1371/journal.pone.0120346.g009

Peptide oligomers form ion channels and permeabilize the lipid vesicles

It was previously suggested that many amyloid oligomers permeabilize lipid bilayers and form ion channels in the cell membrane, thereby disruptimg the cellular homeostasis eventually causing amyloid diseases such as Alzheimer’s and Parkinson’s [53–55]. To further explore the toxicity mechanism of these oligomers, we analyzed whether Mel and PP oligomers, which were formed in the presence of heparin can form channel/pore in a model membrane. To do this, artificial bilayer was constructed from 1, 2-diphytamoyl-sn-glycero-3-phosphocholine (DPhPC). The peptide oligomers were added to these lipid membranes and the channel activity was monitored at different voltages. Our data showed that oligomers of PP and Mel (formed in presence of heparin) readily formed channels in artificial bilayer lipid membrane (BLM) within 5–10 min of their addition to cis chamber (Fig. 10A). In similar experimental condition, PP that was incubated in the absence of heparin, did not exhibit any channel activity (S8 Fig.), suggesting that channel formation activity of PP is associated with its oligomerization. In fully open state, single channel conductance of Mel oligomers (formed in the presence of heparin) was about 320 ± 0.04 pS (n = 7) in 1M KCl. Mel oligomers showed one prominent sub-conductance state of 200 ± 0.02 pS (n = 7). However, PP showed several sub-conductance states of which one of the 17.5 ± 0.04 pS (n = 3) was observed frequently. Mel oligomers, which were formed after two weeks of incubation in the absence of heparin also formed channel, however with approximately 30 times lesser single channel conductance, compared to Mel oligomers formed in presence of heparin (S8 Fig.).

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Fig 10. Membrane damage by oligomers.

(A) Representative single channel current traces; exhibited by oligomeric species at different holding potentials. Channel insertion was initiated by adding 1 μM of Mel and PP oligomers to the cis chamber. All point histogram of the corresponding current trace is shown at the right side. Clamping potentials (mV) are indicated along the right side of the current traces. Conductance values (in pS) of different states are indicated on the right side of current traces. Red horizontal line represents a base line (0 pA). (B) Calcein release assay showing leakage of the calcein dye after addition of oligomers to the calcein-loaded liposomes. A high calcein fluorescence was observed when calcein was released to the solution. (C) Cryo-SEM images of liposomes showing the direct visualization of pore and membrane damage in the presence of oligomers. Arrows indicate the pore-like structures in the liposomes. Scale bars are 100 nm.

https://doi.org/10.1371/journal.pone.0120346.g010

To further reveal the channel forming capability of these oligomers, calcein release assay was performed using calcein-loaded liposomes. If these oligomers are forming channel/pores in the liposomes; the fluorescent calcein dye will leak out from the liposome in the solution. The leakage of calcein, from the liposomes, was detected by measuring the time-dependent calcein fluorescence in the solution (Fig. 10B). The addition of oligomers (10 μM) to the calcein-loaded liposomes at RT showed prominent increase of calcein fluorescence in the solution. For positive control (for 100% calcein release), 0.5% Triton X-100 was also used. The background calcein fluorescence from calcein-loaded liposomes was very less during the entire measurement time (30 min) and it was subtracted from the calcein fluorescence values obtained after oligomer treatment. Addition of Mel oligomers (formed in the presence of heparin) to calcein-loaded liposomes showed ~80% calcein release (as evident from calcein fluorescence in solution). Similarly, addition PP oligomers (formed in the presence of heparin) showed ~20% calcein fluorescence in solution (Fig. 10B). Two weeks incubated Mel alone sample induced ~ 60% calcein release, consistent with its toxic oligomer formation tendency. However, PP incubated for two weeks in the absence of heparin, showed negligible calcein fluorescence when added to calcein-loaded liposome solution (data not shown). The dye leakage assay, therefore, supports the electrical conductance data, suggesting channel/pore formation in the lipid vesicles by oligomers.

Furthermore, to visually observe any pore formation or membrane disruption by these different oligomers, we analyzed the morphology of liposomes in presence and absence of oligomers. The liposomes were incubated with 10 μM oligomers for 30 min at RT and the morphology of liposomes were analyzed using cryo-SEM (Fig. 10C). The data suggested that the oligomer treatment damaged/distorted the liposomes and some pores were also observed on the liposome (Fig. 10C). The electrical conductance, calcein release data, and liposome damage experiment collectively suggest that both Mel and PP oligomers interact with membrane (probably due to their exposed hydrophobic surfaces) and damage the membrane integrity, which subsequently lead to the leakage of inner content. Similar mechanism could be assumed for SH-SY5Y neuronal death in the presence of these oligomers.

Comparison of Mel and PP oligomers with PD associated AS oligomers

Mel and PP oligomers (formed in the presence of heparin) were cytotoxic and showed amyloid specific tinctorial properties (ThT and CR binding). Furthermore, Zyggregator calculation also suggested that these peptides possess an intrinsic amyloidogenic propensity. Therefore, we compared the biophysical properties of these oligomers with PD associated AS oligomers. We also compared the toxicity mechanism of Mel and PP oligomers with AS oligomers. For this purpose, preformed AS oligomers were isolated using SEC and used. Similar to Mel and PP oligomers, which were formed in presence of heparin, preformed AS oligomers also showed globular morphology along with some small protofilament like species under EM (Fig. 11A) and AFM (Fig. 11B). The high ThT (Fig. 11C) and CR binding (Fig. 11D) of these oligomers revealed their amyloidogenic nature. Furthermore, like Mel and PP oligomers, AS oligomers also induced death of SH-SY5Y cells in concentration-dependent manner. However, AS monomers did not show such toxic effect (Fig. 11E and S5 Fig.). Similarly, AS oligomers also have more exposed hydrophobic surfaces compared to monomeric AS (as measured by NR binding assay) (Fig. 11F). These data collectively suggest that the non-disease associated oligomers of Mel and PP share some biophysical parameters with PD associated AS oligomers.

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Fig 11. Biophysical characterization and cytotoxicity of AS oligomers.

(A) EM (B) AFM images showing globular morphology with presence of some protofilaments by preformed AS oligomers (isolated from SEC). (C) ThT fluorescence and (D) CR absorbance of AS monomers and oligomers, respectively. (E) Toxicity assay measured by LDH showing ~ 45% cell death by AS oligomers; whereas no substantial toxicity was observed for AS monomers. (F) NR binding showing AS oligomers have higher NR binding (higher hydrophobic surface exposure) compared to the monomers. (G) Calcein release profile after addition of AS oligomers to calcein-loaded liposome solution. (H) Representative single channel current traces; exhibited by AS oligomers, suggesting channel formation in BLM. AS monomers did not show any channel activity. All point histogram of the corresponding current trace is presented at the right side. (I) Hydrodynamic radius (Rh) of AS oligomers (major population).

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Moreover, like PP and Mel oligomers, AS oligomers also released the calcein dye from calcein-loaded liposomes (Fig. 11G), suggesting a common mode of toxicity for these oligomers. Addition of AS oligomers to calcein-loaded liposome solution induced ~40% calcein release in solution (as evident from calcein fluorescence in solution). However, addition of AS monomers to calcein-loaded liposome solution showed a negligible increase in calcein fluorescence in solution (Fig. 11G). To further explore a common mode of toxicity, we also studied the channel activity of AS oligomers in BLM. The data suggests that AS oligomers also formed channels in BLM within 5–10 min of their addition to cis chamber in planar bilayer lipid recording (Fig. 11H), consistent with the previous observations of pore formation by amyloidogenic oligomers [54,55]. However, the channel conductance of AS oligomers was lesser than Mel and PP oligomers formed in the presence of heparin. In fully open state, single channel conductance of Mel was about 320 ± 0.04 pS (n = 7) in 1M KCl, whereas AS showed the conductance of about 6.25 ± 0.06 pS (n = 4). The monomeric AS did not show any channel activity in similar experimental condition (Fig. 11H). When we analyzed the Rh of oligomeric AS, we found that AS oligomeric sample has average Rh of 74±1.5 nm (Fig. 11I). Collectively, we found that not only the extent of toxicity but the other biophysical characteristics for toxicity mechanism were comparable for non-disease associated Mel, PP oligomers and PD associated AS oligomers.