Paola Allettoa,
Ana M. Garciab,
Federica Piccirilli*c and
Silvia Marchesan
*a
aDepartment of Chemical and Pharmaceutical Sciences, University of Trieste, Via. Giorgieri 1, 34127 Trieste, Italy. E-mail: smarchesan@units.it
bFacultad de Ciencias y Tecnologías Químicas, Instituto Regional de Investigación Científica Aplicada (IRICA), Universidad de Castilla-La Mancha, Ciudad Real 13071, Spain
cArea Science Park, Padriciano 99, Trieste, Italy. E-mail: federica.piccirilli@areasciencepark.it
First published on 21st February 2025
Supramolecular hydrogels composed of self-assembling short peptides are gaining momentum for enzyme mimicry. In particular, multicomponent systems that feature similar peptides with a self-assembling motif (e.g., Phe–Phe) and catalytic residues (e.g., His, Asp) offer a convenient approach to organize in space, functional residues that typically occur at enzymatic active sites. However, characterisation of these systems, and especially understanding whether the different peptides co-assemble or self-sort, is not trivial. In this work, we study two-component hydrogels composed of similar tripeptides and describe how nano-IR can reveal important details of their packing, thus demonstrating it to be a useful technique to characterise multicomponent, nanostructured gels.
However, the detailed characterisation of such systems, especially the localisation of the different components, is not always trivial. On the one hand, constituents of very different nature, such as metal nanostructures6–8 or nanocarbons9–12 and organic assemblies, can be easily identified by microscopy. On the other hand, organic components are far more challenging to distinguish at the nanoscale. Furthermore, hydrogels composed of similar molecules that self-organise into nanofibrillar matrices may arise from different types of assemblies, such as those composed exclusively of either gelator through a self-sorting mechanism, or those composed of different gelators (i.e., coassemblies).13 On the one hand, self-sorting in supramolecular systems is important to enable the co-existence of distinct architectures that can function independently, and it is widely used in nature to create the required compartmentalization for complex systems; such as a living cell, to orchestrate several reactions simultaneously.14 Self-sorted systems can display sophisticated behaviour, such as evolution in response to a trigger,15 simultaneous targeting of multiple cell organelles,16 and chemical signalling in protocells.17 In the case of gels, one convenient strategy employs gelators with pH-responsive behaviour within distinct pH ranges, and/or the use of gelators that respond to different stimuli, so that specific gelation triggers can be used to exert selective control over the organization of each gelator.18 Dynamic and evolving self-sorted gels can be obtained through accurate choice of the assembly triggers, and the mutual influence that one gelator self-organization can exert onto another.19
On the other hand, co-assembly can be attractive to tailor supramolecular organization towards specific properties and functions that cannot be achieved by a single component, for instance to control biomolecular conformation and stability,20 to attain and transfer specific responses such as chiroptical switches,21 or for synergistic behaviour, as demonstrated for example to attain broad antibacterial activity.22 A particularly interesting approach derives from the finding that racemic mixtures of gelators can yield co-assemblies with peculiar properties, and stronger gel networks.23 In particular, self-assembling peptides are attractive gelators, thanks to their easy modular design and synthesis, and the possibility to include diverse amino acids, thus functional groups, chirality, properties, and functions.24 Schneider and collaborators reported in 2011 the racemic assembly of a peptide gelator with remarkably enhanced rigidity relative to gels formed by each enantiomer alone.25 The elucidation of how the two enantiomers were interacting was very challenging, since no significant differences were found by spectroscopic or microscopic investigations. It took a few years, and an arsenal of advanced techniques, including isotope labelling and small-angle neutron scattering, to address such a formidable challenge. In 2017, Schneider and collaborators reported the finding that the two enantiomers were alternating in stacks forming a rippled-beta sheet,26 which is a structure that had been predicted by Pauling and Corey back in 1953.27 Interestingly, peptide stacks were held together by a network of hydrogen bonds between amide groups, whilst forming peculiar hydrophobic interactions that are nested between enantiomers in the dry interior of racemic fibrils.26
Inspired by these studies, we reasoned that the maximization of such hydrophobic regions could enhance hydrophobic substrate binding for catalysis and find scope in enzyme mimicry. Therefore, we took the heterochiral peptide gelator D-His-L-Phe-L-Phe-NH2 (ref. 28) (hFF) and studied its co-assembly in equimolar mixtures with its enantiomer (Hff). This gelator can mimic esterases and catalyse the hydrolysis of p-nitrophenylacetate, a convenient chromogenic substrate,29 only when it is present in the self-assembled state. We found that the racemic hydrogel not only displayed increased viscoelastic moduli and resistance against applied stress, as expected for a rippled-beta sheet, but also enhanced catalysis with over 50% improvement of the reaction rate under analogous conditions to the enantiopure assemblies. The presence of more hydrophobic regions in the racemic gel relative to enantiopure analogs was confirmed by ANS fluorescence.30
Considering that hydrolases typically feature catalytic dyads or triads, including not only His, as the above peptide sequence, but also other catalytically active residues, we thus wondered whether we could extend this approach to also include other functional residues. In particular, we focused our interest in aspartate (Asp), which is a key acidic residue in esterase catalytic sites31 that plays key roles in proton transfer and in positioning the correct His tautomer for catalysis.32 Furthermore, the Asp sidechain features a carboxylate group whose stretching has characteristic signals in the infrared regions corresponding to 1574–1595 (asymmetric) and 1392–1425 (symmetric).33 While the first one falls in a crowded region where aromatic signals are also present, the latter one is in a promising range for correct identification, also in the presence of other amino acids, such as His and Phe. Combination of infrared spectroscopy with AFM analysis in a nano-IR setup could thus provide a convenient tool to investigate whether L-Asp-D-Phe-D-Phe-NH2 (Dff) co-assembles with Hff or with hFF (Scheme 1).
In particular, Dff gelled within a few seconds at both concentrations, while it took each enantiomer with His, ∼1 h to form stable hydrogels at 10 mM, thus highlighting the favourable role of Asp for gelation. At 25 mM, Dff yielded a hydrogel with G′ = 75.1 ± 0.02 kPa and G′′ = 6.78 ± 1.11 kPa that underwent a gel-to-sol transition at ∼18 Pa in stress sweeps (Fig. 1A, B and ESI†). For comparison, Hff yielded hydrogels with G′ = 34.9 ± 3.4 kPa and hFF with G′ = 34.3 ± 5.0 kPa, with both displaying moduli that dropped at ∼70 Pa in stress sweeps.30 Having established that each peptide is a gelator under analogous conditions, we analysed the rheological behaviour of their co-assemblies (Fig. 1).
![]() | ||
Fig. 1 Rheological analysis. Frequency sweeps (left panels) and stress sweeps (right panels) of Dff (A and B), and its co-assembled hydrogels with Hff (C and D) or hFF (E and F). |
Maintaining the same D–L–L stereoconfiguration in the tripeptide design resulted in hydrogels with G′ = 35.3 ± 2.9 kPa that withstood an applied stress of up to 70 Pa (Fig. 1D), demonstrating that addition of Dff to Hff surprisingly did not significantly alter either its elastic modulus (Fig. 1C) or its kinetics (see ESI†). Instead, when Dff was added to the other enantiomer, hFF, the co-assembled hydrogel reached a lower elastic modulus of G′ = 15.0 ± 0.4 kPa, it displayed increased resistance to applied stress up to 100 Pa (Fig. 1E and F), but also significantly slower gelation kinetics (i.e., ∼33 min see ESI Section S4†). Thermoreversibility tests revealed a self-healing ability for all hydrogels (see ESI†). In particular, tripeptide hydrogels (25 mM) with His displayed a Tm = 42 °C and reformed within 20 min, while those composed of Dff had a Tm = 55 °C and reformed within 15 min. Dff + Hff hydrogels (25 mM each) displayed a Tm = 58 °C and reformed within 10 min, thus surpassing those composed of each tripeptide alone in both resistance against heating and kinetics of re-assembly. Therefore, these properties of this multicomponent hydrogel were not simply the sum of the individual components, which is in agreement with the presence of co-assembled fibrils. Analogously, when peptides with opposite stereoconfiguration were mixed (i.e., Dff and hFF, 25 mM each), the Tm was similar (56 °C), while the re-assembly was slower (20 min). We inferred that the differences in the viscoelastic properties of the co-assemblies could be ascribed to more heterogeneity and defects in the supramolecular packing of Dff and hFF, which are two peptides that differ not only in the N-terminal sidechain, but also in stereoconfiguration. To verify this hypothesis, we thus undertook microscopic analysis of the co-assemblies to ascertain whether the viscoelastic differences could be correlated to nanomorphology.
Transmission electron microscopy (TEM) revealed a dense nanofibrillar network in both cases (Fig. 2A–D). However, the size distribution (Fig. 2E) was significantly wider for the gel formed by Dff and hFF, further supporting the hypothesis that changing amino acid sequence and chirality leads to higher heterogeneity within the nanofibrillar network. This finding raised the question of whether such nanomorphological diversity could be ascribed to self-sorting as opposed to co-assembly. Therefore, we sought Fourier-transformed infrared (FT-IR) spectroscopic investigations coupled to atomic force microscopy (AFM).
![]() | ||
Fig. 2 TEM micrographs of Dff + Hff (A and B) and Dff + hFF (C and D) gels and their nanofibrillar width distribution (E) with mean ± standard deviation values (n = 100 counts). |
Firstly, we acquired attenuated total reflectance (ATR) spectra on assemblies in bulk (Fig. 3A) and compared the two-component samples to those of the individual tripeptides. Infrared spectra showed a prominent band in the 1750–1600 cm−1 range, mainly due to amide I modes, and a minor one peaked at 1553 cm−1, ascribed to amide II modes. The comparison between the spectra revealed that the presence of Asp could be traced unambiguously by the signals in the 1400–1360 cm−1 range, which were ascribed to the symmetric stretching of the COO− group.33 Conversely, the antisymmetric stretching of COO− was assigned to the shoulder at 1586 cm−1 that occurred in a crowded region, thus making it difficult to interpret unambiguously. The 2nd-derivative analysis (Fig. 3B) did not highlight significant differences in the amide I profiles, suggesting similarities in the overall arrangement of peptide bonds in the fibrils, as expected for β-sheets formed by this type of gelator.
To reveal finer structural details, we conducted a nanoscopic analysis by acquiring infrared spectra on single fibers imaged by AFM (see ESI†). We exploited s-SNOM spectroscopy (scattering type scanning near-field optical microscopy) that is based on the coupling of AFM to cutting-edge infrared technologies, to obtain information on nanoscale topography with chemical sensitivity. In particular, a typical s-SNOM spectrum is representative of the vibrational profile of sample surfaces that are 20 nm wide, with a penetration depth of up to 100 nm.34,35 Moreover, the interaction of the incoming radiation with the metallic tip of the AFM results in a strong polarization of the electromagnetic radiation along the direction perpendicular to the sample.36 Thus, s-SNOM peak intensities strongly depend on the orientation of covalent bonds. Fig. 4A shows the nano-IR average absorption measured on different fibers of the two-component assemblies. Fig. 4B shows the corresponding data acquired for the racemic gel composed of Hff and hFF and devoid of the Asp signal, as a control. First of all, all spectra measured on different fibers of the two-component samples of Fig. 4A show the Asp signals, and in particular the distinctive signature below 1400 cm−1 that indeed is absent in the control without Asp (Fig. 4B), while it is present in the spectrum of Dff (see ESI, Section S6†). This data supports the hypothesis of co-assembled systems in both cases, as opposed to self-sorted ones, where two populations of fibers with distinctive profiles with and without Asp signals would be expected. Interestingly, despite showing similar frequency, the profile spectra showed clear differences in peak intensities. Based on ATR results, which confirmed similar absorption profiles for the different samples (Fig. 3), and given the polarized nature of the s-SNOM signal, this evidence hinted at differences in the three-dimensional arrangement of the assembled tripeptides that were likely to display a strong alignment of IR-active functional groups. To deepen this aspect, we performed principal component analysis (PCA) on single nano-IR absorbance spectra, the results are shown in Fig. 4C and D. The first three components, PC1, PC2 and PC3, whose scores and loadings are shown respectively in Fig. 4C and D, were taken into account, covering respectively 38%, 16% and 14% of the total data variance. The two-component systems have been compared to the Dff assembly too (maroon markers). We first observed that Dff–Hff spectral distribution appeared to be more homogeneous compared to the other samples, as revealed by the area of the variance ellipses shown in Fig. 4C. This is likely related to a higher structural order of Dff–Hff in the assembly network compared to Dff–hFF, as expected, and surprisingly to Hff–hFF too. It is possible that the negative charge on the Asp sidechain establishes ionic interactions with the cationic N-terminal groups, thus contributing to the organisation of the assemblies. This hypothesis was further supported by 1H-NMR studies, which showed significant shifts for Dff–Hff relative to spectra of the individual components (i.e., Dff or Hff) at neutral pH, but not at pH 2.0, where a different ionization state is expected (see ESI, Section S7†).
Score plots revealed the clear separation of Dff-Hff from the other samples, toward positive values of PC1, of the Dff toward positive values of PC2, and of the racemic samples toward positive values of PC3. As shown in Fig. 4D, where PCA loadings are reported, PC1 shows a prominent peak around 1690–1700 cm−1 likely related to amide I modes37 that have been described for primary amides (i.e. terminal CONH2 groups),38 or to H-bound COO− groups.39 PC2 scores, whose loading shows a main peak at 1645 cm−1, representative of amide I modes, group together the two-component systems in a slightly negative value area, suggesting similarities in their amide 3D arrangements with damped amide I intensity compared to Dff, conversely showing positive PC2 values. Similarly to amyloid fibrils, the high alignment of amide bonds along the fiber axis indeed produced the reduction of the amide I band intensity.40 PC3 showed a main peak at 1550 cm−1, ascribed to the amide II band and minor negative contributions of Asp COO− modes at 1586 and 1380 cm−1. It can thus be considered as a fingerprint of Asp, as also suggested by the grouping together of all Asp-containing samples.
In terms of catalytic activity, the racemic co-assembled fibrils composed of Hff and hFF (each one at 12.5 mM) displayed a kobs = 7.0 × 10−4 s−1 for the hydrolysis of p-nitrophenylacetate (pNPA, 1 mM) that was over 50% higher relative to that displayed by each enantiomer alone at the same overall concentration (25 mM, kobs = 5.0 × 10−4 s−1). This improvement of activity was ascribed to the increased presence of hydrophobic pockets, to accommodate the reaction substrate in the racemic rippled β-sheets, as confirmed by a fluorescence assay and molecular models.30 In contrast, addition of an equimolar amount of Dff (25 mM) to hFF led to a kobs = 4.8 × 10−4 s−1, thus with a marginal improvement relative to the tripeptide with His alone (see ESI Section S8†). Unfortunately, the analogous mixture of Dff with Hff (same stereoconfiguration) resulted in a significantly lower kobs = 1.8 × 10−4 s−1 (see ESI, Section S8†). It is plausible that the more organized packing of Dff + Hff, relative to the more disordered Dff + hFF shown by the PCA analysis on Nano-IR data and TEM data, does not accommodate the reaction substrate as well and/or that the interaction between Hff and Dff renders the catalytic sites less reactive.
Dff was concentrated under argon flow and then dissolved in a mixture of acetonitrile (MeCN, 30%) and milliQ water (70%) with 0.05% trifluoroacetic acid (TFA), these were also the solvents used for HPLC purification. The sample was centrifuged at 15000 rpm for 10 min, then 0.2 μm filtered prior to injection into the HPLC. The peptide was purified on an Agilent 1260 with a C-18 column (Kinetex, 5 μm, 100 Å, 250 × 10 mm, Phenomenex), T = 35 °C, flow = 3 mL min−1 with the following method: t = 0–2 min, 30% MeCN (0.05% TFA); t = 15 min, 56% MeCN (0.05% TFA), t = 15–18 min, 95% MeCN (0.05% TFA), t = 18–20 min, 95% MeCN (0.05% TFA). Rt = 4.7 min.
Footnote |
† Electronic supplementary information (ESI) available: Spectroscopic, rheological, and microscopic data. See DOI: https://doi.org/10.1039/d4fd00193a |
This journal is © The Royal Society of Chemistry 2025 |