Minimalist Prion-Inspired Polar Self-Assembling Peptides

Abstract

Nature provides copious examples of self-assembling supramolecular nanofibers. Among them, amyloid structures have found amazing applications as advanced materials in fields such as biomedicine and nanotechnology. Prions are a singular subset of proteins able to switch between a soluble conformation and an amyloid state. The ability to transit between these two conformations is encoded in the so-called prion domains (PrDs), which are long and disordered regions of low complexity, enriched in polar and uncharged amino acids such as Gln, Asn, Tyr, Ser, and Gly. The polar nature of PrDs results in slow amyloid formation, which allows kinetic control of fiber assembly. This approach has been exploited for fabrication of multifunctional materials because in contrast to most amyloids, PrDs lack hydrophobic stretches that can nucleate their aggregation, their assembly depends on the establishment of a large number of weak interactions along the complete domain. The length and low complexity of PrDs make their chemical synthesis for applied purposed hardly affordable. Here, we designed four minimalist polar binary patterned peptides inspired in PrDs, which include the [Q/N/G/S]-Y-[Q/N/G/S] motif frequently observed in these domains: NYNYNYN, QYQYQYQ, SYSYSYS, and GYGYGYG. Despite their small size, they all recapitulate the properties of full-length PrDs, self-assembling into nontoxic amyloids under physiological conditions. Thus, they constitute small building blocks for the construction of tailored prion-inspired nanostructures. We exploited Tyr residues in these peptides to generate highly stable dityrosine cross-linked assemblies for the immobilization of metal nanoparticles in the fibrils surface and to develop an electrocatalytic amyloid scaffold. Moreover, we show that the shorter and more polar NYNNYN, QYQQYQ, and SYSSYS hexapeptides also self-assemble into amyloid-like structures, consistent with the presence of these tandem motifs in human prion-like proteins.

Relevance of Electrostatic Charges in Compactness, Aggregation, and Phase Separation of Intrinsically Disordered Proteins

“…In this subclass of amyloids, which are self-perpetuating and infectious, sequence determinants have been elusive for years, since cryptically encoded by rather long (at least 60 residues) and disordered sequences, containing a few amino acid types (i.e., low-complexity regions) rich of Tyr, Gly, and polar residues (mostly Gln and Asn) [90,[93][94][95], which argue for the involvement of hydrogen bonds, van der Waals, and π-π stacking interactions [96][97][98]. Short linear sequence motifs rich in polar residues (e.g., SYSGYS from human FUS protein, or GNNQQNY from yeast Sup35) have also been recognized as "nucleation centers" or "soft-amyloid cores", effectively promoting both spontaneous and seeded aggregation in proteins [99,100], and natural and synthetic peptides [101][102][103].…”

Guiding the Morphology of Amyloid Assemblies by Electrostatic Capping: from Polymorphic Twisted Fibrils to Uniform Nanorods

“…The rational design and usage of defined amyloid‐based nanostructures are still being hindered by several issues, which include the high aggregation propensity of amyloidogenic β‐sheet‐forming sequences, the lack of control over the self‐assembly process and the difficulty of predicting the final supramolecular architecture from the primary sequence . In contrast to polymers built on covalent bonds, bottom‐up polypeptide amyloid self‐assembly relies on the formation of a complex and organized network of intermolecular noncovalent interactions . The difficulty of controlling amyloid formation arises from this delicate interplay between several factors triggering nucleation and elongation,7,13a including hydrophobic interactions, hydrogen bonding, electrostatic interactions, and environmental conditions .…”

Prion-based nanomaterials and their emerging applications

“…Nevertheless, the de novo design of prion-inspired self-assembling peptides for nanotechnology applications remained essentially unexplored. To fill this gap we rationally designed four minimalist polar binary patterned peptides bioinspired on prion sequences and exploited them for the obtention of biomaterials with unique properties [66]. The design combined the five most enriched residues in PrDs, Asn, Gln, Ser, Gly and Tyr in a binary pattern, with only seven residues in length, resulting in four heptapeptides: NYNYNYN, QYQYQYQ, SYSYSYS and GYGYGYG.…”

“…We assessed the electrocatalytic ability of our four self-assembled nanostructures by exposing them to copper (II) as an oxidizing agent, in the presence of distilled pyrrole vapor. The fibrils catalyzed efficiently the polymerization of individual pyrrol moieties into a macromolecular polypyrrole (PPy) material ( Figure 2) [66]. Importantly, not all the peptides exhibited the same electrocatalytic activity, which indicated that this property was sequence dependent and, accordingly, that it can be potentially tuned to develop synthetic prion-inspired nanodevices with different catalytic properties.…”

“…In second place, the aggregated state is reversible under certain conditions, offering the possibility to design tunable materials that can be polymerized or depolymerized on demand. This feature can be exploited, for instance, in the obtention of nanomaterials which functionality can be controlled by switching the temperature, the ionic strength or the pH of the solution, Nevertheless, if a more stable fibrillar structure is required, this reversibility can be easily tuned off introducing post-assembly covalent interactions, either by including Cys residues in the sequence, which allows disulfide bridge formation [70] or by artificially inducing post-translational modifications such as Di-Tyr cross-links [66]. It is also important to highlight that, in contrast to the harsh conditions usually employed to induce the partial unfolding of classical amyloid proteins, the transition from the soluble to the fibrillar state in natural, but also in designed prionic sequences occurs under mild conditions.…”