A Matter of Charge: Electrostatically Tuned Coassembly of Amphiphilic Peptides

Coassembly of peptide biomaterials offers a compelling avenue to broaden the spectrum of hierarchically ordered supramolecular nanoscale structures that may be relevant for biomedical and biotechnological applications. In this work coassemblies of amphiphilic and oppositely charged, anionic and cationic, β-sheet peptides are studied, which may give rise to a diverse range of coassembled forms. Mixtures of the peptides show significantly lower critical coassembly concentration (CCC) values compared to those of the individual pure peptides. Intriguingly, the highest formation of coassembled fibrils is found to require excess of the cationic peptide whereas equimolar mixtures of the peptides exhibited the maximum folding into β-sheet structures. Mixtures of the peptides coassembled sequentially from solutions at concentrations surpassing each peptide's intrinsic critical assembly concentration (CAC), are also found to require a higher portion of the cationic peptide to stabilize hydrogels. This study illuminates a systematic investigation of oppositely charged β-sheet peptides over a range of concentrations, in solutions and in hydrogels. The results may be relevant to the fundamental understanding of such intricate charge-driven assembly systems and to the formulation of peptide-based nanostructures with diverse functionalities.

Developing Isomeric Peptides for Mimicking the Sequence-Activity Landscapes of Enzyme Evolution

Enzymes catalyze almost all material conversion processes within living organisms, yet their natural evolution remains unobserved. Short peptides, derived from proteins and featuring active sites, have emerged as promising building blocks for constructing bioactive supramolecular materials that mimic native proteins through self-assembly. Herein, we employ histidine-containing isomeric tetrapeptides KHFF, HKFF, KFHF, HFKF, FKHF, and FHKF to craft supramolecular self-assemblies, aiming to explore the sequence-activity landscapes of enzyme evolution. Our investigations reveal the profound impact of peptide sequence variations on both assembly behavior and catalytic activity as hydrolytic simulation enzymes. During self-assembly, a delicate balance of multiple intermolecular interactions, particularly hydrogen bonding and aromatic-aromatic interactions, influences nanostructure formation, yielding various morphologies (e.g., nanofibers, nanospheres, and nanodiscs). Furthermore, the analysis of the structure-activity relationship demonstrates a strong correlation between the distribution of the His active site on the nanostructures and the formation of the catalytic microenvironment. This investigation of the sequence-structure-activity paradigm reflects how natural enzymes enhance catalytic activity by adjusting the primary structure during evolution, promoting fundamental research related to enzyme evolutionary processes.

Metal Ion-Induced Unusual Stability of the Metastable Vesicle-like Intermediates Evolving during the Self-Assembly of Phenylalanine: Prominent Role of Surface Charge Inversion

The underlying mechanism and intermediate formation in the self-assembly of aromatic amino acids, peptides, and proteins remain elusive despite numerous reports. We, for the first time, report that one can stabilize the intermediates by tuning the metal ion-amino acid interaction. Microscopic and spectroscopic investigations of the self-assembly of carboxybenzyl (Z)-protected phenylalanine (ZF) reveal that the bivalent metal ions eventually lead to the formation of fibrillar networks similar to blank ZF whereas the trivalent ions develop vesicle-like intermediates that do not undergo fibrillation for a prolonged time. The time-lapse measurement of surface charge reveals that the surface charge of blank ZF and in the presence of bivalent metal ions changes from a negative value to zero, implying unstable intermediates leading to the fibril network. Strikingly, a prominent charge inversion from an initial negative value to a positive value in the presence of trivalent metal ions imparts unusual stability to the metastable intermediates.

Martinoid: the peptoid martini force field

Many exciting innovations have been made in the development of assembling peptoid materials. Typically, these have utilised large oligomeric sequences, though elsewhere the study of peptide self-assembly has yielded numerous examples of assemblers below 6-8 residues in length, evidencing that minimal peptoid assemblers are not only feasible but expected. A productive means of discovering such materials is through the application of in silico screening methods, which often benefit from the use of coarse-grained molecular dynamics (CG-MD) simulations. At the current level of development, CG models for peptoids are insufficient and we have been motivated to develop a Martini forcefield compatible peptoid model. A dual bottom-up and top-down parameterisation approach has been adopted, in keeping with the Martini parameterisation methodology, targeting the reproduction of atomistic MD dynamics and trends in experimentally obtained log D7.4 partition coefficients, respectively. This work has yielded valuable insights into the practicalities of parameterising peptoid monomers. Additionally, we demonstrate that our model can reproduce the experimental observations of two very different peptoid assembly systems, namely peptoid nanosheets and minimal tripeptoid assembly. Further we can simulate the peptoid helix secondary structure relevant for antimicrobial sequences. To be of maximum usefulness to the peptoid research community, we have developed freely available code to generate all requisite simulation files for the application of this model with Gromacs MD software.

Minimal Peptoid Dynamics Inform Self-Assembly Propensity

Peptoids are structural isomers of natural peptides, with side chain attachment at the amide nitrogen, conferring this class of compounds with the ability to access both cis and trans ω torsions as well as an increased diversity of ψ/φ states with respect to peptides. Sampling within these dimensions is controlled through side chain selection, and an expansive set of viable peptoid residues exists. It has been shown recently that "minimal" di- and tripeptoids with aromatic side chains can self-assemble into highly ordered structures, with size and morphological definition varying as a function of sequence pattern (e.g., XFF and FXF, where X = a nonaromatic peptoid monomer). Aromatic groups, such as phenylalanine, are regularly used in the design of minimal peptide assemblers. In recognition of this, and to draw parallels between these compounds classes, we have developed a series of descriptors for intramolecular dynamics of aromatic side chains to discern whether these dynamics, in a preassembly condition, can be related to experimentally observed nanoscale assemblies. To do this, we have built on the atomistic peptoid force field reported by Weiser and Santiso (CGenFF-WS) through the rigorous fitting of partial charges and the collation of Charmm General Force Field (CGenFF) parameters relevant to these systems. Our study finds that the intramolecular dynamics of side chains, for a given sequence, is dependent on the specific combination of backbone ω torsions and that homogeneity of sampling across these states correlates well with the experimentally observed ability to assemble into nanomorphologies with long-range order. Sequence patterning is also shown to affect sampling, in a manner consistent for both tripeptoids and tripeptides. Additionally, sampling similarities between the nanofiber forming tripeptoid, Nf-Nke-Nf in the cc state, and the nanotube forming dipeptide FF, highlight a structural motif which may be relevant to the emergence of extended linear assemblies. To assess these properties, a variety of computational approaches have been employed.

Hybrid Hydrogels of FKF-Peptide Assemblies and Gelatin for Sustained Antimicrobial Activity

The growing resistance of pathogenic bacteria to conventional antibiotics promotes the development of new antimicrobial agents, including peptides. Hydrogels composed of antimicrobial peptides (AMPs) may be applied as topical treatments for skin infection and wound regeneration. The unique antimicrobial and ultrashort-peptide FKF (Phe-Lys-Phe) was recently demonstrated to form bactericidal hydrogels. Here, we sought to improve the cyto-biocompatibility of FKF by combining FKF hydrogels with gelatin. Homogeneous hybrid hydrogels of FKF:gelatin were developed based on a series of self-assembly steps that involved mixing solutions of the two components with no covalent cross-linkers. The hydrogels were characterized for their structural features, dissolution, cyto-biocompatibility, and antibacterial properties. These hybrid hydrogels first release the antibacterial FKF assemblies, leaving the gelatinous fraction of the hydrogel to serve as a scaffold for tissue regeneration. Sponges of these hybrid hydrogels, obtained by lyophilization and rehydrated prior to application, exhibited enhanced antimicrobial activity compared to the hydrogels' formulations.

Modulating defibrillation by tryptophan-mediated photo cleavage of disulfide bonds

Dibenzyloxycarbonyl-l-cystine forms amyloid-like fibers and a hydrogel; however, on UV irradiation, Trp-mediated disulfide bond cleavage occurs, leading to defibrillation and a gel to sol transition.

Expanding the Conformational Landscape of Minimalistic Tripeptides by Their O-Glycosylation

We report on the supramolecular self-assembly of tripeptides and their O-glycosylated analogues, in which the carbohydrate moiety is coupled to a central serine or threonine flanked by phenylalanine residues. The substitution of serine with threonine introduces differential side-chain interactions, which results in the formation of aggregates with different morphology. O-glycosylation decreases the aggregation propensity because of rebalancing of the π interactions. The glycopeptides form aggregates with reduced stiffness but increased thermal stability. Our results demonstrate that the designed minimalistic glycopeptides retain critical functional features of glycoproteins and therefore are promising tools for elucidation of molecular mechanisms involved in the glycoprotein interactome. They can also serve as an inspiration for the design of functional glycopeptide-based biomaterials.

Assembly of cationic and amphiphilic β-sheet FKF tripeptide confers antibacterial activity

The race drawn against bacteria facing the evolution of antimicrobial resistance fuels research for new drugs and therapeutic strategies. FKF, a tripeptide that is cationic and amphiphilic was examined in light of its potential antimicrobial activity. Acid titration of purified peptide solution, 6% w/v (136 mM), yielded a hydrogel at pH~ 4. Cryo-TEM images of FKF revealed distinct phases formed upon increase in pH, ranging from elongated needles, uniform width fibers, sheets and tubular structures. ¹H NMR attested FKF charged states as function of pH, and CD and FTIR measurements indicated that FKF β-sheet assemblies are held by both π-π stacking and H-bonds. FKF hydrogel displayed bactericidal activity against E. coli and P. aeruginosa with a 3-log reduction in bacterial counts. The hydrogel was also found effective in reducing P. aeruginosa contamination in a skin lesion model in rats. FKF forms a unique antimicrobial peptide-hydrogel, showing neglectable effect in dissolved state, yet only when fibrillary assembled it gains functionality. STATEMENT OF SIGNIFICANCE: Ultra-short peptides are at the frontier of peptide self-assembly research. The tripeptide FKF assumes distinct assembly forms that are a function of pH, for which we have pinpointed the accompanying changes in charge. Made of natural amino acids, FKF forms a pure peptide hydrogel phase, which is intrinsically antimicrobial. We demonstrate that antimicrobial effect is only assumed by the peptide assemblies, posing self-assembly as a pre-requisite for FKF's bactericidal effect. This system provides evidence for the link between specific microscopic peptide assembled structures, macroscopic gel formation and antimicrobial effect, utilized to alleviate bacterial contamination in vivo.

Smart Thixotropic Hydrogels by Disulfide-Linked Short Peptides for Effective Three-Dimensional Cell Proliferation

Supramolecular assembly of short peptides is a crucial process and has shown numerous potential applications as biomaterials. In the present work, the hydrogelation process of short peptides containing C-terminal "Lys-Cys" (KC) residues have been studied in detail. The N-terminal capping is found to be essential for effective gelation. Out of 12 peptides we studied, two of them could form hydrogels efficiently: Ac-VVKC-NH₂ and Ac-FFKC-NH₂. In both cases, the monomer-to-dimer formation through disulfide linkages by Cys residues controls the aggregation process. Interestingly, the presence of H₂O₂ facilitated the dimerization and thereby reduced the gelation time but could not impart much effect on the mechanical properties of the gels. Detailed rheological study revealed that both hydrogels are thixotropic in nature. Moreover, they are responsive to glutathione (GSH) due to the presence of disulfide linkages. However, the hydrogel of Ac-FFKC-NH₂ is found to be stronger and more effective for biological applications. The thixotropic nature as well as a model drug release study in response to varying GSH concentration indicates the possible use of the hydrogel as an injectable local drug delivery vehicle. The hydrogel of Ac-FFKC-NH₂ is noncytotoxic in nature. Three-dimensional cell proliferation has been found to be more effective than 2D, as it mimics the in vivo situation more closely if not exactly. In the present study, we have shown that both differentiated RAW macrophages and undifferentiated THP-1 monocytes could proliferate significantly within the 3D matrix of the hydrogel, without depicting any apparent cytotoxicity. Thus, the hydrogel of Ac-FFKC-NH₂ has potential for application in localized drug administration and as a supporting biomaterial to study basic phenomena involving cell behavior.

H2S-releasing amphiphilic dipeptide hydrogels are potent S. aureus biofilm disruptors

As a gasotransmitter, hydrogen sulfide (H2S) has been studied to treat wounds and inflammation, but its potential antimicrobial effects in this context have not been evaluated. An H2S-releasing dipeptide hydrogel (S-FE), and several non-H2S-releasing control dipeptides, (C-FE, C-GE, FBA-FE, and FE where S = S-aroylthiooxime, an H2S donor; C = control, an oxime incapable of H2S release; FBA = 4-formylbenzamide, also incapable of H2S release; and E, F, G = glutamic acid, phenylalanine, and glycine, respectively), were studied to correlate differences in their chemical structures and H2S-releasing abilities with their antimicrobial effects on Staphylococcus aureus bacteria. Dipeptides with Phe (S-FE, C-FE, and FE) self-assembled into nanoribbons in water and displayed β-sheet formation and enhanced fluorescence, while the other two dipeptides (FBA-FE and C-GE) did not form assemblies in water. In vitro experiments with Staphylococcus aureus, which is a commonly found bacterium associated with wounds, showed significant antimicrobial effects from some of the dipeptides. Dipeptide S-FE inhibited bacterial growth more effectively than any of the controls, thereby limiting biofilm formation or disrupting established biofilms. These antimicrobial H2S-releasing dipeptide hydrogels provide a promising new approach to treat wound infections.

Self-Assembly of Minimal Peptoid Sequences

Peptoids are biofunctional N-substituted glycine peptidomimics. Their self-assembly is of fundamental interest because they demonstrate alternatives to conventional peptide structures based on backbone chirality and beta-sheet hydrogen bonding. The search for self-assembling, water-soluble "minimal" sequences, be they peptide or peptidomimic, is a further challenge. Such sequences are highly desired for their compatibility with biomacromolecules and convenient synthesis for broader application. We report the self-assembly of a set of trimeric, water-soluble α-peptoids that exhibit a relatively low critical aggregation concentration (CAC ∼ 0.3 wt %). Cryo-EM and angle-resolved DLS show different sequence-dependent morphologies, namely uniform ca. 6 nm wide nanofibers, sheets, and clusters of globular assemblies. Absorbance and fluorescence spectroscopies indicate unique phenyl environments for π-interactions in the highly ordered nanofibers. Assembly of our peptoids takes place when the sequences are fully ionized, representing a departure from superficially similar amyloid-type hydrogen-bonded peptide nanostructures and expanding the horizons of assembly for sequence-specific bio- and biomimetic macromolecules.

Amphiphilic hydrogels for biomedical applications

We highlight the recent advances in the fabrication and biomedical application of amphiphilic hydrogels.

Structural Polymorphism in a Self-Assembled Tri-Aromatic Peptide System

Self-assembly is a process of key importance in natural systems and in nanotechnology. Peptides are attractive building blocks due to their relative facile synthesis, biocompatibility, and other unique properties. Diphenylalanine (FF) and its derivatives are known to form nanostructures of various architectures and interesting and varied characteristics. The larger triphenylalanine peptide (FFF) was found to self-assemble as efficiently as FF, forming related but distinct architectures of plate-like and spherical nanostructures. Here, to understand the effect of triaromatic systems on the self-assembly process, we examined carboxybenzyl-protected diphenylalanine (z-FF) as a minimal model for such an arrangement. We explored different self-assembly conditions by changing solvent compositions and peptide concentrations, generating a phase diagram for the assemblies. We discovered that z-FF can form a variety of structures, including nanowires, fibers, nanospheres, and nanotoroids, the latter were previously observed only in considerably larger or co-assembly systems. Secondary structure analysis revealed that all assemblies possessed a β-sheet conformation. Additionally, in solvent combinations with high water ratios, z-FF formed rigid and self-healing hydrogels. X-ray crystallography revealed a "wishbone" structure, in which z-FF dimers are linked by hydrogen bonds mediated by methanol molecules, with a 2-fold screw symmetry along the c-axis. All-atom molecular dynamics (MD) simulations revealed conformations similar to the crystal structure. Coarse-grained MD simulated the assembly of the peptide into either fibers or spheres in different solvent systems, consistent with the experimental results. This work thus expands the building block library for the fabrication of nanostructures by peptide self-assembly.

Oligonucleotide promoted peptide bond formation using a tRNA mimicking approach

TransferRNA's role in protein translation is the prime example of an Informational Leaving Group (ILG). A simplified model produced oligophenylalanine with a modified uracil as an ILG in the presence of specific oligonucleotides. Our preliminary studies contribute to the importance of hybrid species in bridging the gap between peptides and nucleic acids.

RGD-presenting peptides in amphiphilic and anionic β-sheet hydrogels for improved interactions with cells

The interest in developing functional biomaterials based on designed peptides has been increasing in recent years. The amphiphilic and anionic β-sheet peptide Pro-Asp-(Phe-Asp)5-Pro, denoted FD, was previously shown to assemble into a hydrogel that induces adsorption of calcium and phosphate ions and formation of the bone mineral hydroxyapatite. In this study the integrin binding peptide, Arg-Gly-Asp (RGD), was incorporated into the hydrogel to assess its influence on an osteoblast culture. In solutions and in hydrogels FD fibrils dominated the assembly structures for up to 25 mol% FD-RGD incorporation. The cellular density of osteoblasts cultured in hydrogels composed of 25 mol% FD-RGD in FD was higher than that of only FD hydrogel cultures. These results demonstrate that RGD and possibly other cell binding motifs can be combined into amphiphilic and anionic β-sheet hydrogels, using the design principles of FD and FD-RGD systems, to enhance interactions with cells.