Phenylalanine-based fibrillar systems.

Phenylketonuria (PKU) is an inborn metabolic disorder characterized by excess accumulation of phenylalanine (Phe) and its fibril formation, resulting in progressive intellectual disability. Several research groups have approached from various directions to understand the formation of toxic amyloid fibrils from the essential amino acid Phe. Different parameters like the nature of the solvent, pH, Phe concentration, temperature, etc. influence the fibril formation kinetics. In this article, we have summarized all major findings regarding the formation of Phe-based fibrils in aqueous and organic media and discussed how non-covalent interactions are involved in the self-assembly process using spectroscopic and microscopic techniques. The toxicity of Phe-based fibrils is compared with other neurodegenerative peptides. It is noted that the Phe-based fibrils can also induce various globular proteins into toxic fibrils. Later, we discuss the different approaches to inhibit fibril formation and reduce its toxicity. The presence of polyphenolic compounds, drugs, amino acids, nanoparticles, metal ions, crown ethers, and others showed a remarkable inhibitory effect on fibril formation. To the best of our knowledge, this is the first-ever etymological analysis of the Phe-fibrillar system and its inhibition to create a strong database against PKU.

Probing Molecular Chirality on the Self-Assembly and Gelation of Naphthalimide-Conjugated Dipeptides.

In this work, 1,8-naphthalimide (NMI)-conjugated three hybrid dipeptides constituted of a ß-amino acid and an α-amino acid have been designed, synthesized, and purified. Here, in the design, the chirality of the α-amino acid was varied to study the effect of molecular chirality on the supramolecular assembly. Self-assembly and gelation of three NMI conjugates were studied in mixed solvent systems [water and dimethyl sulphoxide (DMSO)]. Interestingly, chiral NMI derivatives [NMI-ßAla-lVal-OMe (NLV) and NMI-ßAla-dVal-OMe (NDV)] formed self-supported gels, while the achiral NMI derivative [NMI-ßAla-Aib-OMe, (NAA)] failed to form any kind of gel at 1 mM concentration and in a mixed solvent (70% water in DMSO medium). Self-assembly processes were thoroughly investigated using UV-vis spectroscopy, nuclear magnetic resonance (NMR), fluorescence, and circular dichroism (CD) spectroscopy. A J-type molecular assembly was observed in the mixed solvent system. The CD study indicated the formation of chiral assembled structures for NLV and NDV, which were mirror images of one another, and the self-assembled state by NAA was CD-silent. The nanoscale morphology of the three derivatives was studied using scanning electron microscopy (SEM). In the case of NLV and NDV, left- and right-handed fibrilar morphologies were observed, respectively. In contrast, a flake-like morphology was noticed for NAA. The DFT study indicated that the chirality of the α-amino acid influenced the orientation of π-π stacking interactions of naphthalimide units in the self-assembled structure that in turn regulated the helicity. This is a unique work where molecular chirality controls the nanoscale assembly as well as the macroscopic self-assembled state.

Tuning of the Supramolecular Helicity of Peptide-Based Gel Nanofibers.

Helical supramolecular architectures play important structural and functional roles in biological systems. The helicity of synthetic molecules can be tuned mainly by the chiral manipulation of the system. However, tuning of helicity by the achiral unit of the molecules is less studied. In this work, the helicity of naphthalimide-capped peptide-based gel nanofibers is tuned by the alteration of methylene units present in the achiral amino acid. The inversion of supramolecular helicity has been extensively studied by CD spectroscopy and morphological analysis. The density functional theory (DFT) study indicates that methylene spacers influence the orientation of π-π stacking interactions of naphthalimide units in the self-assembled structure that regulates the helicity. This work illustrates a new approach to tuning the supramolecular chirality of self-assembled biomaterials.

Single Amino-Acid Based Self-Assembled Biomaterials with Potent Antimicrobial Activity.

The design and development of soft biomaterials based on amino acid and short-peptide have gained much attention due to their potent biomedical applications. A slight alteration in the side-chain of single amino acid in a peptide or protein sequence has a huge impact on the structure and function. Phenylalanine is one of the most studied amino acids, which contains an aromatic phenyl group connected through a flexible -CH2 - unit. In this work, we have examined whether flexibility and aromatic functionality of phenylalanine (Phe) are important in gel formation of model gelator Fmoc-Phe-OH or not. To examine this hypothesis, we synthesized Fmoc-derivatives of three analogues unnatural amino acids including cyclohexylalanine, phenylglycine, and homophenylalanine; which are slightly varied from Phe. Interestingly, all these three new analogues formed hydrogels in phosphate buffer at pH 7.0 having different gelation efficacy and kinetics. This study suggests that the presence of aromatic side-chain and flexibility are not mandatory for the gelation of this model gelator. Newly synthesized unnatural amino acid derivatives have also exhibited promising antimicrobial activity towards gram-positive bacteria by inhibiting cellular oxygen consumption. We further determined the biocompatibility of these amino acid derivatives by using a hemolysis assay on human blood cells. Overall studies described the development of single amino acid-based new injectable biomaterials with improved antimicrobial activity by the slight alteration in the side-chain of amino acid.

Supramolecular Antiparallel ß-Sheet Formation by Tetrapeptides Based on Amyloid Sequence.

Self-assembly of short peptides has emerged as an interesting research field for a wide range of applications. Recently, several truncated fragments of long-chain peptides or proteins responsible for different neurodegenerative diseases were studied to understand whether they can mimic the property and function of native peptides or not. It was reported that such a kind of peptide adopts a ß-sheet structure in the disease state. It was observed that aromatic amino acid-rich peptide fragments possess a high tendency to adopt a ß-sheet conformation. In this article, we are first time reporting the crystal structure of two tetrapeptides: Boc-GAII-OMe (Peptide 1) and Boc-GGVV-OMe (Peptide 2), composed of aliphatic amino acids, and the sequences are similar to the Aß-peptide fragments Aß29-32 and Aß37-40 , respectively. In the solid-state, they are self-assembled in an antiparallel ß-sheet fashion. The peptide units are connected by the strong amide hydrogen-bonding (N-H···O) interactions. Apart from that, other noncovalent interactions are also present, which help to stabilize the cross-ß-sheet arrangement. Interestingly, in the crystal structure of Peptide 1, noncovalent C···C interaction between the electron-deficient carbonyl carbon, and the electron-rich sp3-carbon atom is observed, which is quite rare in the literature. The calculated torsion angles for these peptides are lying in the ß-sheet region of the Ramachandran plot. FT-IR studies also indicate the formation of an antiparallel ß-sheet structure in the solid-state. Circular dichroism of the peptides in the aqueous solution also suggests the presence of predominantly ß-sheet-like conformation in the aqueous solution. Under cross-polarized light, Congo Red stained both peptides showed green-gold color due to birefringence indicating their amyloidogenic nature. This result indicates that the short peptide composed of aliphatic amino acid is capable of forming a ß-sheet structure in the absence of aromatic amino acid and also can mimic the function of the native amyloid peptide.

Self-assembling behaviour of a modified aromatic amino acid in competitive medium.

Aromatic amino acid, specifically phenylalanine (Phe), is one of the most studied building blocks in peptide synthesis due to its importance in biology. It is reported in the literature that Phe-containing peptides have a high tendency to form different self-assembled materials due to efficient aromatic-aromatic interactions. In this article, we have tuned the supramolecular interactions of phenylalanine by making it electron-deficient upon introduction of the nitro group in the ring. The presence of the nitro group has a profound influence on the self-assembly process. It has been observed that 4-nitrophenylalanine (4NP) is a highly efficient gelator compared with the native phenylalanine in DMSO solvent in terms of minimum gelation concentration and it forms hydrogen bonding mediated crystals in water. The change of self-assembling patterns of 4NP in these solvents was studied using X-ray diffraction, UV-Vis spectroscopy, FE-SEM and other techniques. With the help of different experimental data and density functional theory (DFT), we have simulated the theoretical structure of 4NP in DMSO. The theoretical structure of 4NP in DMSO is different compared with that of crystals in water. We then studied the self-assembly process of 4NP in the mixed solvent of DMSO (polar aprotic) and water (polar protic). Different competitive non-covalent interactions of solvents as well as the ratio of the solvent mixture guide the final self-assembly state of 4NP.

Supramolecular Hydrogel from an Oxidized Byproduct of Tyrosine.

Herein we report for the first time the supramolecular hydrogelation of a derivative of 3-nitrotyrosine (3-NT), which is an oxidized byproduct of tyrosine, produced in the presence of reactive nitrogen species in the cell. The 9-fluorenylmethyloxycarbonyl (Fmoc) derivative of 3-NT, FNT, can form self-supported hydrogels at a wide range of pH values (4.5-8.5) in 50 mM phosphate buffer solutions. Hydrogels prepared at pH 7.0 are yellow, transparent, and thixotropic in nature. A yellow hydrogel was obtained by changing the pH from 4.5 to 8.5. Moreover, the gelation efficiency of the FNT gelator was enhanced by lowering the pH of the buffer solution. pH-Dependent self-assembly properties of the gelator were studied by using UV-vis, fluorescence, and circular dichroism spectroscopy and wide-angle X-ray diffraction techniques. Field-emission-scanning electron microscopy and transmission electron microscopy studies of the self-assembled FNT hydrogel showed a nanofibrillar network structure. Interestingly, the hydrogel showed injectable behavior at physiological pH. The low cytotoxicity value and high antimicrobial properties of the hydrogel indicated that it is a potential material for biomedical applications.

Emergence of native peptide sequences in prebiotic replication networks.

Biopolymer syntheses in living cells are perfected by an elaborate error correction machinery, which was not applicable during polymerization on early Earth. Scientists are consequently striving to identify mechanisms by which functional polymers were selected and further amplified from complex prebiotic mixtures. Here we show the instrumental role of non-enzymatic replication in the enrichment of certain product(s). To this end, we analyzed a complex web of reactions in ß-sheet peptide networks, focusing on the formation of specific intermediate compounds and template-assisted replication. Remarkably, we find that the formation of several products in a mixture is not critically harmful, since efficient and selective template-assisted reactions serve as a backbone correction mechanism, namely, for keeping the concentration of the peptide containing the native backbone equal to, or even higher than, the concentrations of the other products. We suggest that these findings may shed light on molecular evolution processes that led to current biology.The synthesis of biopolymers in living cells is perfected by complex machinery, however this was not the case on early Earth. Here the authors show the role of non-enzymatic replication in the enrichment of certain products within prebiotically relevant mixtures.

The Strong Influence of Structure Polymorphism on the Conductivity of Peptide Fibrils.

Peptide fibril nanostructures have been advocated as components of future biotechnology and nanotechnology devices. However, the ability to exploit the fibril functionality for applications, such as catalysis or electron transfer, depends on the formation of well-defined architectures. Fibrils made of peptides substituted with aromatic groups are described presenting efficient electron delocalization. Peptide self-assembly under various conditions produced polymorphic fibril products presenting distinctly different conductivities. This process is driven by a collective set of hydrogen bonding, electrostatic, and π-stacking interactions, and as a result it can be directed towards formation of a distinct polymorph by using the medium to enhance specific interactions rather than the others. This method facilitates the detailed characterization of different polymorphs, and allows specific conditions to be established that lead to the polymorph with the highest conductivity.

Peptide based hydrogels for cancer drug release: modulation of stiffness, drug release and proteolytic stability of hydrogels by incorporating d-amino acid residue(s).

Synthetic tripeptide based noncytotoxic hydrogelators have been discovered for releasing an anticancer drug at physiological pH and temparature. Interestingly, gel stiffness, drug release capacity and proteolytic stability of these hydrogels have been successfully modulated by incorporating d-amino acid residues, indicating their potential use for drug delivery in the future.

Emergent Catalytic Behavior of Self-Assembled Low Molecular Weight Peptide-Based Aggregates and Hydrogels.

We report a series of short peptides possessing the sequence (FE)n or (EF)n and bearing l-proline at their N-terminus that self-assemble into high aspect ratio aggregates and hydrogels. We show that these aggregates are able to catalyze the aldol reaction, whereas non-aggregated analogues are catalytically inactive. We have undertaken an analysis of the results, considering the accessibility of catalytic sites, pKa value shifts, and the presence of hydrophobic pockets. We conclude that the presence of hydrophobic regions is indeed relevant for substrate solubilization, but that the active site accessibility is the key factor for the observed differences in reaction rates. The results presented here provide an example of the emergence of a new chemical property caused by self-assembly, and support the relevant role played by self-assembled peptides in prebiotic scenarios. In this sense, the reported systems can be seen as primitive aldolase I mimics, and have been successfully tested for the synthesis of simple carbohydrate precursors.

Multi-stimuli responsive self-healing metallo-hydrogels: tuning of the gel recovery property.

A series of amphiphilic tyrosine based self-healable, multi-stimuli responsive metallo-hydrogels have been discovered. Formation of these hydrogels is highly selective to Ni(2+) ions. The self-healing property and the stiffness of these metallo-hydrogels can be tuned by varying the chain length of the corresponding gelator amphiphile.

Assembly of naphthalenediimide conjugated peptides: aggregation induced changes in fluorescence.

Naphthalenediimide appended peptide based self-assembly was studied. Interestingly, an aggregation induced drastic change in the fluorescence property and gel formation were observed depending on the solvent composition (chloroform : methylcyclohexane) at a fixed concentration of 1.6 mM at room temperature.

Formation of hybrid hydrogels consisting of tripeptide and different silver nanoparticle-capped ligands: modulation of the mechanical strength of gel phase materials.

An N-terminally Boc (tert-butyloxycarbonyl) group-protected synthetic tripeptide (Boc-Phe-Phe-Ala-OH) has been found to form a translucent hydrogel in basic aqueous medium. This hydrogel material has been characterized using field emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), Fourier transformed infrared spectroscopy, differential scanning calorimetric, X-ray diffraction (XRD), and rheological studies. FE-SEM and TEM studies have revealed the formation of a nanofibrillar network structure upon gelation. Thiol (-SH) containing ligands (amino acid/peptide) have been used to stabilize small silver nanoparticles (AgNPs), and these thiol-capped silver nanoparticles have been incorporated into this hydrogel to prepare hybrid hydrogels. Morphological study of silver nanoparticles containing a hybrid hydrogel (using TEM experiments) has indicated the nice fabrication of AgNPs along the gel nanofibers. Fabrication of nanoparticles upon the gel nanofibers is due to noncovalent interactions between the capping ligands of the nanoparticles and the peptide-based hydrogel nanofibers. Rheological investigations of these hybrid hydrogels have shown the weakening of the mechanical strength of the hydrogel after incorporation of AgNPs within the native hydrogel system. Our studies have vividly shown the dependence of the elastic modulus (G') and yield stress (σ(y)) on three factors: (a) the nature of the stabilizing ligands used for AgNPs, (b) the size of the AgNPs, and (c) the amount of AgNPs used for the preparation of hybrid hydrogel systems. Modulation of the mechanical strength of the hybrid hydrogel can be successfully achieved by varying these above-mentioned factors. This modulation of the mechanical properties keeps a future promise to make tunable soft materials with interesting properties.

Pyrene-containing peptide-based fluorescent organogels: inclusion of graphene into the organogel.

The N-terminally pyrene-conjugated oligopeptide, Py-Phe-Phe-Ala-OMe, (Py=pyrene 1-butyryl acyl) forms transparent, stable, supramolecular fluorescent organogels in various organic solvents. One of these organogels was thoroughly studied using various techniques including transmission electron microscopy (TEM), field-emission scanning electron microscopy (FESEM), atomic force microscopy (AFM), Fourier-transform infrared (FTIR) spectroscopy, photoluminescence (PL) spectroscopy, and rheology. Unfunctionalized and non-oxidized graphene was successfully incorporated into this fluorescent organogel in o-dichlorobenzene (ODCB) to form a stable hybrid organogel. Graphene is well dispersed into the gel medium by using non-covalent π-π stacking interactions with the pyrene-conjugated gelator peptide. In the presence of graphene, the minimum gelation concentration (mgc) of the hybrid organogel was lowered significantly. This suggests that there is a favorable interaction between the graphene and the gelator peptide within the hybrid organogel system. This hybrid organogel was characterized using TEM, AFM, FTIR, PL, and rheological studies. The TEM study of graphene-containing hybrid organogel revealed the presence of both graphene sheets and entangled gel nanofibers. The AFM study indicated the presence of 3 to 4 layers in exfoliated graphene in ODCB and the presence of both graphene nanosheets and the network of gel nanofibers in the hybrid gel system. The rheological investigation suggested that the flow of the hybrid organogel had become more resistant towards the applied angular frequency upon the incorporation of graphene into the organogel. The hybrid gel is about seven times more rigid than that of the native gel.

Organogels from different self-assembling new dendritic peptides: morphology, rheology, and structural investigations.

Three new peptide based dendrimers with different generations were synthesized, purified, and characterized. Each of these dendrimers form efficient organogels under suitable conditions and these gels were characterized by field emission scanning electron microscopy (FE-SEM), high resolution transmission electron microscopy (HR-TEM), atomic force microscopy (AFM), Fourier transformed infrared (FT-IR) spectroscopy, differential scanning calorimetry (DSC) and rheology. It has been observed that gel forming propensity increases from first to second generation dendrimer and it decreases from second to third generation. The hydrogen bonding interaction is the main driving force for the formation of aggregated structure that leads to the formation of a fibrillar network, responsible for gelation. The morphology is network type consisting of taped or twisted fibrils spanning throughout the space. DSC measurements show the thermoreversible first-order phase transition. Rheological studies indicate that flow behavior and segmental motion of these gels are different for different peptidic gels, obtained from various generations of dendritic peptides.

Fabrication of luminescent CdS nanoparticles on short-peptide-based hydrogel nanofibers: tuning of optoelectronic properties.

The pH-induced self-assembly of three synthetic tripeptides in water medium is used to immobilize luminescent CdS nanoparticles. These peptides form a nanofibrillar network structure upon gelation in aqueous medium at basic pH values (pH 11.0-13.0), and the fabrication of CdS nanoparticles on the gel nanofiber confers the luminescent property to these gels. Atomic force microscopy, field-emission scanning electron microscopy, and high-resolution transmission electron microscopy clearly reveal the presence of CdS nanoparticles in a well-defined array on the gel nanofibers. This is a convenient way to make organic nanofiber-inorganic nanoparticle hybrid nanocomposite systems. The size of the CdS nanoparticles remains almost same before and after deposition on the gel nanofiber. Photoluminescence (PL) measurement of the CdS nanoparticles upon deposition on the gel nanofibers shows a significant blue shift in the emission spectrum of the nanoparticles, and there is a considerable change in the PL gap energy of the CdS nanoparticles after immobilization on different gel nanofibrils. This finding suggests that the optoelectronic properties of CdS nanoparticles can be tuned upon deposition on gel nanofibers without changing the size of the nanoparticles.