Controlled aggregation of peptide–DNA hybrids into amyloid-like fibrils

Self-assembly of a peptide sequence, EKKE, composed of exclusively charged amino acids: Role of charge in morphology and lead binding

The self-assembly of peptides is influenced by their amino acid sequence and other factors including pH, charge, temperature, and solvent. Herein, we explore whether a four-residue sequence, EKKE, consisting of exclusively charged amino acids shows the propensity to form self-assembled ordered nanostructures and whether the overall charge plays any role in morphological and functional properties. From a combination of experimental data provided by Thioflavin T fluorescence, Congo red absorbance, circular dichroism spectroscopy, dynamic light scattering, field emission-scanning electron microscopy, atomic force microscopy, and confocal microscopy, it is clear that the all-polar peptide and charged EKKE sequence shows a pH-dependent tendency to form amyloid-like structures, and the self-assembled entities under acidic, basic and neutral conditions exhibit morphological variation. Additionally, the ability of the self-assembled amyloid nanostructures to bind to the toxic metal, lead (Pb²⁺ ), was demonstrated from the analysis of the ultraviolet absorbance and X-ray photoelectron spectroscopy data. The modulation at the sequence level for the amyloid-forming EKKE scaffold can further extend its potential role not only in the remediation of other toxic metals but also towards biomedical applications.

Tuning dynamic DNA- and peptide-driven self-assembly in DNA-peptide conjugates

DNA-peptide conjugates offer an opportunity to marry the benefits of both biomolecular classes, combining the high level of programmability found with DNA, with the chemical diversity of peptides. These hybrid systems offer potential in fields such as therapeutics, nanotechnology, and robotics. Using the first DNA-β-turn peptide conjugate, we present three studies investigating the self-assembly of DNA-peptide conjugates over a period of 28 days. Time-course studies, such as these have not been previously conducted for DNA-peptide conjugates, although they are common in pure peptide assembly, for example in amyloid research. By using aging studies to assess the structures produced, we gain insights into the dynamic nature of these systems. The first study explores the influence varying amounts of DNA-peptide conjugates have on the self-assembly of our parent peptide. Study 2 explores how DNA and peptide can work together to change the structures observed during aging. Study 3 investigates the presence of orthogonality within our system by switching the DNA and peptide control on and off independently. These results show that two orthogonal self-assemblies can be combined and operated independently or in tandem within a single macromolecule, with both spatial and temporal effects upon the resultant nanostructures.

Nutrient-sensing amyloid metastasis

Amyloids are organized suprastructural polypeptide arrangements. The prevalence of amyloid-related processes of pathophysiological relevance has been linked to aging-related degenerative diseases. Besides the role of genetic polymorphisms on the relative risk of amyloid diseases, the contributions of nongenetic ontogenic cluster of factors remain elusive. In recent decades, mounting evidences have been suggesting the role of essential micronutrients, in particular transition metals, in the regulation of amyloidogenic processes, both directly (such as binding to amyloid proteins) or indirectly (such as regulating regulatory partners, processing enzymes, and membrane transporters). The features of transition metals as regulatory cofactors of amyloid proteins and the consequences of metal dyshomeostasis in triggering amyloidogenic processes, as well as the evidences showing amelioration of symptoms by dietary supplementation, suggest an exaptative role of metals in regulating amyloid pathways. The self- and cross-talk replicative nature of these amyloid processes along with their systemic distribution support the concept of their metastatic nature. The role of amyloidosis as nutrient sensors would act as intra- and transgenerational epigenetic metabolic programming factors determining health span and life span, viability, which could participate as an evolutive selective pressure.

A new aggregation induced emission enhancement (AIEE) dye which self-assembles to panchromatic fluorescent flowers and has application in sensing dichromate ions

We report for the very first time the crystal structure and self-assembly of a new aggregation-induced emission enhancement (AIEE) dye 4-(5-methoxythiazolo[4,5-b]pyridin-2-yl)-N,N-dimethylaniline (TPA) and its application in sensing dichromate ions. TPA reveals cyan blue emission under UV and visible light. The self-assembly properties of TPA were studied extensively by scanning electron microscopy (SEM) which revealed the formation of beautiful flower-like morphologies. These structures revealed both green and red fluorescence under FITC and rhodamine filters respectively when observed through fluorescence microscopy connoting the panchromatic emission properties of TPA from blue to red. The interactions which cause self-assembled structure formation in TPA were also validated theoretically using density functional theory (DFT) calculations. Crystal and molecular structure analysis of TPA was carried out via single-crystal X-ray diffraction to visualize the intermolecular interactions occurring in the solid-state and to study the structure-photophysical property relationship in the aggregated state. The photophysical properties of TPA were also studied extensively by UV-visible and fluorescence spectroscopy and its quantum yield and fluorescence lifetime were calculated by time-correlated single-photon counting (TCSPC). Interestingly, TPA could efficiently sense dichromate (Cr₂O₇^2-) ions in an acidic medium and an interesting morphological transition from a fluorescent flower to non-fluorescent disassembled structures could also be observed. The limit of detection of TPA for Cr₂O₇^2- ions was found to be as low as 5.5 nM, suggesting its exceptional sensitivity. More importantly, TPA could selectively sense Cr₂O₇^2- ions in real water samples even in the presence of other metal ions routinely present in polluted water, hence making it practically useful for water quality monitoring.

Controlled aggregation properties of single amino acids modified with protecting groups

The self-assembling properties of single amino acids modified with protecting groups under controlled conditions of temperature and concentration are illustrated.

Unusual Aggregates Formed by the Self-Assembly of Proline, Hydroxyproline, and Lysine

There is a plethora of significant research that illustrates toxic self-assemblies formed by the aggregation of single amino acids, such as phenylalanine, tyrosine, tryptophan, cysteine, and methionine, and their implication on the etiology of inborn errors of metabolisms (IEMs), such as phenylketonuria, tyrosinemia, hypertryptophanemia, cystinuria, and hypermethioninemia, respectively. Hence, studying the aggregation behavior of single amino acids is very crucial from the chemical neuroscience perspective to understanding the common etiology between single amino acid metabolite disorders and amyloid diseases like Alzheimer's and Parkinson's. Herein we report the aggregation properties of nonaromatic single amino acids l-proline (Pro), l-hydroxyproline (Hyp), and l-lysine hydrochloride (Lys). The morphologies of the self-assembled structures formed by Pro, Hyp, and Lys were extensively studied by various microscopic techniques, and controlled morphological transitions were observed under varied concentrations and aging times. The mechanism of structure formation was deciphered by concentration-dependent ¹H NMR analysis, which revealed the crucial role of hydrogen bonding and hydrophobic interactions in the structure formation of Pro, Hyp, and Lys. MTT assays on neural (SHSY5Y) cell lines revealed that aggregates formed by Pro, Hyp, and Lys reduced cell viability in a dose-dependent manner. These results may have important implications in the understanding of the patho-physiology of disorders such as hyperprolinemia, hyperhydroxyprolinemia, and hyperlysinemia since all these IEMs are associated with severe neurodegenerative symptoms, including intellectual disability, seizures, and psychiatric problems. Our future studies will endeavor to study these biomolecular assemblies in greater detail by immuno-histochemical analysis and advanced biophysical assays.

Chemical Perspective of the Mechanism of Action of Antiamyloidogenic Compounds Using a Minimalistic Peptide as a Reductionist Model

The diphenylalanine (FF) residue which is present at the 19 and 20 positions of the amyloid beta (1-42) (Aβ42) peptide sequence is considered as a reductionist model for studying Aβ42 aggregation. FF self-assembles into well-ordered tubular structures via aromatic π-π stacking. Herein the manuscript, we have presented a chemical perspective on the mechanism of action of antiamyloid compounds by assessing their interaction with FF. Therefore, we first coincubated FF fibers with single amino acids, since they are constituted of different R side chains yet have a common structural unit. This study revealed a crucial role of aromatic rings and functional groups like thiol (-SH) in causing destabilization of FF assembly via their interaction with π-electrons participating in π-π stacking present in FF. We further studied the interaction of different nonsteroidal anti-inflammatory drugs (NSAIDs), other known antiamyloidogenic compounds, and host-guest inclusion compounds like cyclodextrin (CD) to assess their mechanism of action and to decipher the functional moiety present in these compounds which could cause destabilization of π-π stacking. From the coincubation experiments, we could surmise a crucial role of aromatic rings present in these compounds for causing interference in aromatic stacking. We further consolidated our observations through microscopy analysis by various spectroscopic methods such as aggregation-induced emission enhancement (AIEE), fluorescence spectroscopy, solution-state ¹H NMR, FTIR, and circular dichroism. The studies presented in the manuscript thus provide significant insights into the role of functional groups in imparting antiamyloid action and open new avenues for an efficient design of antiamyloid drugs in the future.

Sequential and cellular detection of copper and lactic acid by disaggregation and reaggregation of the fluorescent panchromatic fibres of an acylthiourea based sensor

We report, for the first time, the self-assembly of an acyl-thiourea based sensor, N-{(6-methoxy-pyridine-2-yl) carbamothioyl}benzamide (NG1), with panchromatic fluorescent fibres and its dual-sensing properties for the sequential detection of Cu2+ ions and lactic acid. The panchromatic fibres formed by NG1 were disrupted in the presence of Cu2+ ions and this was accompanied by a visible colour change in the solution from colourless to yellow. The addition of lactic acid to the NG1 + Cu2+ solution, on the other hand, induced re-aggregation to fibrillar structures and the colour of the solution again changed to colourless. Hence, it may be surmised that the disaggregation and re-aggregation impart unique dual-sensing properties to NG1 for the sequential detection of Cu2+ ions and lactic acid. The application of NG1 as a selective sensor for Cu2+ ions and lactic acid has been assessed in detail by UV-visible and fluorescence spectroscopy. Furthermore, two structural variants of NG1, namely, NG2 and NG3, were synthesized, which suggest the crucial role of pyridine in imparting panchromatic emission properties and of both pyridine and acyl-thiourea side chain in the binding of Cu2+ ions. The O-methoxy group plays an important part in making NG1 the most sensitive probe of its structural analogs. Finally, the utility of NG1 for the sequential and cellular detection of Cu2+ ions and lactic acid was studied in human RPE cells. The experimental results of the interaction of NG1 with Cu2+ ions and lactic acid have also been validated theoretically by using quantum chemical calculations based on density functional theory (DFT). To the best of our knowledge, this is the first report wherein a dual sensor for Cu2+ ions and lactate ions is synthesized. More importantly, the aggregation properties of the sensor have been studied extensively and an interesting correlation of the photophysical properties of the probe with its self-assembling behavior has been elucidated.

Self-assembly of a benzothiazolone conjugate into panchromatic fluorescent fibres and their application in cellular imaging

We report self assembly of a benzothiazolone conjugate (CBT) into fluorescent panchromatic fibres and their application as a panchromatic dye in bioimaging.

Self-assembly of novel Fmoc-cardanol compounds into hydrogels - analysis based on rheological, structural and thermal properties

Hydrogels of low molecular weight molecules are particularly appealing for various biomedical applications such as drug delivery, tissue engineering, and antitumor therapy due to their excellent biocompatibility, biodegradability, and easy availability. Fmoc-peptide hydrogels form an essential category of these hydrogels. Herein we report a new class of Fmoc hydrogels in which cardanol (3-pentadecyl phenol (PDP)) is covalently linked with fluorenylmethyloxycarbonyl group. Cardanol is a plant-based renewable raw material, readily obtained from Cashew Nut Shell Liquid (CNSL). The long aliphatic chain of pentadecyl phenol helps in bringing a structural incompatibility and generates different nanostructures such as nanospheres, nanotapes, and nanofibers depending on Fmoc substitution and the solvents used. Stable hydrogels were formed from Fmoc-PDP in DMSO/H2O, and the critical aggregation concentration (CAC) and critical gelation concentration (CGC) were determined. The role of non-covalent forces such as hydrogen-bonding, hydrophobicity, and π-π stacking interactions in governing self-assembly to hydrogel formation was studied for Fmoc, DiFmoc and Boc groups attached to PDP. The thermal properties were analyzed, and smectic and nematic phases were identified for the molecules depending on the substitutions involved. Overall the study supports the mechanisms of aggregation and gelation in novel Fmoc-cardanol derivatives.

Achieving biopolymer synergy in systems chemistry

Synthetic and materials chemistry initiatives have enabled the translation of the macromolecular functions of biology into synthetic frameworks. These explorations into alternative chemistries of life attempt to capture the versatile functionality and adaptability of biopolymers in new orthogonal scaffolds. Information storage and transfer, however, so beautifully represented in the central dogma of biology, require multiple components functioning synergistically. Over a single decade, the emerging field of systems chemistry has begun to catalyze the construction of mutualistic biopolymer networks, and this review begins with the foundational small-molecule-based dynamic chemical networks and peptide amyloid-based dynamic physical networks on which this effort builds. The approach both contextualizes the versatile approaches that have been developed to enrich chemical information in synthetic networks and highlights the properties of amyloids as potential alternative genetic elements. The successful integration of both chemical and physical networks through β-sheet assisted replication processes further informs the synergistic potential of these networks. Inspired by the cooperative synergies of nucleic acids and proteins in biology, synthetic nucleic-acid-peptide chimeras are now being explored to extend their informational content. With our growing range of synthetic capabilities, structural analyses, and simulation technologies, this foundation is radically extending the structural space that might cross the Darwinian threshold for the origins of life as well as creating an array of alternative systems capable of achieving the progressive growth of novel informational materials.

Triblock peptide-oligonucleotide chimeras (POCs): programmable biomolecules for the assembly of morphologically tunable and responsive hybrid materials

Triblock peptide-oligonucleotide chimeras (POCs) consisting of peptides and oligonucleotides interlinked by an organic core are presented and their assembly behaviour is investigated. Several factors influence POC assembly, resulting in the formation of either vesicles or fibres. Design rules are introduced and used to predict and alter POC assembly morphology.