Search

Liquid-liquid phase separation (LLPS) is involved in both physiological and pathological processes. The intrinsically disordered protein Tau and its K18 construct can undergo LLPS in a distinct temperature-dependent manner, and the LLPS of Tau protein can initiate Tau aggregation. However, the underlying mechanism driving Tau LLPS remains largely elusive. To understand the temperature-dependent LLPS behavior of Tau at the monomeric level, we explored the conformational ensemble of Tau at different temperatures by performing all-atom replica-exchange molecular dynamic simulation on K18 monomer with an accumulated simulation time of 26.4 μs. Our simulation demonstrates that the compactness, β-structure propensity, and intramolecular interaction of K18 monomer exhibit nonlinear temperature-dependent behavior. 295DNIKHV300/326GNIHHK331/337VEVKSE342 make significant contributions to the temperature dependence of the β propensity of K18 monomer, while the two fibril-nucleating cores display relatively high β propensity at all temperatures. At a specific temperature, K18 monomer adopts the most collapsed state with exposed sites for both persistent and transient interactions. Given that more collapsed polypeptide chains were reported to be more prone to phase separate, our results suggest that K18 monomer inherently possesses conformational characteristics favoring LLPS. Our simulation predicts the importance of 295DNIKHV300/326GNIHHK331/337VEVKSE342 to the temperature-dependent conformational properties of K18, which is corroborated by CD spectra, turbidity assays, and DIC microscopy. Taken together, we offer a computational and experimental approach to comprehend the structural basis for LLPS by amyloidal building blocks.

Despite the fundamental clinical importance of amyloid fibril formation, its mechanism is still enigmatic. Crystallography of minimal amyloid models was a milestone in the understanding of the architecture and biological activities of amyloid fibers. However, the crystal structure of ultimate dipeptide-based amyloids is not yet reported. Herein, we present the crystal structure of a typical amyloid-forming minimal dipeptide, Ac-Phe-Phe-NH2 (Ac-FF-NH2 ), showing a canonical β-sheet structure at the atomic level. The simplicity of the structure helped in investigating amyloid-inhibition using crystallography, never previously reported for larger peptide models. Interestingly, in the presence of an inhibitor, the supramolecular packing of Ac-FF-NH2 molecules rearranged into a supramolecular 2-fold helix (21 helix). This study promotes our understanding of the mechanism of amyloid formation and of the structural transitions that occur during the inhibition process in a most fundamental model.

Summary Liquid-liquid phase separation (LLPS) of proteins mediates the assembly of biomolecular condensates involved in physiological and pathological processes. Identifying the minimalistic building blocks and the sequence determinant of protein phase separation is an urgent need but remains challenging partially due to lack of methodologies to characterize the phase behavior. Here, we demonstrate computational tools to efficiently quantify the microscopic fluidity of liquid condensates and the temperature-dependent phase diagram of peptides. We comprehensively explore the LLPS abilities of all 400 dipeptide combinations of coded amino acids and observe the occurrences of spontaneous LLPS in three categories of dipeptides. Our predictions are validated by turbidity assays and differential interference contrast (DIC) microscopy. We demonstrate that dipeptides, minimal but complete, possess multivalent interactions sufficient for LLPS, suggesting LLPS is a general property of peptides and proteins, independent of their sequence length. This study paves the way for the prediction and characterization of peptide phase behavior at the molecular level.

Most natural biomolecules may exist in either of two enantiomeric forms. Although in nature, amino acid biopolymers are characterized by l-type homochirality, incorporation of d-amino acids in the design of self-assembling peptide motifs has been shown to significantly alter enzyme stability, conformation, self-assembly behavior, cytotoxicity, and even therapeutic activity. However, while functional metabolite assemblies are ubiquitous throughout nature and play numerous important roles including physiological, structural, or catalytic functions, the effect of chirality on the self-assembly nature and function of single amino acids is not yet explored. Herein, we investigated the self-assembly mechanism of amyloid-like structure formation by two aromatic amino acids, phenylalanine (Phe) and tryptophan (Trp), both previously found as extremely important for the nucleation and self-assembly of aggregation-prone peptide regions into functional structures. Employing d-enantiomers, we demonstrate the critical role that amino acid chirality plays in their self-assembly process. The kinetics and morphology of pure enantiomers is completely altered upon their coassembly, allowing to fabricate different nanostructures that are mechanically more robust. Using diverse experimental techniques, we reveal the different molecular arrangement and self-assembly mechanism of the dl-racemic mixtures that resulted in the formation of advanced supramolecular materials. This study provides a simple yet sophisticated engineering model for the fabrication of attractive materials with bionanotechnological applications.

Porous microspheres from discotic tripeptides have been investigated as potential candidates for drug delivery vehicles. The C3 symmetric discotic tripeptide adopts a supramolecular helical column structure by three fold intermolecular hydrogen bonding interactions as well as face to face π–π stacking interactions. But the C2 symmetric discotic tripeptide adopts a supramolecular dimer like structure by six-fold intermolecular hydrogen bonding interactions and face to face π–π stacking interactions. Field emission scanning electron microscopy (FE-SEM) revealed that the C3 symmetric discotic tripeptide exhibits bird nest-like porous microsphere morphology formed by the assembly of the individual columns. However the C2 symmetric discotic tripeptide forms round clay pitcher like porous microspheres. These porous microspheres have been used as potential carriers for the sustained release of a bacteriostatic antibiotic sulfamethoxazole. The spectroscopic studies as well as the growth inhibition of E. coli reveal that the round clay pitcher-like porous microspheres are more efficient than the bird nest-like porous microspheres for the sustained release of drugs. The report highlights the importance of the self-assembly pattern for the fabrication of advanced functional materials.

High levels of homocysteine are reported as a risk factor for Alzheimer’s disease (AD). Correspondingly, inborn hyperhomocysteinemia is associated with an increased predisposition to the development of dementia in later stages of life. Yet, the mechanistic link between homocysteine accumulation and the pathological neurodegenerative processes is still elusive. Furthermore, despite the clear association between protein aggregation and AD, attempts to develop therapy that specifically targets this process have not been successful. It is envisioned that the failure in the development of efficacious therapeutic intervention may lie in the metabolomic state of affected individuals. We recently demonstrated the ability of metabolites to self-assemble and cross-seed the aggregation of pathological proteins, suggesting a role for metabolite structures in the initiation of neurodegenerative diseases. Here, we provide a report of homocysteine crystal structure and self-assembly into amyloid-like toxic fibrils, their inhibition by polyphenols, and their ability to seed the aggregation of the AD-associated β-amyloid polypeptide. A yeast model of hyperhomocysteinemia indicates a toxic effect, correlated with increased intracellular amyloid staining that could be rescued by polyphenol treatment. Analysis of AD mouse model brain sections indicates the presence of homocysteine assemblies and the interplay between β-amyloid and homocysteine. This work implies a molecular basis for the association between homocysteine accumulation and AD pathology, potentially leading to a paradigm shift in the understanding of AD initial pathological processes.

Realization of a self-assembled, nontoxic and eco-friendly piezoelectric device with high-performance, sensitivity and reliability is highly desirable to complement conventional inorganic and polymer based materials. Hierarchically organized natural materials such as collagen have long been posited to exhibit electromechanical properties that could potentially be amplified via molecular engineering to produce technologically relevant piezoelectricity. Here, by using a simple, minimalistic, building block of collagen, we fabricate a peptide-based piezoelectric generator utilising a radically different helical arrangement of Phe-Phe-derived peptide, Pro-Phe-Phe and Hyp-Phe-Phe, based only on proteinogenic amino acids. The simple addition of a hydroxyl group increases the expected piezoelectric response by an order of magnitude (d35 = 27 pm V−1). The value is highest predicted to date in short natural peptides. We demonstrate tripeptide-based power generator that produces stable max current >50 nA and potential >1.2 V. Our results provide a promising device demonstration of computationally-guided molecular engineering of piezoelectricity in peptide nanotechnology. Piezoelectric materials which are non-toxic and eco-friendly are of interest. Here, the authors report on the creation of collagen-mimetic peptides which can be self-assembled into piezoelectric materials and study the design characteristics required for optimized power generation.

Liquid-liquid phase separation (LLPS) of proteins mediates the assembly of biomolecular condensates involved in physiological and pathological processes. Identifying the minimalistic building blocks and the sequence determinant of protein phase separation is of urgent importance but remains challenging due to the enormous sequence space and difficulties of existing methodologies in characterizing the phase behavior of ultrashort peptides. Here we demonstrate computational tools to efficiently quantify the microscopic fluidity and density of liquid-condensates/solid-aggregates and the temperature-dependent phase diagram of peptides. Utilizing our approaches, we comprehensively predict the LLPS abilities of all 400 dipeptide combinations of coded amino acids based on 492 micro-second molecular dynamics simulations, and observe the occurrences of spontaneous LLPS. We identify 54 dipeptides that form solid-like aggregates and three categories of dipeptides with high LLPS propensity. Our predictions are validated by turbidity assays and differential interference contrast (DIC) microscopy on four representative dipeptides (WW, QW, GF, and VI). Phase coexistence diagrams are constructed to explore the temperature dependence of LLPS. Our results reveal that aromatic moieties are crucial for a dipeptide to undergo LLPS, and hydrophobic and polar components are indispensable. We demonstrate for the first time that dipeptides, minimal but complete, possess multivalent interactions sufficient for LLPS, suggesting that LLPS is a general property of peptides/proteins, independent of their sequence length. This study provides a computational and experimental approach to the prediction and characterization of the phase behavior of minimalistic peptides, and will be helpful for understanding the sequence-dependence and molecular mechanism of protein phase separation.SignificanceProtein liquid-liquid phase separation (LLPS) is associated with human health and diseases. Identifying the minimalistic building blocks and sequence determinants of LLPS is of urgent importance but remains computationally challenging partially due to the lack of methodologies characterizing the liquid condensates. Herein we provide approaches to evaluate LLPS ability of dipeptides, and screen all 400 dipeptides by MD simulations combined with multi-bead-per-residue models which capture key interactions driving LLPS that are missing in one-bead-per-residue models. Three categories of LLPS dipeptides are identified and the experimentally-verified QW dipeptide is by far the smallest LLPS system. Our results suggest that dipeptides, minimal but complete, possess multivalent interactions sufficient for LLPS, and LLPS is a general property of peptides/proteins, independent of their length.

A series of discotic tripeptides containing a rigid aromatic core and l-phenylalanine have been developed. The orientation of the amide bonds yielded variations of the structure and self-assembly properties of the compounds. The aggregation behavior of the discotic tripeptides was studied by various spectroscopic techniques. The morphology of the resulting aggregates was studied by field emission electron microscopy and atomic force microscopy. These studies showed that the orientation of the amide bonds has a strong influence on the intermolecular interactions, resulting in huge differences in the aggregation properties, and morphology of the discotic tripeptides. Only the C3-symmetric discotic tripeptides formed organogels. The supramolecular aggregation mechanism of N-centered and C[double bond, length as m-dash]O-centered discotic tripeptides for forming 3-fold intermolecular H-bonded helical column were the same, there was only a smaller enthalpy change due to the occurrence of longer distances for the N-HO[double bond, length as m-dash]C bonds of the N-centered discotic tripeptide. Whereas, the C2-symmetric discotic tripeptides 2 and 3 adopted a 6-fold intermolecular H-bonded dimer structure. Thus, this report presents a valuable approach for the fine-tuning of the discotic tripeptide based functional material.

Collagen, the most abundant protein in mammals, possesses notable cohesion and elasticity properties and efficiently induces tissue regeneration. The Gly-Pro-Hyp canonical tripeptide repeating unit of the collagen superhelix has been well-characterized. However, to date, the shortest tripeptide repeat demonstrated to attain a helical conformation contained 3-10 peptide repeats. Here, taking a minimalistic approach, we studied a single repeating unit of collagen in its protected form, Fmoc-Gly-Pro-Hyp. The peptide formed single crystals displaying left-handed polyproline II superhelical packing, as in the native collagen single strand. The crystalline assemblies also display head-to-tail H-bond interactions and an "aromatic zipper" arrangement at the molecular interface. The coassembly of this tripeptide, with Fmoc-Phe-Phe, a well-studied dipeptide hydrogelator, produced twisted helical fibrils with a polyproline II conformation and improved hydrogel mechanical rigidity. The design of these peptides illustrates the possibility to assemble superhelical nanostructures from minimal collagen-inspired peptides with their potential use as functional motifs to introduce a polyproline II conformation into hybrid hydrogel assemblies.

The amino acid sequence plays an essential role in amyloid formation. Here, using the central core recognition module of the Aβ peptide and its reverse sequence, we show that although both peptides assemble into β-sheets, their morphologies, kinetics and cell toxicities display marked differences. In addition, the native peptide, but not the reverse one, shows notable affinity towards bilayer lipid model membranes that modulates the aggregation pathways to stabilize the oligomeric intermediate states and function as the toxic agent responsible for neuronal dysfunction.

An α–α corner mimetic self-assembles to form a rod-like supramolecular structure which bends and closes end-to-end like a cyclization reaction to form uniform toroids. Each peptide fragment containing L-leucine, α-aminoisobutyric acid (Aib) and L-tyrosine forms rigid 310 helical structures stabilized by multiple intramolecular N–H⋯O hydrogen bonds. Two 310 helices are connected by the spacer 3-aminomethyl-benzylamine and maintain an angular distance of 120° and therefore mimic the α–α corner motif of a protein super secondary structure. The individual α–α corner subunits are themselves regularly interlinked through multiple water mediated intermolecular hydrogen-bonding interactions to form the rod-like supramolecular structure and toroids. The formation of the supramolecular structure has been proven with X-ray crystallography and other spectroscopic techniques. The cyclization of the supramolecular structure and toroid formation were studied by optical microscope, AFM and FE-SEM experiments. Despite other assignments such as exfoliation of graphene from graphite, the compound exhibits significant memory to finally produce the toroids.

Amino acid chirality plays an important role in conveying directionality and specificity to their supramolecular organization. However, the impact of enantiopure and racemic amino acids on the favorable packing and macroscopic properties of organic cocrystals with nonchiral coformers is poorly understood. Herein, we performed a systematic study of the effect of chirality on the macroscopic properties of acetylated alanine (AcA) single crystals and cocrystals with a nonchiral photo-sensitive bipyridine derivative (BPE). Cocrystallization with BPE produced a marked morphology transition that improved the supramolecular chirality, thermal stability and mechanical strength of AcA crystals. The distinct supramolecular packing modes were analyzed by X-ray crystallography. The highest rigidity was observed for BPE/ dl -AcA, while BPE/ d -AcA and BPE/ l -AcA crystals exhibited higher efficiency of photo-induced emission for fluorescent imprinting, as well as significantly higher piezoelectricity. This work provides a striking illustration that subtle differences in amino acid stereochemistry translate into tunable macroscopic properties of organic cocrystals for future applications in rigid solids, fluorescent imprinting, and energy harvesting.

Conformational transition of proteins and peptides into highly stable, β-sheet-rich structures is observed in many amyloid-associated neurodegenerative disorders, yet the precise mechanism of amyloid formation at the molecular level remains poorly understood due to the complex molecular structures. Short peptides provide simplified models for studying the molecular basis of the assembly mechanism that governs β-sheet fibrillation processes underlying the formation and inhibition of amyloid-like structures. Herein, we report a supramolecular coassembly strategy for the inhibition and transformation of stable β-sheet-rich amyloid-derived dipeptide self-assemblies into adaptable secondary structural fibrillar assemblies by mixing with bipyridine derivatives. The interplay between the type and mixing ratio of bipyridine derivatives allowed the variable coassembly process with stimuli-responsive functional properties, studied by various experimental characterizations and computational methods. Furthermore, the resulting coassemblies showed functional redox- and photoresponsive properties, making them promising candidates for controllable drug release and fluorescent imprint. This work presents a coassembly strategy not only to explore the mechanism of amyloid-like structure formation and inhibition at the molecular level but also to manipulate amyloid-like structures into responsive supramolecular coassemblies for material science and biotechnology applications.

Diphenylalanine (FF) represents the simplest peptide building block that self-assembles into ordered nanostructures with interesting physical properties. Among self-assembled peptide structures, FF nanotubes display notable stiffness and piezoelectric parameters (Young’s modulus = 19–27 GPa, strain coefficient d33 = 18 pC/N). Yet, inorganic alternatives remain the major materials of choice for many applications due to higher stiffness and piezoelectricity. Here, aiming to broaden the applications of the FF motif in materials chemistry, we designed three phenyl-rich dipeptides based on the β,β-diphenyl-Ala-OH (Dip) unit: Dip-Dip, cyclo-Dip-Dip, and tert-butyloxycarbonyl (Boc)-Dip-Dip. The doubled number of aromatic groups per unit, compared to FF, produced a dense aromatic zipper network with a dramatically improved Young’s modulus of ∼70 GPa, which is comparable to aluminum. The piezoelectric strain coefficient d33 of ∼73 pC/N of such assembly exceeds that of poled polyvinylidene-fluoride (PVDF) polymers and compares well to that of lead zirconium titanate (PZT) thin films and ribbons. The rationally designed π–π assemblies show a voltage coefficient of 2–3 Vm/N, an order of magnitude higher than PVDF, improved thermal stability up to 360 °C (∼60 °C higher than FF), and useful photoluminescence with wide-range excitation-dependent emission in the visible region. Our data demonstrate that aromatic groups improve the rigidity and piezoelectricity of organic self-assembled materials for numerous applications.

The variety and complexity of DNA-based structures make them attractive candidates for nanotechnology, yet insufficient stability and mechanical rigidity, compared to polyamide-based molecules, limit their application. Here, we combine the advantages of polyamide materials and the structural patterns inspired by nucleic-acids to generate a mechanically rigid fluorenylmethyloxycarbonyl (Fmoc)-guanine peptide nucleic acid (PNA) conjugate with diverse morphology and photoluminescent properties. The assembly possesses a unique atomic structure, with each guanine head of one molecule hydrogen bonded to the Fmoc carbonyl tail of another molecule, generating a non-planar cyclic quartet arrangement. This structure exhibits an average stiffness of 69.6 ± 6.8 N m−1 and Young’s modulus of 17.8 ± 2.5 GPa, higher than any previously reported nucleic acid derived structure. This data suggests that the unique cation-free “basket” formed by the Fmoc-G-PNA conjugate can serve as an attractive component for the design of new materials based on PNA self-assembly for nanotechnology applications., DNA is an attractive nanomaterial, yet limited compared to polyamides due to low stability and mechanical issues. Here, the authors combine polyamide and DNA characteristics to form mechanically rigid self-assembled peptide nucleic acid based materials with high stiffness and Young’s modulus.

Summary The understanding and prediction of the solubility of biomolecules, even of the simplest ones, reflect an open question and unmet need. Short aromatic tripeptides are among the most highly aggregative biomolecules. However, in marked contrast, Ala-Phe-Ala (AFA) was surprisingly found to be non-aggregative and could be solubilized at millimolar concentrations. Here, aiming to uncover the underlying molecular basis of its high solubility, we explore in detail the solubility, aggregation propensity, and atomic-level structure of the tripeptide. We demonstrate an unexpectedly high water solubility of AFA reaching 672 mM, two orders of magnitude higher than reported previously. The single crystal structure reveals an anti-parallel β sheet conformation devoid of any aromatic interactions. This study provides clear mechanistic insight into the structural basis of solubility and suggests a simple and feasible tool for its estimation, bearing implications for design of peptide drugs, peptides materials, and advancement of peptide nanotechnology., Graphical abstract, Highlights Balance between solubility versus aggregation of aromatic peptides is examined Significant differences in solubility are observed for analogous tripeptides Solid-state packing is found to be underlying molecular basis for high solubility Revealing the importance of biology at the solid state in physiology and pathology, The solubility of biomolecules in aqueous solutions is a central issue with regard to their physiological and pathological activities. Bera et al. provide insight into the solid-state packing-solubility relationship of biomolecules. This work may further extend the importance of solid-state biology for basic and applied science.

Metabolite materials are extremely useful to obtain functional bioinspired assemblies with unique physical properties for various applications in the fields of material science, engineering, and medicine by self-assembly of the simplest biological building blocks. Supramolecular co-assembly has recently emerged as a promising extended approach to further expand the conformational space of metabolite assemblies in terms of structural and functional complexity. Yet, the design of synergistically co-assembled amino acids to produce tailor-made functional architectures is still challenging. Herein, we propose a design rule to predict the supramolecular co-assembly of naturally occurring amino acids based on their interlayer separation distances observed in single crystals. Using diverse experimental techniques, we demonstrate that amino acids with comparable interlayer separation strongly interact and co-assemble to produce structural composites distinctly different from their individual properties. However, such an interaction is hampered in a mixture of differentially layer-separated amino acids, which self-sort to generate individual characteristic structures. This study provides a different paradigm for the modular design of supramolecular assemblies based on amino acids with predictable properties.

The formation of ordered nanostructures by metabolites is gaining increased interest due to the simplicity of the building blocks and their natural occurrence. Specifically, aromatic amino acids possess the ability to form ordered supramolecular interactions due to their limited solubility in aqueous solution. Unexpectedly, l-tyrosine (l-Tyr) is almost 2 orders of magnitude less soluble in water compared to l-phenylalanine (l-Phe). However, the underlying mechanism is not fully understood as l-Tyr is more polar. Here, we explore the utilization of insoluble tyrosine assemblies for technological applications and their molecular basis by manipulating the basic building blocks of tightly packed dimers. We show that the addition of an amyloid inhibition agent increases l-Tyr solubility due to the disruption of the dimer formation. The molecular organization grants the l-Tyr crystal higher thermal stability and mechanical properties between three amino acids. Additionally, l-Tyr crystals are shown to generate high and stable piezoelectric power outputs under mechanical pressure in a sandwich device. By incorporating the rigid l-Tyr crystals into a soft polymer, a mechano-responsive bending composite was fabricated. Furthermore, the l-Tyr crystalline needles exhibit an active photowaveguiding property, making them promising candidates for the generation of photonic biomaterial-based devices. The present work exemplifies a feasible strategy to explore physical properties of supramolecular self-assemblies comprises minimalistic naturally occurring building blocks and their applications in energy harvesting, photonic devices, stretchable electronics, and soft robotics.

The unique physiochemical properties and multiscale organization of layered materials draw the attention of researchers across a wide range of scientific disciplines. Layered structures are commonly found in diverse biological systems where they fulfill various functions. A prominent example of layered biological materials is the organization of proteins and polypeptides into the archetypal aggregated amyloidal structures. While the organization of proteins into amyloid structures was initially associated with various degenerative disorders, it was later revealed that proteins not related to any disease could also form identical layered assemblies. Thus, it appears that the ability of peptides and proteins to produce amyloid-like aggregates represents a generic property of polyamides to assemble into higher order fibrillar structures. In the aggregated state, the peptide backbone forms β-sheet structures which are further organized into layered arrangements. We have recently extended the identified amyloidogenic building blocks to include not only peptides or proteins, but also single amino acids and other metabolites. High resolution spectroscopy and crystallography analyses confirm the clear potential of amino acids and other metabolites to form layered amyloid-like aggregates showing biophysical and biochemical properties similar to protein amyloids. Therefore, the generic propensity of peptides and proteins backbones to assemble into layered organizations may emanate from their basic building block, the amino acid. In this Account, we aim to introduce the concept of supramolecular β-sheet organization of single amino acids and to present an analysis of their layered-structure organization based on single crystal structures. We demonstrate that, despite the different side-chains that considerably vary in their chemical properties, all coded amino acids display a layer-like assembly stabilized by α-amine to α-carboxyl H-bonds, resembling supramolecular β-sheet structures, while the side-chains determine the higher order organization of the layers. Our work presents the first analysis of the β-sheet propensity of single amino acids in their unbound form, indicating an evolutionary predisposition. We classify the amino acids β-sheet propensity on the basis of the interlayer separation distance in the crystal packing, which correlates well with previously reported classifications based on various criteria, such as hydrophobicity, steric bulkiness, and folding. In addition, we demonstrate that the relative direction of α-amine to α-carboxyl H-bonding pattern provides critical insights regarding the stabilization of parallel versus antiparallel β-sheet structures by the various amino acids. Taken together, our analysis of amino acid crystals provides substantial information regarding protein folding and dynamics and could serve as basic rules set for the design of potential building blocks for molecular self-assembly to produce functional materials of tunable properties, an important objective of bottom-up nanotechnology.

Quinolinic acid (QA), a downstream neurometabolite in the kynurenine pathway, the biosynthetic pathway of tryptophan, is associated with neurodegenerative diseases pathology. Mutations in genes encoding kynurenine pathway enzymes, which control the level of QA production, are linked with elevated risk of developing Parkinson's disease. Recent findings have revealed the accumulation and deposition of QA in post-mortem samples, as well as in cellular models of Alzheimer's disease and related disorders. Furthermore, intrastriatal inoculation of mice with QA results in increased levels of phosphorylated α-synuclein and neurodegenerative pathological and behavioral characteristics. However, the cellular and molecular mechanisms underlying the involvement of QA accumulation in protein aggregation and neurodegeneration remain elusive. We recently established that self-assembled ordered structures are formed by various metabolites and hypothesized that these "metabolite amyloids" may seed amyloidogenic proteins. Here we demonstrate the formation of QA amyloid-like fibrillar assemblies and seeding of α-synuclein aggregation by these nanostructures both in vitro and in cell culture. Notably, α-synuclein aggregation kinetics was accelerated by an order of magnitude. Additional amyloid-like properties of QA assemblies were demonstrated using thioflavin T assay, powder X-ray diffraction and cell apoptosis analysis. Moreover, fluorescently labeled QA assemblies were internalized by neuronal cells and co-localized with α-synuclein aggregates. In addition, we observed cell-to-cell propagation of fluorescently labeled QA assemblies in a co-culture of treated and untreated cells. Our findings suggest that excess QA levels, due to mutations in the kynurenine pathway, for example, may lead to the formation of metabolite assemblies that seed α-synuclein aggregation, resulting in neuronal toxicity and induction of Parkinson's disease.

The stimuli responsive assembly of small molecules that can modulate the physical properties of a supramolecular system may have potential as futuristic materials. The dimethyl dipicolinate in alcohol, when combined with 3 equiv. of potassium hydroxide and water, aggregates to a strong self-healing transparent gel. The instant gelation is highly selective towards potassium hydroxide and does not need any heating–cooling or sonication. The gelation is also selective for solvent systems such as 9 : 1 methanol–water or ethanol–water. The rheological stepstrain measurements under varying strain at room temperature show that the gel is thixotropic in nature. The gel can be shaped like any free-standing objects due to its high mechanical strength. The gel exhibits remarkable self-healing properties when damaged and diffusion of methyl orange through the gel suggests the dynamic nature of the gel. We found that the non-explosive gel can be packaged in a polyethylene tube and used as a safe fuel for indoor and outdoor heating without any special stove or burner. The gelator retains strong memory even after burning which makes it rechargeable up to four times by the addition of (9 : 1) methanol–water.

The diverse assembly of encapsulated water molecules in hybrid bisamide hosts has been investigated. Hybrid bisamides containing aromatic terminal groups and flexible aliphatic spacers restrict the intermolecular amide–amide hydrogen bonding and π-stacking interactions. However, the addition of water promotes the self-assembly processes by bridging between the bisamide molecules and the stabilized helical or zigzag one dimensional water chains. The bisamide 1 containing ethylenediamine adopted an extended shape and stabilized one-dimensional hydrogen bonded helical water chain inside the supramolecular frameworks. In contrast, bisamide 2 containing trimethylenediamine adopted a U-shape structure and entrapped an isolated water molecule. X-ray crystallography reveals that the bisamide 4 containing cadaverine adopted an extended structure and a stabilized one-dimensional hydrogen bonded zigzag water chain in a higher order packing. Moreover, by U-tube experiments using the pH gradient as the driving force across a liquid chloroform phase, bisamide 4 was found to be considerably active proton transporter than bisamide 1.

The self-assembly of two naphthalene-bisimide based nonionic bolaamphiphiles containing two terminal tripeptide moieties has been investigated. The bisimide 1 containing a core of adjacent aromatic rings and two termini of folded tripeptide moieties (-Tyr-Aib-Leu-OMe) adopts a dumbbell shape conformation, and it self-assembles through noncovalent interactions to fabricate microspheres. In contrast, the bisimide 2 containing two termini of extended tripeptide moieties (-Phe-Phe-Tyr-OMe) adopts a wrist band shape structure, and it self-assembles to produce elongated fibrils. The X-ray crystallography reveals that the bisimide 1 adopts a dumbbell shape with two terminal β-turns, and it self-associates to form a rhombus-like structure in higher order packing. Moreover, the conductivity of the bisimide 2 is 2 orders of magnitude higher than that of the bisimide 1 in room light. The secondary structures of the terminal tripeptides of bisimide systems and the peptide–peptide interactions are the driving forces f...

The self-assemblies of diphenylalanine and its tyrosine analogues have been investigated. The peptide Boc-Phe-Phe-OMe (1), having a sequence identity with the central hydrophobic cluster (CHC) of Alzheimer’s β-amyloid diphenylalanine motif, self-assembles to produce twisted fibrils. In contrast, the tyrosine-modified analogues Boc-Phe-Tyr-OMe (2), Boc-Tyr-Phe-OMe (3), and Boc-Tyr-Tyr-OMe (4), self-assemble to form microspheres. The X-ray crystallography reveal that the peptide 1 adopts an inverse γ-turn structure and self-associates as a hydrogen-bonded chain of molecules along a 2-fold screw axis, whereas the tyrosine-modified analogues exhibit parallel β-sheet aggregation and cyclic packing in higher-order assembly. The structural analysis of the peptides as described here can serve as a basis for de novo design and therapeutics.

A peptidomimetic compound containing leucine, tyrosine and malonic acid self-assembles through various noncovalent interactions to form spider silk-like fibers at ambient temperature. From the high-density liquid, a liquid-solid phase transition is initiated at 20 °C and solidification occurs upon contact with air. The fiber has comprehensive mechanical strength and optical properties similar to spider silk, and can be used to mimic a natural spider web.

The molecular self-assembly, growth and nonlinear thermo-optical properties of three synthetic aromatic–aliphatic hybrid nitropeptides have been investigated. The X-ray crystallography of nitropeptide 2 containing a glutamic acid moiety shows that the peptide adopts a dimeric structure using intermolecular hydrogen bonding as well as face to face π–π stacking interactions. Moreover, nitropeptide 2 exhibits nonlocal nonlinear optical properties. When a Gaussian laser beam passes through nitropeptide 2, the peptide shows several concentric rings due to spatial self-phase modulation (SSPM). However, the homologous peptide 1 containing an aspartic acid moiety and peptide 3 containing an achiral α-aminoisobutyric acid (Aib) moiety adopt sheet-like structures and have no self-phase modulation effect. The report describes the thermo-optical properties consistent with assumption and calculation and is promising for their applications in nonlinear optical modulation devices.

The benzene-1,3,5-tricarboxyamide containing three l-methionine (1) self-assemble through 3-fold amide–amide hydrogen bonds and π–π stacking to fabricate one-dimensional nanorod like structure. However, the tyrosine analogue (2) carrying multiple H-bonding side chains lost the C3 symmetry and 3-fold amide–amide hydrogen bonds and developed a porous structure. The porous material exhibits ten times more N2 sorption (155 cc/g) than the columnar one, indicating that side chain–core interactions have a drastic effect on structure and function.

The self-assembly of peptidomimetic compounds containing urea and dipicolinic acid was studied to develop a targeted drug delivery vehicle using hydrogen peroxide as a stimulus. Peptidomimetic compound 1 capped with N,N′-dicyclohexylurea mimicked a peptide turn structure, while compound 2 adopted a rigid planar structure through intramolecular N–H⋯O and N–H⋯N hydrogen bonding interactions. The AFM and FE-SEM images revealed that peptidomimetic compound 1 formed microspheres, whereas compound 2 formed a tape-like structure. These microspheres were loaded with the anticancer drug nicotinamide. The microspheres disassembled in the presence of hydrogen peroxide. Hydrogen peroxide ruptured the microspheres composed of peptidomimetic compound 1, thereby enhancing the proportional release of the loaded drug molecules. The reported peptidomimetic microspheres hold future prospects for use as targeted drug delivery vehicles for cancer cells with high levels of H2O2.

The Boc and N,N'-dicyclohexylurea capped γ-amino acid upon monobromination showed phosphorescence in the solid state. The compound exhibited different photoluminescence intensity and lifetimes in crystals obtained from ethyl acetate and methanol. X-ray crystallography revealed that the intermolecular C=O…Br halogen bond directs the heavy atom effect to produce the phosphorescence.

Donor acceptor π–π stacking and hydrogen bond mediated self-assembly of two synthetic naphthalene bisimides containing L-amino acids are illustrated. The solution studies exhibit a blue shift in UV/vis spectrum with increasing concentration for both phenylalanine and tyrosine-appended naphthalene bisimides. The single crystal X-ray reveals that both the Phe and Tyr side chains are in the trans position in the reported naphthalene bisimides 1 and 2. In higher order packing, the bisimide 2 molecules self-assemble through intermolecular hydrogen bonds between side chain Tyr –OH and ester –CO, and donor acceptor π–π stacking interactions between the electron deficient central naphthalene moiety and side chain tyrosine ring to generate a staircase architecture. Atomic force microscopy revealed microsphere morphology with diameters of 200–300 nm for bisimides 1 and 2. The microspheres have significant green emission upon excitation at 400 nm. Moreover these two naphthalene bisimides can be used as turn on fluoride sensor in aqueous medium.

The self-assembly of three peptides containing various conformationally flexible and rigid γ-amino acids has been investigated. In the solid state, peptide 1 adopts an extended backbone conformation, peptide 2 forms a turn-like structure and peptide 3 adopts a kink-like conformation, which are consistent with the increasing rigidity of the N-terminal γ-amino acids. In methanol–water (19 : 1) solution the peptides self-assembled and formed polydisperse porous microspheres. AFM and FE-SEM images show that the microspheres have diameters ranging from 500 nm–1 μm. Moreover, these microspheres have encapsulated a potent anticonvulsant and mood stabilizing drug carbamazepine. The dissolution of the peptide capsule in water leads to the sustained release of the encapsulated hydrophobic drug.

The compounds capable of blocking the aggregation of amyloidogenic proteins may have therapeutic potentials. We report on the synthesis of 2-acetyl amino-3-[4-(2-amino-5-sulfo-phenylazo)-phenyl]-propionic acid as an HEWL (hen egg white lysozyme) amyloid inhibitor starting from phenylalanine. The compounds arrest the monomers and exhibit anti-aggregating activity. Moreover, the acetyl derivative 1 served as a better inhibitor than the trifluoroacetyl derivative 2 against in vitro amyloid fibrillogenesis of the HEWL model system.

The sonication induced organogelation of a tripodal peptide has been investigated. The tripodal peptide does not form a gel in organic solvents after heating, cooling and ageing. Ultrasound has been used as a source of energy to tune the molecular assembly and organogelation. CD, NMR and fluorescence spectroscopies indicate distinct structural changes before and after sonication. FE-SEM and AFM of the xerogels reveal the nanofibrillar morphology. Moreover, the sonication responsive organogelation has been used to fabricate novel lanthanide nanocrystal decorated fibers. This gelation selectively quenches the viable emissions from the nanocryatsls as well the FRET observed between Tm3+/Yb3+-doped LiYF4 nanocrystals and ketocyanine dye occurring near 550 nm without affecting the NIR emissions of the nanocrystals.

The structural versatility, biocompatibility and dynamic range of the mechanical properties of protein materials have been explored in functional biomaterials for a wide array of biotechnology applications. Typically, such materials are made from self-assembled peptides with a predominant β-sheet structure, a common structural motif in silk and amyloid fibrils. However, collagen, the most abundant protein in mammals, is based on a helical arrangement. Here we show that Pro-Phe-Phe, the most aggregation-prone tripeptide of natural amino acids, assembles into a helical-like sheet that is stabilized by the dry hydrophobic interfaces of Phe residues. This architecture resembles that of the functional PSMα3 amyloid, highlighting the role of dry helical interfaces as a core structural motif in amyloids. Proline replacement by hydroxyproline, a major constituent of collagen, generates minimal helical-like assemblies with enhanced mechanical rigidity. These results establish a framework for designing functional biomaterials based on ultrashort helical protein elements. The structural foundation of self-assembled peptide materials is typically the β-sheet. Here the authors describe peptides made of three natural amino acids that self-assemble into helical-like superstructures with enhanced mechanical rigidity.

The self-assembly of short peptide building blocks into well-ordered nanostructures is a key direction in bionanotechnology. The formation of β -sheet organizations by short peptides is well explored, leading to the development of a wide range of functional assemblies. Likewise, many natural proteinaceous materials, such as silk and amyloid fibrils, are based on β-sheet structures. In contrast, collagen, the most abundant protein in mammals, is based on helical arrangement. Similar to β-sheet structures, short helical peptides have been recently discovered to possess a diverse set of functionalities with the potential to fabricate artificial self-assembling materials. Here, we outline the functional roles of self-assembled nanostructures formed by short helical peptides and their potential as artificial materials. We focus on the association between self-assembled mesoscale structures and their material function and demonstrate the way by which this class of building blocks bears the potential for diverse applications, such as the future fabrication of smart devices.