Catalytic peptide assemblies

De novo designed peptides form a highly catalytic ordered nanoarchitecture on a graphite surface

Here we demonstrate that short peptides, de novo designed from first principles, self-assemble on the surface of graphite to produce a highly robust and catalytic nanoarchitecture, which promotes peroxidation reactions with activities that rival those of natural enzymes in both single and multi-substrate reactions. These designable peptides recapitulate the symmetry of the underlying graphite surface and act as molecular scaffolds to immobilize hemin molecules on the electrode in a hierarchical self-assembly manner. The highly ordered and uniform hybrid graphite-peptide-hemin nanoarchitecture shows the highest faradaic efficiency of any hybrid electrode reported. Given the explosive growth of the types of chemical reactions promoted by self-assembled peptide materials, this new approach to creating complex electrocatalytic assemblies will yield highly efficient and practically applicable electrocatalysts.

Localized Enzyme-Assisted Self-Assembly of low molecular weight hydrogelators. Mechanism, applications and perspectives

Nature uses systems of high complexity coordinated by the precise spatial and temporal control of associated processes, working from the molecular to the macroscopic scale. This living organization is mainly ensured by enzymatic actions. Herein, we review the concept of Localized Enzyme-Assisted Self-Assembly (LEASA). It is defined and presented as a straightforward and insightful strategy to achieve high levels of control in artificial systems. Indeed, the use of immobilized enzymes to drive self-assembly events leads not only to the local formation of supramolecular structures but also to tune their kinetics and their morphologies. The possibility to design tailored complex systems taking advantage of self-assembled networks through their inherent and emergent properties offers new perspectives for the design of novel, more adaptable materials. As a result, some applications have already been developed and are gathered in this review. Finally, challenges and perspectives of LEASA are introduced and discussed.

Supramolecular assemblies of histidine-containing peptides with switchable hydrolase and peroxidase activities through Cu(II) binding and co-assembling

Modulating enzyme activities or functionalities is one of the primary features of biological systems, which is, however, a great challenge for artificial enzyme systems. In this work, we designed and synthesized a series of self-assembling peptides from histidine and other amino acids (Asp, Ser, Lys or Arg), which exist in the active site of natural enzymes. These peptides could undergo a conformational transition from random coils to β-sheet structures under physiological conditions and formed self-assembled nanotubes with obvious hydrolase activities. After incorporation of transition metal ions such as Cu²⁺, these peptides could coordinate with Cu²⁺ ions, switch molecular conformations, and self-assemble into hybrid nanomaterials with altered morphologies and peroxidase-like activities. This work illustrates a facile approach for constructing artificial enzymes from self-assembling peptides with histidine residues whose catalytic functions could be modulated by incorporation of Cu²⁺ ions.

Electricity, chemistry and biomarkers: an elegant and simple package: The potential of electrochemical biosensors for developing novel point-of-care diagnostics: The potential of electrochemical biosensors for developing novel point-of-care diagnostics

Electrochemical sensors to measure biomarkers from complex samples are a tried and tested technology with large untapped potential for addressing important public health needs.

Mapping the Morphological Landscape of Oligomeric Di-block Peptide-Polymer Amphiphiles

Peptide-polymer amphiphiles (PPAs) are tunable hybrid materials that achieve complex assembly landscapes by combining the sequence-dependent properties of peptides with the structural diversity of polymers. Despite their promise as biomimetic materials, determining how polymer and peptide properties simultaneously affect PPA self-assembly remains challenging. We herein present a systematic study of PPA structure-assembly relationships. PPAs containing oligo(ethyl acrylate) and random-coil peptides were used to determine the role of oligomer molecular weight, dispersity, peptide length, and charge density on self-assembly. We observed that PPAs predominantly formed spheres rather than anisotropic particles. Oligomer molecular weight and peptide hydrophilicity dictated morphology, while dispersity and peptide charge affected particle size. These key benchmarks will facilitate the rational design of PPAs that expand the scope of biomimetic functionality within assembled soft materials.

Selective Fluorescence Imaging of Cancer Cells Based on ROS-Triggered Intracellular Cross-Linking of Artificial Enzyme

Inside living cells, regulation of catalytic activity of artificial enzymes remains challenging due to issues such as biocompatibility, efficiency, and stability of the catalyst, by which the practical applications of artificial enzymes have been severely hindered. Here, an artificial enzyme, PTT-SGH, with responsiveness to reactive oxygen species (ROS), was obtained by introducing a catalytic histidine residue to pentaerythritol tetra(3-mercaptopropionate) (PTT). The artificial enzyme formed large aggregates in cells via the intracellular ROS-mediated oxidation of thiol groups. The process was significantly facilitated in tumor cells because of the higher ROS concentration in the tumor microenvironment. The catalytic activity of this artificial enzyme was intensively enhanced through deprotonation of cross-linked PTT-SGH, which showed typical esterase activities. Selective fluorescence imaging of tumor cells was achieved using the artificial enzyme to trigger the cleavage of the ester bond of the caged fluorophore inside living cells.

Systems chemistry of peptide-assemblies for biochemical transformations

During the billions of years of the evolutionary journey, primitive polymers, involved in proto metabolic pathways with low catalytic activity, played critical roles in the emergence of modern enzymes with remarkable substrate specificity. The precise positioning of amino acid residues and the complex orchestrated interplay in the binding pockets of evolved enzymes promote covalent and non-covalent interactions to foster a diverse set of complex catalytic transformations. Recent efforts to emulate the structural and functional information of extant enzymes by minimal peptide based assemblies have attempted to provide a holistic approach that could help in discerning the prebiotic origins of catalytically active binding pockets of advanced proteins. In addition to the impressive sets of advanced biochemical transformations, catalytic promiscuity and cascade catalysis by such small molecule based dynamic systems can foreshadow the ancestral catalytic processes required for the onset of protometabolism. Looking beyond minimal systems that work close to equilibrium, catalytic systems and compartments under non-equilibrium conditions utilizing simple prebiotically relevant precursors have attempted to shed light on how bioenergetics played an essential role in chemical emergence of complex behaviour. Herein, we map out these recent works and progress where diverse sets of complex enzymatic transformations were demonstrated by utilizing minimal peptide based self-assembled systems. Further, we have attempted to cover the examples of peptide assemblies that could feature promiscuous activity and promote complex multistep cascade reaction networks. The review also covers a few recent examples of minimal transient catalytic assemblies under non-equilibrium conditions. This review attempts to provide a broad perspective for potentially programming functionality via rational selection of amino acid sequences leading towards minimal catalytic systems that resemble the traits of contemporary enzymes.

Single amino acid bionanozyme for environmental remediation

Enzymes are extremely complex catalytic structures with immense biological and technological importance. Nevertheless, their widespread environmental implementation faces several challenges, including high production costs, low operational stability, and intricate recovery and reusability. Therefore, the de novo design of minimalistic biomolecular nanomaterials that can efficiently mimic the biocatalytic function (bionanozymes) and overcome the limitations of natural enzymes is a critical goal in biomolecular engineering. Here, we report an exceptionally simple yet highly active and robust single amino acid bionanozyme that can catalyze the rapid oxidation of environmentally toxic phenolic contaminates and serves as an ultrasensitive tool to detect biologically important neurotransmitters similar to the laccase enzyme. While inspired by the laccase catalytic site, the substantially simpler copper-coordinated bionanozyme is ∼5400 times more cost-effective, four orders more efficient, and 36 times more sensitive compared to the natural protein. Furthermore, the designed mimic is stable under extreme conditions (pH, ionic strength, temperature, storage time), markedly reusable for several cycles, and displays broad substrate specificity. These findings hold great promise in developing efficient bionanozymes for analytical chemistry, environmental protection, and biotechnology.

Development of a hydrolase mimicking peptide amphiphile and its immobilization on silica surface for stereoselective and enhanced catalysis

Biocatalysis is an important area of modern research and is extensively explored by various industries to attain greener methods in various applications. Supramolecular interactions of short peptides have been under the scanner for developing artificial smart materials inspired from natural systems. Peptide-based artificial enzymes have been proved to show various enzyme-like activities. Therefore, immobilization of catalytic peptides on solid surfaces can be an extremely useful breakthrough for development of cost-effective catalytic formulations. In this work, a series of peptide amphiphiles (PAs) have been systematically analyzed to find the most effective catalyst with esterase like activity. The PA, containing a catalytic triad, 'Asp(Ser)His' in a branched manner, was further immobilized onto silica nanoparticles through covalent bonding method to obtain surface coated catalytic silica nanoparticles. The heterogenous catalytic formulation not only showed enhanced esterase activity than the self-assembled PA in homogenous phase, but also exceeded the activity of natural CV lipase. The catalytic formulation showed high stereoselectivity towards chiral esters. Moreover, the catalyst remained stable at higher temperature, in presence of various denaturant and retained its activity after several catalytic cycles. The ease of separation, robust nature, reusability and high stereoselectivity of the catalyst opens up the possibility of creating new generation heterogeneous catalysts for further industrial applications.

Computational methods to predict protein aggregation

In most cases, protein aggregation stems from the establishment of non-native intermolecular contacts. The formation of insoluble protein aggregates is associated with many human diseases and is a major bottleneck for the industrial production of protein-based therapeutics. Strikingly, fibrillar aggregates are naturally exploited for structural scaffolding or to generate molecular switches and can be artificially engineered to build up multi-functional nanomaterials. Thus, there is a high interest in rationalizing and forecasting protein aggregation. Here, we review the available computational toolbox to predict protein aggregation propensities, identify sequential or structural aggregation-prone regions, evaluate the impact of mutations on aggregation or recognize prion-like domains. We discuss the strengths and limitations of these algorithms and how they can evolve in the next future.

Enzyme-Instructed Self-Assembly of Peptides: From Concept to Representative Applications

Enzyme-instructed self-assembly, integrating enzymatic reaction and molecular self-assembly, has drawn noticeable attention over the last decade with the intension of being used in valuable applications. Recent advances in the field allow it possible to spatiotemporally control peptide self-assembly in cellular milieu, broadening the potential applications of peptide assemblies to cancer therapy and subcellular delivery. In this minireview, the concept of enzyme-instructed self-assembly of peptide, containing enzymatic trigger and spatiotemporal control, is described. Representative applications in cells are also discussed, followed by outlook on the field of enzyme-instructed self-assembly.

An Approach to the De Novo Synthesis of Life

As the remit of chemistry expands beyond molecules to systems, new synthetic targets appear on the horizon. Among these, life represents perhaps the ultimate synthetic challenge. Building on an increasingly detailed understanding of the inner workings of living systems and advances in organic synthesis and supramolecular chemistry, the de novo synthesis of life (i.e., the construction of a new form of life based on completely synthetic components) is coming within reach. This Account presents our first steps in the journey toward this long-term goal. The synthesis of life requires the functional integration of different subsystems that harbor the different characteristics that are deemed essential to life. The most important of these are self-replication, metabolism, and compartmentalization. Integrating these features into a single system, maintaining this system out of equilibrium, and allowing it to undergo Darwinian evolution should ideally result in the emergence of life. Our journey toward de novo life started with the serendipitous discovery of a new mechanism of self-replication. We found that self-assembly in a mixture of interconverting oligomers is a general way of achieving self-replication, where the assembly process drives the synthesis of the very molecules that assemble. Mechanically induced breakage of the growing replicating assemblies resulted in their exponential growth, which is an important enabler for achieving Darwinian evolution. Through this mechanism, the self-replication of compounds containing peptides, nucleobases, and fully synthetic molecules was achieved. Several examples of evolutionary dynamics have been observed in these systems, including the spontaneous diversification of replicators allowing them to specialize on different food sets, history dependence of replicator composition, and the spontaneous emergence of parasitic behavior. Peptide-based replicator assemblies were found to organize their peptide units in space in a manner that, inadvertently, gives rise to microenvironments that are capable of catalysis of chemical reactions or binding-induced activation of cofactors. Among the reactions that can be catalyzed by the replicators are ones that produce the precursors from which these replicators grow, amounting to the first examples of the assimilation of a proto-metabolism. Operating these replicators in a chemically fueled out-of-equilibrium replication-destruction regime was found to promote an increase in their molecular complexity. Fueling counteracts the inherent tendency of replicators to evolve toward lower complexity (caused by the fact that smaller replicators tend to replicate faster). Among the remaining steps on the road to de novo life are now to assimilate compartmentalization and achieve open-ended evolution of the resulting system. Success in the synthesis of de novo life, once obtained, will have far-reaching implications for our understanding of what life is, for the search for extraterrestrial life, for how life may have originated on earth, and for every-day life by opening up new vistas in the form living technology and materials.

Supramolecular assembly of protein building blocks: from folding to function

Several phenomena occurring throughout the life of living things start and end with proteins. Various proteins form one complex structure to control detailed reactions. In contrast, one protein forms various structures and implements other biological phenomena depending on the situation. The basic principle that forms these hierarchical structures is protein self-assembly. A single building block is sufficient to create homogeneous structures with complex shapes, such as rings, filaments, or containers. These assemblies are widely used in biology as they enable multivalent binding, ultra-sensitive regulation, and compartmentalization. Moreover, with advances in the computational design of protein folding and protein-protein interfaces, considerable progress has recently been made in the de novo design of protein assemblies. Our review presents a description of the components of supramolecular protein assembly and their application in understanding biological phenomena to therapeutics.

Mariz B, Moreira IP, Kalafatovic D, Morais Faustino BM, Narang V, Wang T, Pappas CG, Ferreira I, Roque ACA, Ulijn RV. Discovery of phosphotyrosine-binding oligopeptides with supramolecular target selectivity

Phage-display screening on self-assembled tyrosine-phosphate ligands enables the identification of oligopeptides selective to dynamic supramolecular targets, with the lead peptide showing a preferred hairpin-like conformation and catalytic activity.

The effect of temperature on the kinetics of enhanced amide bond formation from lactic acid and valine driven by deep eutectic solvents

Deep eutectic solvents have been found to facilitate the copolymerization of hydroxy acids and amino acids through an ester-amide exchange reaction, and to drive the formation of amino acid-enriched oligomers with peptide backbones. The complexity of oligomer distribution is significantly reduced in deep eutectic solvents and amide-linked oligomers can be selectively produced. In the present study, we investigated the kinetics of amide bond formation in deep eutectic solvents to understand how the solvents regulate the pathways of complex copolymerization. A mathematical model successfully simulated the reaction of a lactic acid/valine mixture in deep eutectic solvents at different temperatures and provided insight into the activation energy of each step. Our findings indicated that the esterification and the evaporation of hydroxy acids were greatly suppressed in deep eutectic solvents because of the strong interaction between the quaternary ammonium salts and the hydroxy acids. In contrast, the ester-amide exchange reaction in deep eutectic solvents was significantly enhanced by lowering the activation entropies. The synergic effect of reduced esterification and increased exchange leads to amino acid-enriched oligomers with high yield and high selectivity. Furthermore, the reduced evaporation of hydroxy acids in deep eutectic solvents may preserve limited reactants in the prebiotic scenario. These results reveal deep eutectic solvents as sustainable media for the simple synthesis of amide bonds.

Catalytic amyloids: Is misfolding folding?

Originally regarded as a disease symptom, amyloids have shown a rich diversity of functions, including biologically beneficial ones. As such, the traditional view of polypeptide aggregation into amyloid-like structures being 'misfolding' should rather be viewed as 'alternative folding.' Various amyloid folds have been recently used to create highly efficient catalysts with specific catalytic efficiencies rivaling those of enzymes. Here we summarize recent developments and applications of catalytic amyloids, derived from both de novo and bioinspired designs, and discuss how progress in the last 2 years reflects on the field as a whole.

Peptide-Based Supramolecular Systems Chemistry

Peptide-based supramolecular systems chemistry seeks to mimic the ability of life forms to use conserved sets of building blocks and chemical reactions to achieve a bewildering array of functions. Building on the design principles for short peptide-based nanomaterials with properties, such as self-assembly, recognition, catalysis, and actuation, are increasingly available. Peptide-based supramolecular systems chemistry is starting to address the far greater challenge of systems-level design to access complex functions that emerge when multiple reactions and interactions are coordinated and integrated. We discuss key features relevant to systems-level design, including regulating supramolecular order and disorder, development of active and adaptive systems by considering kinetic and thermodynamic design aspects and combinatorial dynamic covalent and noncovalent interactions. Finally, we discuss how structural and dynamic design concepts, including preorganization and induced fit, are critical to the ability to develop adaptive materials with adaptive and tunable photonic, electronic, and catalytic properties. Finally, we highlight examples where multiple features are combined, resulting in chemical systems and materials that display adaptive properties that cannot be achieved without this level of integration.

Atomistic insights into the structure of heptapeptide nanofibers

Artificial amyloid-like nanofibers formed from short peptides are emerging as new supramolecular structures for catalysis and advanced materials. In this work, we analyze, by means of computational approaches, the preferred atomistic fibrillar architectures that result from the self-assembly of polar NY7, NF7, SY7, SF7, and GY7 peptides into steric zippers formed by two β-sheets (describing an individual steric zipper) and by four β-sheets. For all heptapeptides, except GY7, parallel β-sheet organizations with polar residues packed at the steric zipper appear to be the preferred assemblies for the two β-sheets system due to the formation of a strong network of hydrogen bonds. For GY7, however, an antiparallel organization with glycine at the steric zipper is the most stable one. The preferred architecture is mostly conserved when enlarging our model from two to four β-sheets. The present work shows that the relative stability of different architectures results from a delicate balance between peptide composition, side chain hydrophobicity, and non-covalent interactions at the interface and provides the basis for a rational design of new improved artificial prion-inspired materials.

Photothermally switchable peptide nanostructures towards modulating catalytic hydrolase activity

Enzymes are the most efficient catalysts in nature that possess an impressive range of catalytic activities, albeit limited by stability in adverse conditions. Functional peptides have emerged as alternative robust biocatalysts to mimic complex enzymes. Here, a rational design of minimalistic amyloid-inspired peptides 1-2 is demonstrated, which leads to pathway-driven self-assembly triggered by heat, light and chemical cues to render 1D and 2D nanostructures by the interplay of hydrogen bonding, host-guest interaction and reversible photodimerization. Such in situ transformable peptide nanostructures by means of external cues are envisaged as a catalytic amyloid for the first time to mimic the hydrolase enzyme activity. Michaelis Menten's enzyme kinetic parameters for the hydrolysis rate correlate the external cue-mediated structure-function augmentation with the twisted bundles, 1_TB being the most efficient biocatalyst among all the dimensionally diverse nanostructures. Unlike the natural enzyme, the peptide nanostructures exhibited the robust nature of the hydrolase activity over a broad range of temperature and pH. Finally, the peptide nanostructures are explored as efficient heterogeneous flow catalysts to improve the turnover number for the hydrolase activity.

New antimicrobial self-assembling short lipopeptides

Lipopeptides are an exceptional example of amphiphilic molecules that self-assemble into functional structures with applications in the areas of nanotechnology, catalysis or medicinal chemistry. Herein, we report a library of 21 short lipopeptides, together with their supramolecular characterization and antimicrobial activity against both Gram-negative (E. coli) and Gram-positive (S. aureus) strains. This study shows that simple lipoamino acids self-assemble into micellar or vesicular structures, while incorporating dipeptides capable of stablishing hydrogen bonds results in the adoption of advanced fibrilar structures. The self-assembly effect has proven to be key to achieve antimicrobial activity.

Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks

Many fundamental cellular and viral functions, including replication and translation, involve complex ensembles hosting synergistic activity between nucleic acids and proteins/peptides. There is ample evidence indicating that the chemical precursors of both nucleic acids and peptides could be efficiently formed in the prebiotic environment. Yet, studies on nonenzymatic replication, a central mechanism driving early chemical evolution, have focused largely on the activity of each class of these molecules separately. We show here that short nucleopeptide chimeras can replicate through autocatalytic and cross-catalytic processes, governed synergistically by the hybridization of the nucleobase motifs and the assembly propensity of the peptide segments. Unequal assembly-dependent replication induces clear selectivity toward the formation of a certain species within small networks of complementary nucleopeptides. The selectivity pattern may be influenced and indeed maximized to the point of almost extinction of the weakest replicator when the system is studied far from equilibrium and manipulated through changes in the physical (flow) and chemical (template and inhibition) conditions. We postulate that similar processes may have led to the emergence of the first functional nucleic-acid-peptide assemblies prior to the origin of life. Furthermore, spontaneous formation of related replicating complexes could potentially mark the initiation point for information transfer and rapid progression in complexity within primitive environments, which would have facilitated the development of a variety of functions found in extant biological assemblies.

Structure optimization of lipopeptide assemblies for aldol reactions in an aqueous medium

Four amphiphilic peptides were synthesized, characterized, and evaluated regarding their efficiency in the catalysis of direct aldol reactions in water. The lipopeptides differ by having a double lipid chain and a guanidinium pyrrole group functionalizing one Lys side chain. All the samples are composed of the amino acids l-proline (P), l-arginine (R), or l-lysine (K) functionalized with the cationic guanidiniocarbonyl pyrrole unit (GCP), l-tryptophan (W), and l-glycine (G), covalently linked to one or two long aliphatic chains, leading to surfactant-like designs with controlled proline protonation state and different stereoselectivity. Critical aggregation concentrations (cac) were higher in the presence of the GCP group, suggesting that self-assembly depends on charge distribution along the peptide backbone. Cryogenic Transmission Electron Microscopy (Cryo-TEM) and Small Angle X-ray Scattering (SAXS) showed a rich polymorphism including spherical, cylindrical, and bilayer structures. Molecular dynamics simulations performed to assess the lipopeptide polymorphs revealed an excellent agreement with core-shell arrangements derived from SAXS data and provided an atomistic view of the changes incurred by modifying head groups and lipid chains. The resulting nanostructures behaved as excellent catalysts for aldol condensation reactions, in which superior conversions (>99%), high diastereoselectivities (ds = 94 : 6), and enantioselectivities (ee = 92%) were obtained. Our findings contribute to elucidate the effect of nanoscale organization of lipopeptide assemblies in the catalysis of aldol reactions in an aqueous environment.

Self-Assembling Peptidic Bolaamphiphiles for Biomimetic Applications

Bolaamphiphile, which is a class of amphiphilic molecules, has a unique structure of two hydrophilic head groups at the ends of the hydrophobic center. Peptidic bolaamphiphiles that employ peptides or amino acids as their hydrophilic groups exhibit unique biochemical activities when they self-organize into supramolecular structures, which are not observed in a single molecule. The self-assembled peptidic bolaamphiphiles hold considerable promise for imitating proteins with biochemical activities, such as specific affinity toward heterogeneous substances, a catalytic activity similar to a metalloenzyme, physicochemical activity from harmonized amino acid segments, and the capability to encapsulate genes like a viral vector. These diverse activities give rise to large research interest in biomaterials engineering, along with the synthesis and characterization of the assembled structures. This review aims to address the recent progress in the applications of peptidic bolaamphiphile assemblies whose densely packed peptide motifs on their surface and their stacked hydrophobic centers exhibit unique protein-like activity and designer functionality, respectively.

Water Microdroplets Allow Spontaneously Abiotic Production of Peptides

The chemistry of abiotic synthesis of peptides in the context of their prebiotic origins is a continuing challenge that arises from thermodynamic and kinetic constraints in aqueous media. Here we reported a strategy of microdroplets' mass spectrometry for peptide bonds formed from pure amino acids or a mixture in the presence of phosphoric acids in aqueous microdroplets. In contrast to bulk experiments, the condensation reactions proceed spontaneously under ambient conditions. The microdroplet gave a negative free-energy change (ΔG ∼ -1.1 kcal/mol), and product yields of ∼75% were obtained at the scale of a few milliseconds. Experiments in which nebulization gas pressure and external charge were varied established dependence of peptide production on the droplet size that has a high surface-to-volume ratio. It is concluded that the condensation reactions occurred at or near the air-water interfaces of microdroplets. This aqueous microdroplets approach also provides a route for chemistry synthesis in the prebiotic era.

Self-Assembled Peptide Nano-Superstructure towards Enzyme Mimicking Hydrolysis

The structural arrangement of amino acid residues in native enzymes underlies their remarkable catalytic properties, thus providing a notable point of reference for designing potent yet simple biomimetic catalysts. Herein, we describe a minimalistic approach to construct a dipeptide-based nano-superstructure with enzyme-like activity. The self-assembled biocatalyst comprises one peptide as a single building block, readily synthesized from histidine. Through coordination with zinc ion, the peptide self-assembly procedure allows the formation of supramolecular β-sheet ordered nanocrystals, which can be used as basic units to further construct higher-order superstructure. As a result, remarkable hydrolysis activity and enduring stability are demonstrated. Our work exemplifies the use of a bioinspired supramolecular assembly approach to develop next-generation biocatalysts for biotechnological applications.

Self-Templated, Enantioselective Assembly of an Amyloid-like Dipeptide into Multifunctional Hierarchical Helical Arrays

Chiral self-assembly of peptides has attracted great interest owing to their promising applications in biomedicine, chemistry, and materials science. However, compared with the rich knowledge about their chiral self-assembly at the molecular or nanoscale, the formation of long-range-ordered hierarchical helical arrays (HHAs) from simple peptides remains a formidable challenge. Herein, we report the self-templated assembly of an amyloid-like dipeptide into long-range-ordered HHAs by their spontaneous fibrillization and hierarchical helical assembly within a confined film. The chiral interactions between the peptide and diamines result in geometry frustration and the phase transition of self-assembling peptide films from achiral spherulite structures into chiral HHAs. By changing the chirality and enantioselective interactions, we can control the phase behavior, handedness, and chiroptics of the self-assembled HHAs precisely. Moreover, the redox activity of the HHAs allows the in situ decoration of nanoparticles with high catalytic activity. These results provide insights into the chiral self-assembly of peptides and the fabrication of highly ordered materials with complex architectures and promising applications in chiroptics and catalysis.

Intracellular artificial supramolecules based on de novo designed Y15 peptides

De novo designed self-assembling peptides (SAPs) are promising building blocks of supramolecular biomaterials, which can fulfill a wide range of applications, such as scaffolds for tissue culture, three-dimensional cell culture, and vaccine adjuvants. Nevertheless, the use of SAPs in intracellular spaces has mostly been unexplored. Here, we report a self-assembling peptide, Y15 (YEYKYEYKYEYKYEY), which readily forms β-sheet structures to facilitate bottom-up synthesis of functional protein assemblies in living cells. Superfolder green fluorescent protein (sfGFP) fused to Y15 assembles into fibrils and is observed as fluorescent puncta in mammalian cells. Y15 self-assembly is validated by fluorescence anisotropy and pull-down assays. By using the Y15 platform, we demonstrate intracellular reconstitution of Nck assembly, a Src-homology 2 and 3 domain-containing adaptor protein. The artificial clusters of Nck induce N-WASP (neural Wiskott-Aldrich syndrome protein)-mediated actin polymerization, and the functional importance of Nck domain valency and density is evaluated.

Diketopiperazine Gels: New Horizons from the Self-Assembly of Cyclic Dipeptides

Cyclodipeptides (CDPs) or 2,5-diketopiperazines (DKPs) can exert a variety of biological activities and display pronounced resistance against enzymatic hydrolysis as well as a propensity towards self-assembly into gels, relative to the linear-dipeptide counterparts. They have attracted great interest in a variety of fields spanning from functional materials to drug discovery. This concise review will analyze the latest advancements in their synthesis, self-assembly into gels, and their more innovative applications.

Facile access to foldable redox-active flavin-peptide conjugates

A convenient approach for the synthesis of foldable redox-active flavin peptide conjugates was established. A model β-hairpin oligopeptide motif was utilized to demonstrate that azidolysine side-chains are readily functionalised with an alkyne-bearing flavine derivative. The folding equilibrium of the peptide backbone as well as the redox behaviour of the flavin moieties remains intact after the conjugation.

Cu-Catalyzed Arylation of Bromo-Difluoro-Acetamides by Aryl Boronic Acids, Aryl Trialkoxysilanes and Dimethyl-Aryl-Sulfonium Salts: New Entries to Aromatic Amides

We describe a mechanism-guided discovery of a synthetic methodology that enables the preparation of aromatic amides from 2-bromo-2,2-difluoroacetamides utilizing a copper-catalyzed direct arylation. Readily available and structurally simple aryl precursors such as aryl boronic acids, aryl trialkoxysilanes and dimethyl-aryl-sulfonium salts were used as the source for the aryl substituents. The scope of the reactions was tested, and the reactions were insensitive to the electronic nature of the aryl groups, as both electron-rich and electron-deficient aryls were successfully introduced. A wide range of 2-bromo-2,2-difluoroacetamides as either aliphatic or aromatic secondary or tertiary amides were also reactive under the developed conditions. The described synthetic protocols displayed excellent efficiency and were successfully utilized for the expeditious preparation of diverse aromatic amides in good-to-excellent yields. The reactions were scaled up to gram quantities.

Biocatalysts Based on Peptide and Peptide Conjugate Nanostructures

Peptides and their conjugates (to lipids, bulky N-terminals, or other groups) can self-assemble into nanostructures such as fibrils, nanotubes, coiled coil bundles, and micelles, and these can be used as platforms to present functional residues in order to catalyze a diversity of reactions. Peptide structures can be used to template catalytic sites inspired by those present in natural enzymes as well as simpler constructs using individual catalytic amino acids, especially proline and histidine. The literature on the use of peptide (and peptide conjugate) α-helical and β-sheet structures as well as turn or disordered peptides in the biocatalysis of a range of organic reactions including hydrolysis and a variety of coupling reactions (e.g., aldol reactions) is reviewed. The simpler design rules for peptide structures compared to those of folded proteins permit ready ab initio design (minimalist approach) of effective catalytic structures that mimic the binding pockets of natural enzymes or which simply present catalytic motifs at high density on nanostructure scaffolds. Research on these topics is summarized, along with a discussion of metal nanoparticle catalysts templated by peptide nanostructures, especially fibrils. Research showing the high activities of different classes of peptides in catalyzing many reactions is highlighted. Advances in peptide design and synthesis methods mean they hold great potential for future developments of effective bioinspired and biocompatible catalysts.

Supramolecular Antiparallel β-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 β-sheet structure in the disease state. It was observed that aromatic amino acid-rich peptide fragments possess a high tendency to adopt a β-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 Aβ-peptide fragments Aβ_29-32 and Aβ_37-40 , respectively. In the solid-state, they are self-assembled in an antiparallel β-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-β-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 β-sheet region of the Ramachandran plot. FT-IR studies also indicate the formation of an antiparallel β-sheet structure in the solid-state. Circular dichroism of the peptides in the aqueous solution also suggests the presence of predominantly β-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 β-sheet structure in the absence of aromatic amino acid and also can mimic the function of the native amyloid peptide.

Biohybrid Systems for Improved Bioinspired, Energy-Relevant Catalysis

Biomimetic catalysts, ranging from small-molecule metal complexes to supramolecular assembles, possess many exciting properties that could address salient challenges in industrial-scale manufacturing. Inspired by natural enzymes, these biohybrid catalytic systems demonstrate superior characteristics, including high activity, enantioselectivity, and enhanced aqueous solubility, over their fully synthetic counterparts. However, instability and limitations in the prediction of structure-function relationships are major drawbacks that often prevent the application of biomimetic catalysts outside of the laboratory. Despite these obstacles, recent advances in synthetic enzyme models have improved our understanding of complicated biological enzymatic processes and enabled the production of catalysts with increased efficiency. This review outlines important developments and future prospects for the design and application of bioinspired and biohybrid systems at multiple length scales for important, biologically relevant, clean energy transformations.

Self-Assembling Catalytic Peptide Nanomaterials Capable of Highly Efficient Peroxidase Activity

The self-assembly of short peptides gives rise to versatile nanomaterials capable of promoting efficient catalysis. We have shown that short, seven-residue peptides bind hemin to produce functional catalytic materials which display highly efficient peroxidation activity, reaching a catalytic efficiency of 3×105  m-1  s-1 . Self-assembly is essential for catalysis as non-assembling controls show no activity. We have also observed peroxidase activity even in the absence of hemin, suggesting the potential to alter redox properties of substrates upon association with the assemblies. These results demonstrate the practical utility of self-assembled peptides in various catalytic applications and further support the evolutionary link between amyloids and modern-day enzymes.

Fluorinated peptide biomaterials

Fluorinated compounds, while rarely used by nature, are emerging as fundamental ingredients in biomedical research, with applications in drug discovery, metabolomics, biospectroscopy, and, as the focus of this review, peptide/protein engineering. Leveraging the fluorous effect to direct peptide assembly has evolved an entirely new class of organofluorine building blocks from which unique and bioactive materials can be constructed. Here, we discuss three distinct peptide fluorination strategies used to design and induce peptide assembly into nano-, micro-, and macrosupramolecular states that potentiate high-ordered organization into material scaffolds. These fluorine-tailored peptide assemblies employ the unique fluorous environment to boost biofunctionality for a broad range of applications, from drug delivery to antibacterial coatings. This review provides foundational tactics for peptide fluorination and discusses the utility of these fluorous-directed hierarchical structures as material platforms in diverse biomedical applications.

Short intrinsically disordered polypeptide-oligonucleotide conjugates for programmed self-assembly of nanospheres with temperature-dependent size controllability

A series of short intrinsically disordered polypeptide conjugated oligonucleotides (IDPOCs) were rationally developed and assembled into well-defined nanospheres. The nanospheres exhibited excellent reversible thermoresponsive regulation of their contraction and expansion. Furthermore, the nanospheres showed biocompatibility, drug encapsulation and effective cellular uptake.